Starting phenix.real_space_refine on Thu Sep 18 14:04:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywa_39627/09_2025/8ywa_39627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywa_39627/09_2025/8ywa_39627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ywa_39627/09_2025/8ywa_39627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywa_39627/09_2025/8ywa_39627.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywa_39627/09_2025/8ywa_39627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywa_39627/09_2025/8ywa_39627.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1018 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 6078 2.51 5 N 1803 2.21 5 O 1960 1.98 5 H 6751 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16619 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 5579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 5579 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 30, 'TRANS': 395} Unresolved chain link angles: 7 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 4, 'TYR:plan': 2, 'GLU:plan': 1, 'TRP:plan': 3, 'ASP:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "X" Number of atoms: 5565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 5565 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 30, 'TRANS': 395} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 2, 'GLU:plan': 1, 'TRP:plan': 3, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 126 Chain: "h" Number of atoms: 518 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 516 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 132 Conformer: "B" Number of residues, atoms: 104, 516 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 132 bond proxies already assigned to first conformer: 512 Chain: "x" Number of atoms: 518 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 516 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 132 Conformer: "B" Number of residues, atoms: 104, 516 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 132 bond proxies already assigned to first conformer: 512 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 2803 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1068 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 1, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 433 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 3, 'PHE:plan': 12, 'ASP:plan': 2, 'HIS:plan': 3, 'TYR:plan': 3, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 191 Chain: "D" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 221 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 221 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.09, per 1000 atoms: 0.19 Number of scatterers: 16619 At special positions: 0 Unit cell: (118.483, 142.397, 175.007, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 1960 8.00 N 1803 7.00 C 6078 6.00 H 6751 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS H 251 " - pdb=" SG CYS H 309 " distance=2.03 Simple disulfide: pdb=" SG CYS H 325 " - pdb=" SG CYS X 237 " distance=2.03 Simple disulfide: pdb=" SG CYS H 355 " - pdb=" SG CYS H 415 " distance=2.04 Simple disulfide: pdb=" SG CYS H 461 " - pdb=" SG CYS H 521 " distance=2.04 Simple disulfide: pdb=" SG CYS X 251 " - pdb=" SG CYS X 309 " distance=2.04 Simple disulfide: pdb=" SG CYS X 355 " - pdb=" SG CYS X 415 " distance=2.04 Simple disulfide: pdb=" SG CYS X 461 " - pdb=" SG CYS X 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 176 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 515.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2808 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 28 sheets defined 22.0% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 273 through 275 No H-bonds generated for 'chain 'H' and resid 273 through 275' Processing helix chain 'H' and resid 298 through 303 Processing helix chain 'H' and resid 341 through 347 Processing helix chain 'H' and resid 403 through 409 Processing helix chain 'H' and resid 483 through 485 No H-bonds generated for 'chain 'H' and resid 483 through 485' Processing helix chain 'H' and resid 510 through 516 removed outlier: 3.824A pdb=" N LYS H 516 " --> pdb=" O GLU H 512 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 277 removed outlier: 3.766A pdb=" N LEU X 276 " --> pdb=" O ASP X 273 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 303 Processing helix chain 'X' and resid 341 through 347 Processing helix chain 'X' and resid 403 through 409 Processing helix chain 'X' and resid 483 through 485 No H-bonds generated for 'chain 'X' and resid 483 through 485' Processing helix chain 'X' and resid 510 through 516 Processing helix chain 'h' and resid 126 through 132 Processing helix chain 'h' and resid 186 through 193 Processing helix chain 'x' and resid 126 through 132 Processing helix chain 'x' and resid 186 through 193 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 201 through 234 Proline residue: A 209 - end of helix Processing helix chain 'B' and resid 18 through 41 removed outlier: 4.368A pdb=" N GLY B 36 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 38 " --> pdb=" O CYS B 34 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 60 through 81 removed outlier: 3.682A pdb=" N GLY B 64 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 123 removed outlier: 3.588A pdb=" N GLY B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 167 removed outlier: 4.291A pdb=" N CYS