Starting phenix.real_space_refine on Mon Nov 18 19:54:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ywa_39627/11_2024/8ywa_39627.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ywa_39627/11_2024/8ywa_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ywa_39627/11_2024/8ywa_39627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ywa_39627/11_2024/8ywa_39627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ywa_39627/11_2024/8ywa_39627.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ywa_39627/11_2024/8ywa_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-5513/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: 8.92, per 1000 atoms: 0.54 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: 4.53 Conformation dependent library (CDL) restraints added in 1.9 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: 1.77 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: 5.97 Time building geometry restraints manager: 5.36 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.390 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.760 Find NCS groups from input model: 0.450 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.180 ------------------------------------------------------------------------------- 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 : 1.463 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: 0.4890 time to fit residues: 95.6836 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 : 1.409 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 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 : 1.377 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: 0.7568 (m) cc_final: 0.7276 (m) REVERT: X 433 THR cc_start: 0.5804 (m) cc_final: 0.5581 (p) REVERT: A 49 LEU cc_start: 0.6814 (pt) cc_final: 0.6573 (pp) outliers start: 6 outliers final: 5 residues processed: 104 average time/residue: 0.4317 time to fit residues: 62.7566 Evaluate side-chains 92 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 50.0000 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 50.0000 chunk 142 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 130 optimal weight: 50.0000 chunk 44 optimal weight: 50.0000 chunk 105 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** ** X 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10029 Z= 0.259 Angle : 0.572 12.834 13763 Z= 0.295 Chirality : 0.044 0.300 1671 Planarity : 0.004 0.065 1838 Dihedral : 5.326 57.853 1736 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.84 % Favored : 94.96 % Rotamer: Outliers : 1.66 % Allowed : 13.14 % Favored : 85.20 % 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: 1.28 (0.23), residues: 1470 helix: 3.22 (0.31), residues: 287 sheet: 1.08 (0.22), residues: 573 loop : -0.56 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 135 HIS 0.008 0.002 HIS X 525 PHE 0.018 0.002 PHE H 466 TYR 0.012 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 90 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.328 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: 0.7762 (OUTLIER) cc_final: 0.7483 (m) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.4209 time to fit residues: 51.6843 Evaluate side-chains 75 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 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 51 CYS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 164 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 50.0000 chunk 99 optimal weight: 50.0000 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 chunk 132 optimal weight: 50.0000 chunk 140 optimal weight: 40.0000 chunk 69 optimal weight: 0.6980 chunk 125 optimal weight: 50.0000 chunk 37 optimal weight: 0.7980 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 298 GLN H 381 HIS H 414 GLN ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 541 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.115 10029 Z= 0.674 Angle : 0.863 9.203 13763 Z= 0.462 Chirality : 0.055 0.278 1671 Planarity : 0.007 0.086 1838 Dihedral : 7.160 59.829 1736 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.49 % Favored : 92.17 % Rotamer: Outliers : 4.01 % Allowed : 17.01 % Favored : 78.98 % 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: 0.17 (0.23), residues: 1470 helix: 2.06 (0.30), residues: 300 sheet: 0.33 (0.22), residues: 562 loop : -1.09 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP X 407 HIS 0.016 0.004 HIS X 419 PHE 0.042 0.004 PHE H 466 TYR 0.038 0.004 TYR A 174 ARG 0.009 0.001 ARG X 486 *********************** 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 113 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8099 (m) REVERT: X 396 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7743 (p) REVERT: X 462 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7233 (tp) REVERT: X 500 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.6259 (m-10) outliers start: 29 outliers final: 20 residues processed: 109 average time/residue: 0.4027 time to fit residues: 62.2515 Evaluate side-chains 93 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 398 SER Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 