Starting phenix.real_space_refine on Tue Jan 21 20:01:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywa_39627/01_2025/8ywa_39627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywa_39627/01_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_39627/01_2025/8ywa_39627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywa_39627/01_2025/8ywa_39627.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywa_39627/01_2025/8ywa_39627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywa_39627/01_2025/8ywa_39627.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG: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, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 3} 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, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} 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, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} 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, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} 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, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} 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: {'GLN:plan1': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU: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: {'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 12, 'GLU:plan': 8, 'ASP:plan': 2} 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, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} 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, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} 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: 9.32, per 1000 atoms: 0.56 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: 4.39 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.96 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: 6.63 Time building geometry restraints manager: 5.20 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 542 or resid 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: 0.690 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.340 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.870 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- 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 10029 Z= 0.288 Angle : 0.606 12.078 13763 Z= 0.333 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 : 10.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.028 0.002 TRP H 513 HIS 0.011 0.001 HIS A 66 PHE 0.016 0.001 PHE H 466 TYR 0.020 0.001 TYR A 174 ARG 0.003 0.000 ARG X 405 *********************** 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 : 1.404 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: 0.4953 time to fit residues: 96.8803 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 : 1.314 ------------------------------------------------------------------------------- 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 122 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 131 optimal weight: 50.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 478 ASN X 487 HIS X 541 ASN A 28 GLN A 46 ASN A 67 ASN A 99 ASN 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 = 0.5030 r_free = 0.5030 target = 0.271271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.234777 restraints weight = 32171.834| |-----------------------------------------------------------------------------| r_work (start): 0.4719 rms_B_bonded: 2.21 r_work: 0.4367 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10029 Z= 0.239 Angle : 0.574 9.706 13763 Z= 0.298 Chirality : 0.044 0.250 1671 Planarity : 0.004 0.047 1838 Dihedral : 6.237 59.900 1739 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 0.83 % Allowed : 10.10 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1470 helix: 2.74 (0.30), residues: 284 sheet: 1.12 (0.23), residues: 564 loop : -0.43 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 513 HIS 0.007 0.001 HIS H 487 PHE 0.022 0.001 PHE X 501 TYR 0.013 0.002 TYR A 146 ARG 0.004 0.001 ARG X 384 *********************** 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 107 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 1.248 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: H 412 THR cc_start: 0.7875 (m) cc_final: 0.7592 (m) REVERT: H 432 LYS cc_start: 0.6742 (ttpt) cc_final: 0.6512 (tptt) REVERT: X 433 THR cc_start: 0.6295 (m) cc_final: 0.5809 (p) REVERT: X 502 VAL cc_start: 0.7372 (t) cc_final: 0.7141 (m) REVERT: A 49 LEU cc_start: 0.7078 (pt) cc_final: 0.6743 (pp) outliers start: 6 outliers final: 5 residues processed: 104 average time/residue: 0.4280 time to fit residues: 62.7752 Evaluate side-chains 93 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 111 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 137 optimal weight: 50.0000 chunk 106 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 143 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 477 HIS ** 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 = 0.4985 r_free = 0.4985 target = 0.265313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.224596 restraints weight = 31236.487| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 2.00 r_work: 0.4248 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10029 Z= 0.227 Angle : 0.544 12.441 13763 Z= 0.280 Chirality : 0.044 0.318 1671 Planarity : 0.004 0.060 1838 Dihedral : 5.079 57.431 1736 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.43 % Favored : 95.37 % Rotamer: Outliers : 1.24 % Allowed : 13.14 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1470 helix: 3.30 (0.31), residues: 287 sheet: 1.12 (0.22), residues: 573 loop : -0.47 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 513 HIS 0.007 0.001 HIS X 525 PHE 0.015 0.001 PHE H 503 TYR 0.011 0.002 TYR A 146 ARG 0.011 0.001 ARG X 457 *********************** 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 87 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.314 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: H 353 ILE cc_start: 0.7871 (pt) cc_final: 0.7635 (tt) REVERT: H 432 LYS cc_start: 0.6789 (ttpt) cc_final: 0.6551 (tptt) REVERT: X 502 VAL cc_start: 0.7943 (t) cc_final: 0.7718 (m) outliers start: 9 outliers final: 8 residues processed: 83 average time/residue: 0.4379 time to fit residues: 51.2036 Evaluate side-chains 73 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 462 LEU Chi-restraints excluded: chain X residue 533 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 108 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 13 optimal weight: 6.9990 chunk 91 optimal weight: 50.0000 chunk 143 optimal weight: 50.0000 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 87 optimal weight: 0.0570 chunk 58 optimal weight: 30.0000 chunk 7 optimal weight: 40.0000 chunk 116 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.263166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.233059 restraints weight = 31127.802| |-----------------------------------------------------------------------------| r_work (start): 0.4728 rms_B_bonded: 1.86 r_work: 0.4292 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4014 r_free = 0.4014 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4014 r_free = 0.4014 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10029 Z= 0.174 Angle : 0.478 4.750 13763 Z= 0.253 Chirality : 0.042 0.151 1671 Planarity : 0.004 0.054 1838 Dihedral : 4.680 54.564 1736 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.22 % Favored : 95.57 % Rotamer: Outliers : 1.24 % Allowed : 14.38 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1470 helix: 3.40 (0.31), residues: 289 sheet: 1.17 (0.22), residues: 570 loop : -0.42 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 513 HIS 0.004 0.001 HIS A 66 PHE 0.012 0.001 PHE H 503 TYR 0.010 0.001 TYR A 146 ARG 0.005 0.000 ARG X 457 *********************** 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 83 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7481 (m) REVERT: H 412 THR cc_start: 0.7960 (m) cc_final: 0.7711 (m) REVERT: H 432 LYS cc_start: 0.6788 (ttpt) cc_final: 0.6496 (tptt) REVERT: X 433 THR cc_start: 0.6630 (m) cc_final: 0.6139 (p) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.4059 time to fit residues: 46.5965 Evaluate side-chains 77 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 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 533 THR Chi-restraints excluded: chain A residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 127 optimal weight: 40.0000 chunk 133 optimal weight: 50.0000 chunk 23 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 124 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 128 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 381 HIS X 248 GLN ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 541 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.253679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.212098 restraints weight = 30970.591| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 1.97 r_work: 0.4074 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 10029 Z= 0.502 Angle : 0.729 8.049 13763 Z= 0.388 Chirality : 0.049 0.241 1671 Planarity : 0.006 0.072 1838 Dihedral : 6.246 59.486 1736 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.02 % Favored : 92.71 % Rotamer: Outliers : 3.60 % Allowed : 15.08 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1470 helix: 2.73 (0.31), residues: 298 sheet: 0.65 (0.22), residues: 571 loop : -0.80 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP X 407 HIS 0.013 0.003 HIS X 419 PHE 0.037 0.003 PHE H 466 TYR 0.028 0.003 TYR A 174 ARG 0.008 0.001 ARG X 486 *********************** 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 107 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8093 (m) REVERT: X 462 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7237 (tp) REVERT: X 500 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.6042 (m-10) REVERT: A 96 GLN cc_start: 0.6976 (tm-30) cc_final: 0.6712 (mp10) outliers start: 26 outliers final: 18 residues processed: 101 average time/residue: 0.4108 time to fit residues: 58.7907 Evaluate side-chains 93 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 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 473 VAL Chi-restraints excluded: chain H residue 502 VAL 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 458 THR Chi-restraints excluded: chain X residue 462 LEU Chi-restraints excluded: chain X residue 500 PHE Chi-restraints excluded: chain A residue 51 CYS 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 164 THR Chi-restraints excluded: chain A residue 174 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 136 optimal weight: 30.0000 chunk 116 optimal weight: 0.9980 chunk 99 optimal weight: 50.0000 chunk 74 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 GLN H 298 GLN ** X 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 532 