B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 52 removed outlier: 4.067A pdb=" N ARG D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 53 removed outlier: 3.666A pdb=" N ALA C 53 " --> pdb=" O GLN C 49 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 123 through 128 Processing sheet with id=AA2, first strand: chain 'H' and resid 123 through 128 Processing sheet with id=AA3, first strand: chain 'H' and resid 156 through 160 Processing sheet with id=AA4, first strand: chain 'H' and resid 277 through 284 removed outlier: 6.128A pdb=" N ALA H 288 " --> pdb=" O GLY H 255 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY H 255 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN H 248 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN X 248 " --> pdb=" O SER X 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 262 through 263 Processing sheet with id=AA6, first strand: chain 'H' and resid 266 through 267 Processing sheet with id=AA7, first strand: chain 'H' and resid 334 through 337 removed outlier: 3.772A pdb=" N ASP H 359 " --> pdb=" O LEU H 394 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU H 394 " --> pdb=" O ASP H 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 368 through 373 removed outlier: 3.725A pdb=" N THR H 430 " --> pdb=" O TYR H 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 441 through 446 Processing sheet with id=AB1, first strand: chain 'H' and resid 441 through 446 removed outlier: 3.568A pdb=" N ARG H 493 " --> pdb=" O PHE H 501 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 480 through 481 Processing sheet with id=AB3, first strand: chain 'X' and resid 123 through 128 removed outlier: 4.100A pdb=" N GLY X 149 " --> pdb=" O TYR X 182 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR X 182 " --> pdb=" O GLY X 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'X' and resid 123 through 128 removed outlier: 4.100A pdb=" N GLY X 149 " --> pdb=" O TYR X 182 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR X 182 " --> pdb=" O GLY X 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'X' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'X' and resid 270 through 271 removed outlier: 3.916A pdb=" N ASN X 262 " --> pdb=" O THR X 312 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 334 through 337 removed outlier: 3.950A pdb=" N ASP X 359 " --> pdb=" O LEU X 394 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU X 394 " --> pdb=" O ASP X 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 414 through 417 Processing sheet with id=AB9, first strand: chain 'X' and resid 441 through 446 Processing sheet with id=AC1, first strand: chain 'X' and resid 480 through 481 Processing sheet with id=AC2, first strand: chain 'h' and resid 119 through 123 removed outlier: 3.808A pdb=" N VAL h 138 " --> pdb=" O PHE h 123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'h' and resid 158 through 159 Processing sheet with id=AC4, first strand: chain 'x' and resid 119 through 123 removed outlier: 3.737A pdb=" N VAL x 138 " --> pdb=" O PHE x 123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'x' and resid 158 through 159 Processing sheet with id=AC6, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.835A pdb=" N LYS A 31 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 40 through 42 removed outlier: 6.824A pdb=" N ILE A 41 " --> pdb=" O PHE A 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AC9, first strand: chain 'A' and resid 113 through 117 Processing sheet with id=AD1, first strand: chain 'A' and resid 150 through 154 removed outlier: 5.116A pdb=" N ALA A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS A 147 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LYS A 142 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS A 179 " --> pdb=" O LYS A 142 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 6751 1.02 - 1.22: 3 1.22 - 1.42: 4141 1.42 - 1.62: 5851 1.62 - 1.82: 34 Bond restraints: 16780 Sorted by residual: bond pdb=" N LYS A 29 " pdb=" CA LYS A 29 " ideal model delta sigma weight residual 1.457 1.573 -0.116 1.41e-02 5.03e+03 6.73e+01 bond pdb=" CA LYS A 29 " pdb=" C LYS A 29 " ideal model delta sigma weight residual 1.524 1.478 0.046 1.26e-02 6.30e+03 1.33e+01 bond pdb=" NZ LYS A 29 " pdb=" HZ2 LYS A 29 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" NZ LYS A 29 " pdb=" HZ3 LYS A 29 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" NZ LYS A 29 " pdb=" HZ1 LYS A 29 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 16775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 29162 2.42 - 4.83: 127 4.83 - 7.25: 9 7.25 - 9.66: 4 9.66 - 12.08: 3 Bond angle restraints: 29305 Sorted by residual: angle pdb=" C LYS A 29 " pdb=" N PRO A 30 " pdb=" CA PRO A 30 " ideal model delta sigma weight residual 119.99 111.21 8.78 1.08e+00 8.57e-01 6.61e+01 angle pdb=" C GLN B 18 " pdb=" N GLU B 19 " pdb=" CA GLU B 19 " ideal model delta sigma weight residual 120.58 111.89 8.69 1.71e+00 3.42e-01 2.58e+01 angle pdb=" N GLN B 18 " pdb=" CA GLN B 18 " pdb=" C GLN B 18 " ideal model delta sigma weight residual 110.80 100.64 10.16 2.13e+00 2.20e-01 2.28e+01 angle pdb=" CA PRO H 245 " pdb=" N PRO H 245 " pdb=" CD PRO H 245 " ideal model delta sigma weight residual 112.00 105.38 6.62 1.40e+00 5.10e-01 2.23e+01 angle pdb=" N LYS A 29 " pdb=" CA LYS A 29 " pdb=" C LYS A 29 " ideal model delta sigma weight residual 109.81 99.46 10.35 2.21e+00 2.05e-01 2.20e+01 ... (remaining 29300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 7917 17.03 - 34.06: 444 34.06 - 51.10: 151 51.10 - 68.13: 49 68.13 - 85.16: 8 Dihedral angle restraints: 8569 sinusoidal: 3849 harmonic: 4720 Sorted by residual: dihedral pdb=" CB CYS X 251 " pdb=" SG CYS X 251 " pdb=" SG CYS X 309 " pdb=" CB CYS X 309 " ideal model delta sinusoidal sigma weight residual 93.00 32.87 60.13 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS A 93 " pdb=" CB CYS A 93 " ideal model delta sinusoidal sigma weight residual 93.00 141.62 -48.62 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" C LYS A 29 " pdb=" N LYS A 29 " pdb=" CA LYS A 29 " pdb=" CB LYS A 29 " ideal model delta harmonic sigma weight residual -122.60 -113.51 -9.09 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 8566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1508 0.076 - 0.152: 160 0.152 - 0.227: 2 0.227 - 0.303: 0 0.303 - 0.379: 1 Chirality restraints: 1671 Sorted by residual: chirality pdb=" CA LYS A 29 " pdb=" N LYS A 29 " pdb=" C LYS A 29 " pdb=" CB LYS A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA LYS B 16 " pdb=" N LYS B 16 " pdb=" C LYS B 16 " pdb=" CB LYS B 16 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE X 463 " pdb=" N ILE X 463 " pdb=" C ILE X 463 " pdb=" CB ILE X 463 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 1668 not shown) Planarity restraints: 3006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN H 474 " -0.240 2.00e-02 2.50e+03 3.26e-01 1.60e+03 pdb=" CD GLN H 474 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN H 474 " 0.231 2.00e-02 2.50e+03 pdb=" NE2 GLN H 474 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN H 474 " 0.509 2.00e-02 2.50e+03 pdb="HE22 GLN H 474 " -0.519 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 601 " -0.352 2.00e-02 2.50e+03 3.03e-01 1.14e+03 pdb=" C7 NAG H 601 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG H 601 " -0.146 2.00e-02 2.50e+03 pdb=" N2 NAG H 601 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG H 601 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 18 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" N GLU B 19 " -0.056 2.00e-02 2.50e+03 pdb=" CA GLU B 19 " 0.012 2.00e-02 2.50e+03 pdb=" H GLU B 19 " 0.027 2.00e-02 2.50e+03 ... (remaining 3003 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 652 2.19 - 2.79: 28407 2.79 - 3.39: 38280 3.39 - 4.00: 50461 4.00 - 4.60: 75371 Nonbonded interactions: 193171 Sorted by model distance: nonbonded pdb=" H GLU H 267 " pdb=" O GLN H 270 " model vdw 1.582 2.450 nonbonded pdb=" O PHE A 206 " pdb=" H LEU A 210 " model vdw 1.601 2.450 nonbonded pdb=" HZ1 LYS X 494 " pdb=" O GLY X 497 " model vdw 1.620 2.450 nonbonded pdb=" H THR H 509 " pdb=" OE1 GLU H 512 " model vdw 1.638 2.450 nonbonded pdb=" O THR X 433 " pdb="HH22 ARG X 437 " model vdw 1.661 2.450 ... (remaining 193166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'H' and ((resid 117 through 224 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 225 through 540 or (resid 541 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name HA )) or (resid 542 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD )) or resid 601)) selection = (chain 'X' and ((resid 117 and (name CA or name C or name O or name CB or name H \ A )) or resid 118 through 328 or (resid 329 and (name N or name CA or name C or \ name O or name CB or name CG or name OD1 or name ND2)) or (resid 330 and (name N \ or name CA or name C or name O or name CB or name CG or name CD )) or resid 331 \ through 601)) } ncs_group { reference = (chain 'h' and (resid 111 through 183 or resid 185 through 214)) selection = (chain 'x' and (resid 111 through 183 or resid 185 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.140 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.850 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 10038 Z= 0.214 Angle : 0.607 12.078 13781 Z= 0.334 Chirality : 0.044 0.379 1671 Planarity : 0.008 0.303 1838 Dihedral : 12.538 85.162 3263 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.86 % Favored : 93.94 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.23), residues: 1470 helix: 2.68 (0.31), residues: 287 sheet: 1.14 (0.23), residues: 562 loop : -0.47 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 405 TYR 0.020 0.001 TYR A 174 PHE 0.016 0.001 PHE H 466 TRP 0.028 0.002 TRP H 513 HIS 0.011 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00432 (10029) covalent geometry : angle 0.60581 (13763) SS BOND : bond 0.00412 ( 9) SS BOND : angle 1.13296 ( 18) hydrogen bonds : bond 0.11613 ( 528) hydrogen bonds : angle 5.55153 ( 1527) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue SER 222 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue LEU 215 is missing expected H atoms. Skipping. Residue ALA 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue VAL 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ALA 93 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue THR 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue MET 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ALA 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 433 THR cc_start: 0.5339 (m) cc_final: 0.4917 (p) outliers start: 1 outliers final: 1 residues processed: 147 average time/residue: 0.1984 time to fit residues: 38.4907 Evaluate side-chains 96 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 474 