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.256996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.216692 restraints weight = 30687.422| |-----------------------------------------------------------------------------| r_work (start): 0.4569 rms_B_bonded: 2.05 r_work: 0.4128 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3892 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10029 Z= 0.175 Angle : 0.500 5.486 13763 Z= 0.267 Chirality : 0.043 0.166 1671 Planarity : 0.004 0.055 1838 Dihedral : 5.197 55.389 1736 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.50 % Favored : 95.30 % Rotamer: Outliers : 1.94 % Allowed : 17.84 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1470 helix: 3.24 (0.31), residues: 296 sheet: 0.96 (0.22), residues: 557 loop : -0.63 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 513 HIS 0.004 0.001 HIS A 66 PHE 0.010 0.001 PHE X 466 TYR 0.012 0.001 TYR A 175 ARG 0.004 0.000 ARG H 405 *********************** 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 94 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7932 (m) REVERT: X 462 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7219 (tp) REVERT: X 500 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.5674 (m-10) REVERT: X 541 ASN cc_start: 0.7869 (m110) cc_final: 0.7528 (m110) outliers start: 14 outliers final: 11 residues processed: 90 average time/residue: 0.3764 time to fit residues: 49.5134 Evaluate side-chains 88 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 399 THR Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 462 LEU Chi-restraints excluded: chain X residue 500 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 VAL 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 69 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 89 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 141 optimal weight: 50.0000 chunk 83 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.259062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.224780 restraints weight = 30657.174| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 2.00 r_work: 0.4240 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10029 Z= 0.173 Angle : 0.480 4.929 13763 Z= 0.255 Chirality : 0.042 0.163 1671 Planarity : 0.004 0.054 1838 Dihedral : 4.925 54.069 1736 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.75 % Rotamer: Outliers : 1.94 % Allowed : 18.53 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1470 helix: 3.42 (0.31), residues: 296 sheet: 1.07 (0.22), residues: 560 loop : -0.55 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 513 HIS 0.004 0.001 HIS A 66 PHE 0.008 0.001 PHE H 466 TYR 0.010 0.001 TYR A 175 ARG 0.006 0.000 ARG H 405 *********************** 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 90 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 369 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8368 (tt) REVERT: H 399 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7963 (m) outliers start: 14 outliers final: 10 residues processed: 87 average time/residue: 0.4379 time to fit residues: 54.1435 Evaluate side-chains 86 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 369 LEU Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 93 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 91 optimal weight: 50.0000 chunk 139 optimal weight: 4.9990 chunk 3 optimal weight: 50.0000 chunk 48 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 138 optimal weight: 40.0000 chunk 53 optimal weight: 0.0040 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- 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 532 GLN ** X 541 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 = 0.4885 r_free = 0.4885 target = 0.250156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.216845 restraints weight = 30568.994| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 1.93 r_work: 0.4161 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.112 10029 Z= 0.699 Angle : 0.802 8.250 13763 Z= 0.427 Chirality : 0.052 0.268 1671 Planarity : 0.007 0.081 1838 Dihedral : 6.556 59.800 1736 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.43 % Favored : 92.23 % Rotamer: Outliers : 3.46 % Allowed : 19.23 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1470 helix: 2.64 (0.31), residues: 299 sheet: 0.38 (0.22), residues: 563 loop : -1.02 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP X 265 HIS 0.014 0.003 HIS X 419 PHE 0.040 0.004 PHE H 466 TYR 0.039 0.004 TYR X 413 ARG 0.012 0.001 ARG A 40 *********************** 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 100 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 369 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8451 (tt) REVERT: H 399 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8258 (m) REVERT: H 507 GLU cc_start: 0.5337 (tp30) cc_final: 0.4856 (tp30) REVERT: X 462 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7029 (tp) REVERT: X 500 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.6824 (m-10) REVERT: A 66 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7123 (p-80) outliers start: 25 outliers final: 16 residues processed: 96 average time/residue: 0.4398 time to fit residues: 58.4074 Evaluate side-chains 91 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 334 SER Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 413 TYR 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 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 164 THR Chi-restraints excluded: chain A residue 174 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 79 optimal weight: 0.6980 chunk 46 optimal weight: 40.0000 chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 40.0000 chunk 125 optimal weight: 50.0000 chunk 69 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.256080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.223484 restraints weight = 30564.713| |-----------------------------------------------------------------------------| r_work (start): 0.4652 rms_B_bonded: 1.90 r_work: 0.4229 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3977 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3965 r_free = 0.3965 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3965 r_free = 0.3965 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10029 Z= 0.177 Angle : 0.520 5.518 13763 Z= 0.277 Chirality : 0.043 0.166 1671 Planarity : 0.005 0.057 1838 Dihedral : 5.556 58.912 1736 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.43 % Favored : 95.37 % Rotamer: Outliers : 2.21 % Allowed : 20.61 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.23), residues: 1470 helix: 3.16 (0.31), residues: 296 sheet: 0.82 (0.22), residues: 551 loop : -0.76 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 513 HIS 0.006 0.001 HIS A 95 PHE 0.009 0.001 PHE X 466 TYR 0.015 0.002 TYR A 174 ARG 0.008 0.001 ARG X 390 *********************** 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 87 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 369 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8494 (tt) REVERT: H 399 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8150 (m) REVERT: H 507 GLU cc_start: 0.5722 (tp30) cc_final: 0.4867 (tp30) outliers start: 16 outliers final: 11 residues processed: 83 average time/residue: 0.4505 time to fit residues: 51.7208 Evaluate side-chains 82 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 369 LEU 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 500 PHE Chi-restraints excluded: chain X residue 504 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 108 VAL 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 36 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.256802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.216511 restraints weight = 30653.714| |-----------------------------------------------------------------------------| r_work (start): 0.4567 rms_B_bonded: 2.10 r_work: 0.4147 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10029 Z= 0.239 Angle : 0.522 5.286 13763 Z= 0.276 Chirality : 0.043 0.166 1671 Planarity : 0.004 0.068 1838 Dihedral : 5.370 58.347 1736 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.79 % Favored : 94.01 % Rotamer: Outliers : 1.94 % Allowed : 21.02 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1470 helix: 3.35 (0.31), residues: 293 sheet: 0.89 (0.22), residues: 556 loop : -0.70 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 513 HIS 0.005 0.001 HIS A 66 PHE 0.012 0.001 PHE H 503 TYR 0.015 0.002 TYR A 174 ARG 0.010 0.001 ARG X 390 ********************** 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 88 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 369 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8337 (tt) REVERT: H 399 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8122 (m) REVERT: H 507 GLU cc_start: 0.5704 (tp30) cc_final: 0.4961 (tp30) REVERT: X 305 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8127 (mpp80) REVERT: X 456 LYS cc_start: 0.7417 (tmmt) cc_final: 0.7149 (tmmt) outliers start: 14 outliers final: 11 residues processed: 85 average time/residue: 0.4672 time to fit residues: 54.4954 Evaluate side-chains 84 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 369 LEU 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 489 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 93 CYS 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 132 optimal weight: 50.0000 chunk 5 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 chunk 123 optimal weight: 40.0000 chunk 113 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 50.0000 chunk 139 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 97 optimal weight: 50.0000 chunk 102 optimal weight: 50.0000 overall best weight: 9.3388 ------------------------------------------------------------------------------- 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 515 GLN ** 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 = 0.4838 r_free = 0.4838 target = 0.245895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.199602 restraints weight = 30291.036| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 2.00 r_work: 0.4014 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.7356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.196 10029 Z= 1.248 Angle : 1.147 10.263 13763 Z= 0.607 Chirality : 0.068 0.374 1671 Planarity : 0.009 0.097 1838 Dihedral : 7.237 57.737 1736 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.47 % Favored : 89.92 % Rotamer: Outliers : 3.32 % Allowed : 19.78 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1470 helix: 1.80 (0.30), residues: 299 sheet: -0.04 (0.22), residues: 561 loop : -1.51 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.006 TRP X 407 HIS 0.025 0.005 HIS X 419 PHE 0.053 0.006 PHE H 466 TYR 0.070 0.007 TYR X 413 ARG 0.016 0.002 ARG X 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12092.61 seconds wall clock time: 212 minutes 12.20 seconds (12732.20 seconds total)