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 478 ASN H 487 HIS X 391 ASN X 487 HIS ** X 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 541 ASN A 28 GLN A 67 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.264199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.234142 restraints weight = 31429.701| |-----------------------------------------------------------------------------| r_work (start): 0.4728 rms_B_bonded: 1.98 r_work: 0.4308 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10038 Z= 0.239 Angle : 0.676 10.136 13781 Z= 0.355 Chirality : 0.048 0.497 1671 Planarity : 0.005 0.062 1838 Dihedral : 6.360 58.801 1739 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.97 % Favored : 94.82 % Rotamer: Outliers : 1.11 % Allowed : 11.62 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.23), residues: 1470 helix: 2.38 (0.31), residues: 284 sheet: 0.95 (0.22), residues: 576 loop : -0.52 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 486 TYR 0.016 0.002 TYR A 174 PHE 0.021 0.002 PHE H 466 TRP 0.017 0.002 TRP H 513 HIS 0.010 0.002 HIS H 487 Details of bonding type rmsd covalent geometry : bond 0.00514 (10029) covalent geometry : angle 0.67244 (13763) SS BOND : bond 0.00764 ( 9) SS BOND : angle 2.12689 ( 18) hydrogen bonds : bond 0.03756 ( 528) hydrogen bonds : angle 4.63211 ( 1527) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue SER 222 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue LEU 215 is missing expected H atoms. Skipping. Residue ALA 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue VAL 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ALA 93 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue THR 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue MET 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ALA 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 353 ILE cc_start: 0.8006 (pt) cc_final: 0.7710 (tt) REVERT: H 432 LYS cc_start: 0.6804 (ttpt) cc_final: 0.6590 (tptt) REVERT: X 433 THR cc_start: 0.6321 (m) cc_final: 0.5870 (p) REVERT: X 493 ARG cc_start: 0.5552 (mmm160) cc_final: 0.5335 (tpp-160) outliers start: 8 outliers final: 6 residues processed: 97 average time/residue: 0.1955 time to fit residues: 25.6936 Evaluate side-chains 82 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain X residue 354 THR Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 459 LEU Chi-restraints excluded: chain X residue 462 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 50.0000 chunk 58 optimal weight: 9.9990 chunk 104 optimal weight: 0.3980 chunk 98 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 48 optimal weight: 50.0000 chunk 130 optimal weight: 50.0000 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 40.0000 chunk 94 optimal weight: 40.0000 chunk 64 optimal weight: 0.0470 overall best weight: 3.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 381 HIS ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.254134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.217431 restraints weight = 31103.866| |-----------------------------------------------------------------------------| r_work (start): 0.4583 rms_B_bonded: 2.06 r_work: 0.4123 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 10038 Z= 0.312 Angle : 0.725 8.344 13781 Z= 0.384 Chirality : 0.049 0.413 1671 Planarity : 0.006 0.083 1838 Dihedral : 6.323 59.229 1736 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.74 % Favored : 93.05 % Rotamer: Outliers : 3.04 % Allowed : 14.80 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.23), residues: 1470 helix: 2.33 (0.31), residues: 294 sheet: 0.58 (0.22), residues: 580 loop : -0.80 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 486 TYR 0.023 0.003 TYR A 174 PHE 0.033 0.003 PHE H 466 TRP 0.019 0.003 TRP X 407 HIS 0.010 0.002 HIS X 419 Details of bonding type rmsd covalent geometry : bond 0.00730 (10029) covalent geometry : angle 0.72042 (13763) SS BOND : bond 0.01087 ( 9) SS BOND : angle 2.32400 ( 18) hydrogen bonds : bond 0.04580 ( 528) hydrogen bonds : angle 4.75584 ( 1527) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue SER 222 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue LEU 215 is missing expected H atoms. Skipping. Residue ALA 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue VAL 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ALA 93 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue THR 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue MET 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ALA 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8130 (m) REVERT: X 462 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7414 (tp) REVERT: X 493 ARG cc_start: 0.5923 (mmm160) cc_final: 0.5659 (mmt-90) REVERT: X 500 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.6879 (m-10) REVERT: A 107 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7164 (mp0) outliers start: 22 outliers final: 16 residues processed: 94 average time/residue: 0.1827 time to fit residues: 23.9297 Evaluate side-chains 85 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 234 GLN Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain X residue 354 THR Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 462 LEU Chi-restraints excluded: chain X residue 472 SER Chi-restraints excluded: chain X residue 500 PHE Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 174 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 80 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 46 optimal weight: 40.0000 chunk 7 optimal weight: 40.0000 chunk 123 optimal weight: 50.0000 chunk 10 optimal weight: 30.0000 chunk 94 optimal weight: 40.0000 chunk 20 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.253720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.220061 restraints weight = 30613.254| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 1.87 r_work: 0.4139 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10038 Z= 0.238 Angle : 0.608 6.419 13781 Z= 0.324 Chirality : 0.045 0.202 1671 Planarity : 0.005 0.075 1838 Dihedral : 5.848 58.836 1736 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.79 % Favored : 94.01 % Rotamer: Outliers : 3.18 % Allowed : 17.98 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.23), residues: 1470 helix: 2.59 (0.31), residues: 295 sheet: 0.63 (0.22), residues: 571 loop : -0.73 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 486 TYR 0.018 0.002 TYR A 174 PHE 0.020 0.002 PHE H 466 TRP 0.014 0.002 TRP X 407 HIS 0.008 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00556 (10029) covalent geometry : angle 0.60620 (13763) SS BOND : bond 0.00548 ( 9) SS BOND : angle 1.36712 ( 18) hydrogen bonds : bond 0.03479 ( 528) hydrogen bonds : angle 4.47412 ( 1527) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue SER 222 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue LEU 215 is missing expected H atoms. Skipping. Residue ALA 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue VAL 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ALA 93 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue THR 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue MET 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ALA 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8015 (m) REVERT: X 462 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7287 (tp) REVERT: X 493 ARG cc_start: 0.5860 (mmm160) cc_final: 0.5615 (mmt-90) REVERT: X 500 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.6041 (m-10) REVERT: X 541 ASN cc_start: 0.7652 (m-40) cc_final: 0.7377 (m110) REVERT: A 96 GLN cc_start: 0.6753 (pp30) cc_final: 0.6365 (mp10) outliers start: 23 outliers final: 18 residues processed: 92 average time/residue: 0.1739 time to fit residues: 22.9846 Evaluate side-chains 90 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 458 THR Chi-restraints excluded: chain X residue 462 LEU Chi-restraints excluded: chain X residue 500 PHE Chi-restraints excluded: chain X residue 508 VAL Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 174 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 90 optimal weight: 50.0000 chunk 103 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 9 optimal weight: 50.0000 chunk 7 optimal weight: 40.0000 chunk 16 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 541 ASN A 39 ASN ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.249840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.208659 restraints weight = 30447.445| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 1.89 r_work: 0.4073 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 10038 Z= 0.379 Angle : 0.769 7.599 13781 Z= 0.410 Chirality : 0.051 0.268 1671 Planarity : 0.006 0.082 1838 Dihedral : 6.586 57.337 1736 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.38 % Favored : 91.42 % Rotamer: Outliers : 6.09 % Allowed : 19.92 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.23), residues: 1470 helix: 2.35 (0.31), residues: 299 sheet: 0.26 (0.22), residues: 564 loop : -1.09 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 486 TYR 0.034 0.004 TYR X 413 PHE 0.027 0.003 PHE H 466 TRP 0.025 0.003 TRP X 407 HIS 0.012 0.003 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00903 (10029) covalent geometry : angle 0.76677 (13763) SS BOND : bond 0.00683 ( 9) SS BOND : angle 1.63530 ( 18) hydrogen bonds : bond 0.04448 ( 528) hydrogen bonds : angle 4.80339 ( 1527) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue SER 222 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue LEU 215 is missing expected H atoms. Skipping. Residue ALA 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue VAL 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ALA 93 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue THR 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue MET 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ALA 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 74 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8193 (m) REVERT: H 507 GLU cc_start: 0.5663 (tp30) cc_final: 0.5182 (tp30) REVERT: X 396 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8058 (p) REVERT: X 493 ARG cc_start: 0.6348 (mmm160) cc_final: 0.5730 (tpp-160) REVERT: X 500 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.6831 (m-10) REVERT: X 512 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6183 (tt0) REVERT: X 541 ASN cc_start: 0.7941 (m110) cc_final: 0.7418 (m110) outliers start: 44 outliers final: 29 residues processed: 110 average time/residue: 0.1712 time to fit residues: 26.4785 Evaluate side-chains 103 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain X residue 295 THR Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 396 VAL Chi-restraints excluded: chain X residue 399 THR Chi-restraints excluded: chain X residue 413 TYR Chi-restraints excluded: chain X residue 458 THR Chi-restraints excluded: chain X residue 461 CYS Chi-restraints excluded: chain X residue 472 SER Chi-restraints excluded: chain X residue 500 PHE Chi-restraints excluded: chain X residue 506 LEU Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 192 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 128 optimal weight: 50.0000 chunk 4 optimal weight: 50.0000 chunk 33 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 50.0000 chunk 133 optimal weight: 50.0000 chunk 139 optimal weight: 9.9990 chunk 125 optimal weight: 50.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.252911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.215823 restraints weight = 30444.195| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 2.03 r_work: 0.4113 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.6662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 10038 Z= 0.294 Angle : 0.664 6.530 13781 Z= 0.354 Chirality : 0.047 0.212 1671 Planarity : 0.006 0.075 1838 Dihedral : 6.315 50.977 1736 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.29 % Favored : 92.44 % Rotamer: Outliers : 4.70 % Allowed : 21.99 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.23), residues: 1470 helix: 2.51 (0.31), residues: 299 sheet: 0.29 (0.22), residues: 558 loop : -1.01 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 348 TYR 0.026 0.003 TYR A 174 PHE 0.018 0.002 PHE H 466 TRP 0.018 0.002 TRP X 407 HIS 0.009 0.002 HIS X 419 Details of bonding type rmsd covalent geometry : bond 0.00693 (10029) covalent geometry : angle 0.66208 (13763) SS BOND : bond 0.00637 ( 9) SS BOND : angle 1.60568 ( 18) hydrogen bonds : bond 0.03750 ( 528) hydrogen bonds : angle 4.57367 ( 1527) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue SER 222 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue LEU 215 is missing expected H atoms. Skipping. Residue ALA 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue VAL 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ALA 93 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue THR 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue MET 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ALA 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8207 (m) REVERT: H 507 GLU cc_start: 0.5743 (tp30) cc_final: 0.5312 (tp30) REVERT: X 238 ASP cc_start: 0.7522 (t0) cc_final: 0.6972 (t70) REVERT: X 396 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8065 (p) REVERT: X 493 ARG cc_start: 0.6617 (mmm160) cc_final: 0.5864 (tpp-160) REVERT: X 500 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.6557 (m-10) REVERT: X 541 ASN cc_start: 0.8094 (m110) cc_final: 0.7862 (t0) outliers start: 34 outliers final: 28 residues processed: 102 average time/residue: 0.2102 time to fit residues: 29.6375 Evaluate side-chains 105 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 396 VAL Chi-restraints excluded: chain X residue 399 THR Chi-restraints excluded: chain X residue 413 TYR Chi-restraints excluded: chain X residue 500 PHE Chi-restraints excluded: chain X residue 506 LEU Chi-restraints excluded: chain X residue 508 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 141 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 134 optimal weight: 50.0000 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 138 optimal weight: 40.0000 chunk 6 optimal weight: 50.0000 chunk 44 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.254976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.215479 restraints weight = 30280.456| |-----------------------------------------------------------------------------| r_work (start): 0.4574 rms_B_bonded: 1.98 r_work: 0.4136 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.6672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10038 Z= 0.113 Angle : 0.515 5.652 13781 Z= 0.274 Chirality : 0.043 0.166 1671 Planarity : 0.005 0.058 1838 Dihedral : 5.527 49.440 1736 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.31 % Favored : 94.48 % Rotamer: Outliers : 2.77 % Allowed : 23.79 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.23), residues: 1470 helix: 2.97 (0.31), residues: 296 sheet: 0.67 (0.22), residues: 553 loop : -0.81 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 390 TYR 0.013 0.001 TYR A 175 PHE 0.008 0.001 PHE X 501 TRP 0.014 0.001 TRP H 513 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00257 (10029) covalent geometry : angle 0.51443 (13763) SS BOND : bond 0.00360 ( 9) SS BOND : angle 0.99341 ( 18) hydrogen bonds : bond 0.02935 ( 528) hydrogen bonds : angle 4.16537 ( 1527) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue SER 222 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue LEU 215 is missing expected H atoms. Skipping. Residue ALA 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue VAL 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ALA 93 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue THR 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue MET 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ALA 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8131 (m) REVERT: H 507 GLU cc_start: 0.6029 (tp30) cc_final: 0.5151 (tp30) REVERT: X 456 LYS cc_start: 0.7048 (tmmt) cc_final: 0.6721 (tmmt) REVERT: X 493 ARG cc_start: 0.6482 (mmm160) cc_final: 0.5798 (mmt-90) REVERT: X 512 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.5987 (tt0) REVERT: X 518 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6621 (tp30) REVERT: X 541 ASN cc_start: 0.7781 (m110) cc_final: 0.7284 (m110) outliers start: 20 outliers final: 15 residues processed: 89 average time/residue: 0.2034 time to fit residues: 24.6909 Evaluate side-chains 86 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 506 LEU Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 174 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 114 optimal weight: 0.9980 chunk 144 optimal weight: 40.0000 chunk 15 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 30.0000 chunk 93 optimal weight: 0.4980 chunk 89 optimal weight: 0.0870 chunk 95 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 100 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.255867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.216453 restraints weight = 30607.315| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 2.09 r_work: 0.4131 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.6749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10038 Z= 0.104 Angle : 0.490 5.003 13781 Z= 0.259 Chirality : 0.042 0.165 1671 Planarity : 0.004 0.075 1838 Dihedral : 5.060 50.737 1736 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.90 % Favored : 94.89 % Rotamer: Outliers : 2.63 % Allowed : 24.48 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.23), residues: 1470 helix: 3.24 (0.31), residues: 296 sheet: 0.87 (0.22), residues: 552 loop : -0.68 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 416 TYR 0.011 0.001 TYR A 175 PHE 0.009 0.001 PHE X 501 TRP 0.019 0.001 TRP X 265 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00244 (10029) covalent geometry : angle 0.48864 (13763) SS BOND : bond 0.00367 ( 9) SS BOND : angle 0.96590 ( 18) hydrogen bonds : bond 0.02795 ( 528) hydrogen bonds : angle 3.95108 ( 1527) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue SER 222 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue LEU 215 is missing expected H atoms. Skipping. Residue ALA 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue VAL 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ALA 93 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue THR 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue MET 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ALA 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8111 (m) REVERT: H 427 MET cc_start: 0.7153 (mmm) cc_final: 0.6874 (tpp) REVERT: H 507 GLU cc_start: 0.5907 (tp30) cc_final: 0.4987 (tp30) REVERT: X 456 LYS cc_start: 0.7037 (tmmt) cc_final: 0.6653 (tmmt) REVERT: X 493 ARG cc_start: 0.6448 (mmm160) cc_final: 0.5766 (mmt-90) REVERT: X 512 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6008 (tt0) REVERT: X 518 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6715 (tp30) REVERT: X 541 ASN cc_start: 0.7743 (m110) cc_final: 0.7260 (m110) REVERT: A 107 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: A 150 GLU cc_start: 0.8197 (tp30) cc_final: 0.7965 (tp30) outliers start: 19 outliers final: 13 residues processed: 90 average time/residue: 0.2139 time to fit residues: 26.2337 Evaluate side-chains 90 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 399 THR Chi-restraints excluded: chain X residue 472 SER Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 50.0000 chunk 85 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 3 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 chunk 80 optimal weight: 4.9990 chunk 141 optimal weight: 50.0000 chunk 51 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.251882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.215998 restraints weight = 30472.181| |-----------------------------------------------------------------------------| r_work (start): 0.4574 rms_B_bonded: 1.96 r_work: 0.4113 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.7041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 10038 Z= 0.344 Angle : 0.683 6.875 13781 Z= 0.361 Chirality : 0.048 0.224 1671 Planarity : 0.006 0.073 1838 Dihedral : 5.922 51.277 1736 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.04 % Favored : 91.83 % Rotamer: Outliers : 4.15 % Allowed : 23.24 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.23), residues: 1470 helix: 2.94 (0.31), residues: 295 sheet: 0.47 (0.22), residues: 558 loop : -0.90 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 390 TYR 0.032 0.003 TYR A 174 PHE 0.030 0.003 PHE H 466 TRP 0.020 0.003 TRP X 407 HIS 0.012 0.002 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00822 (10029) covalent geometry : angle 0.68058 (13763) SS BOND : bond 0.00640 ( 9) SS BOND : angle 1.57855 ( 18) hydrogen bonds : bond 0.03817 ( 528) hydrogen bonds : angle 4.36046 ( 1527) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue SER 222 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue LEU 215 is missing expected H atoms. Skipping. Residue ALA 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue VAL 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ALA 93 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue THR 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue MET 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ALA 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8215 (m) REVERT: X 396 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.7966 (p) REVERT: X 462 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.6811 (tp) REVERT: X 493 ARG cc_start: 0.6810 (mmm160) cc_final: 0.6121 (mmt-90) REVERT: X 512 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6020 (tt0) REVERT: X 518 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6703 (tm-30) outliers start: 30 outliers final: 22 residues processed: 96 average time/residue: 0.2340 time to fit residues: 30.6959 Evaluate side-chains 97 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 396 VAL Chi-restraints excluded: chain X residue 399 THR Chi-restraints excluded: chain X residue 413 TYR Chi-restraints excluded: chain X residue 461 CYS Chi-restraints excluded: chain X residue 462 LEU Chi-restraints excluded: chain X residue 472 SER Chi-restraints excluded: chain X residue 506 LEU Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 174 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 134 optimal weight: 50.0000 chunk 42 optimal weight: 60.0000 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 50.0000 chunk 56 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 118 optimal weight: 0.5980 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.249517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.209362 restraints weight = 30173.309| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 1.94 r_work: 0.4102 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 10038 Z= 0.327 Angle : 0.698 7.026 13781 Z= 0.369 Chirality : 0.048 0.222 1671 Planarity : 0.006 0.078 1838 Dihedral : 6.063 53.952 1736 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.17 % Favored : 91.62 % Rotamer: Outliers : 3.87 % Allowed : 23.65 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.23), residues: 1470 helix: 2.67 (0.31), residues: 299 sheet: 0.23 (0.22), residues: 558 loop : -1.08 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 390 TYR 0.031 0.003 TYR A 174 PHE 0.027 0.003 PHE H 466 TRP 0.032 0.003 TRP X 265 HIS 0.010 0.002 HIS X 419 Details of bonding type rmsd covalent geometry : bond 0.00769 (10029) covalent geometry : angle 0.69642 (13763) SS BOND : bond 0.00646 ( 9) SS BOND : angle 1.63675 ( 18) hydrogen bonds : bond 0.03828 ( 528) hydrogen bonds : angle 4.51914 ( 1527) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue SER 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue MET 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue THR 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue MET 169 is missing expected H atoms. Skipping. Residue THR 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue SER 179 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue ILE 185 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue LYS 196 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue SER 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue SER 222 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue LEU 215 is missing expected H atoms. Skipping. Residue ALA 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue VAL 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ALA 93 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue THR 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue MET 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 155 is missing expected H atoms. Skipping. Residue ALA 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue TYR 35 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8228 (m) REVERT: X 500 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: X 512 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.5984 (tt0) outliers start: 28 outliers final: 21 residues processed: 95 average time/residue: 0.2424 time to fit residues: 30.8809 Evaluate side-chains 94 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 399 THR Chi-restraints excluded: chain X residue 461 CYS Chi-restraints excluded: chain X residue 472 SER Chi-restraints excluded: chain X residue 500 PHE Chi-restraints excluded: chain X residue 506 LEU Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 174 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 95 optimal weight: 50.0000 chunk 92 optimal weight: 6.9990 chunk 2 optimal weight: 50.0000 chunk 112 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 132 optimal weight: 50.0000 chunk 76 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 4 optimal weight: 50.0000 chunk 129 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.252544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.208350 restraints weight = 30098.006| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 2.07 r_work: 0.4091 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.7581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10038 Z= 0.144 Angle : 0.550 5.884 13781 Z= 0.292 Chirality : 0.043 0.174 1671 Planarity : 0.005 0.073 1838 Dihedral : 5.597 51.608 1736 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.54 % Favored : 93.32 % Rotamer: Outliers : 2.90 % Allowed : 25.03 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.23), residues: 1470 helix: 3.03 (0.32), residues: 293 sheet: 0.44 (0.22), residues: 557 loop : -0.91 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 390 TYR 0.015 0.002 TYR A 174 PHE 0.010 0.001 PHE X 501 TRP 0.021 0.002 TRP X 265 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00327 (10029) covalent geometry : angle 0.54902 (13763) SS BOND : bond 0.00456 ( 9) SS BOND : angle 1.17618 ( 18) hydrogen bonds : bond 0.03058 ( 528) hydrogen bonds : angle 4.19907 ( 1527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6288.54 seconds wall clock time: 106 minutes 51.57 seconds (6411.57 seconds total)