414 GLN Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 396 VAL Chi-restraints excluded: chain X residue 430 THR Chi-restraints excluded: chain X residue 458 THR Chi-restraints excluded: chain X residue 462 LEU Chi-restraints excluded: chain X residue 500 PHE Chi-restraints excluded: chain X residue 508 VAL Chi-restraints excluded: chain X residue 540 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 71 optimal weight: 0.8980 chunk 125 optimal weight: 50.0000 chunk 35 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10029 Z= 0.188 Angle : 0.545 6.083 13763 Z= 0.292 Chirality : 0.043 0.165 1671 Planarity : 0.004 0.060 1838 Dihedral : 6.021 58.620 1736 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.43 % Favored : 95.37 % Rotamer: Outliers : 2.35 % Allowed : 20.19 % Favored : 77.46 % 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: 0.81 (0.23), residues: 1470 helix: 2.83 (0.31), residues: 295 sheet: 0.78 (0.22), residues: 558 loop : -0.84 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 407 HIS 0.009 0.001 HIS A 95 PHE 0.011 0.001 PHE H 519 TYR 0.019 0.002 TYR A 174 ARG 0.004 0.001 ARG X 390 *********************** 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 94 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 414 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6216 (mp10) REVERT: X 462 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7079 (tp) REVERT: A 90 GLU cc_start: 0.7109 (pp20) cc_final: 0.6893 (pp20) outliers start: 17 outliers final: 12 residues processed: 91 average time/residue: 0.3704 time to fit residues: 49.3690 Evaluate side-chains 83 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 414 GLN Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 399 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 108 VAL 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 47 optimal weight: 50.0000 chunk 126 optimal weight: 30.0000 chunk 27 optimal weight: 0.0270 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 140 optimal weight: 40.0000 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 50.0000 chunk 73 optimal weight: 1.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- 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 391 ASN ** X 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 532 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10029 Z= 0.237 Angle : 0.527 5.466 13763 Z= 0.279 Chirality : 0.043 0.164 1671 Planarity : 0.004 0.056 1838 Dihedral : 5.370 58.214 1736 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.59 % Favored : 94.21 % Rotamer: Outliers : 2.90 % Allowed : 20.33 % Favored : 76.76 % 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: 3.04 (0.31), residues: 296 sheet: 0.88 (0.22), residues: 552 loop : -0.76 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 513 HIS 0.005 0.001 HIS A 66 PHE 0.011 0.001 PHE H 503 TYR 0.018 0.002 TYR A 174 ARG 0.007 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: 21 poor density : 73 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7918 (m) REVERT: H 414 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6207 (mp10) REVERT: H 507 GLU cc_start: 0.5601 (tp30) cc_final: 0.4785 (tp30) REVERT: X 462 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7155 (tp) REVERT: X 500 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.6100 (m-10) REVERT: A 107 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6621 (mp0) outliers start: 21 outliers final: 13 residues processed: 89 average time/residue: 0.4667 time to fit residues: 58.3291 Evaluate side-chains 90 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 399 THR Chi-restraints excluded: chain H residue 414 GLN Chi-restraints excluded: chain H residue 429 SER 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 383 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 174 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 50.0000 chunk 118 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 139 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10029 Z= 0.270 Angle : 0.536 5.506 13763 Z= 0.285 Chirality : 0.043 0.166 1671 Planarity : 0.004 0.058 1838 Dihedral : 5.340 57.185 1736 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.59 % Favored : 94.21 % Rotamer: Outliers : 2.90 % Allowed : 21.44 % Favored : 75.66 % 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: 0.98 (0.23), residues: 1470 helix: 3.13 (0.31), residues: 296 sheet: 0.79 (0.22), residues: 559 loop : -0.73 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 265 HIS 0.007 0.001 HIS A 66 PHE 0.015 0.002 PHE H 466 TYR 0.018 0.002 TYR A 174 ARG 0.004 0.001 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 99 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 399 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7944 (m) REVERT: H 414 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.5652 (tp40) REVERT: H 507 GLU cc_start: 0.5544 (tp30) cc_final: 0.4771 (tp30) REVERT: X 305 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7891 (mpp80) REVERT: X 500 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6205 (m-10) outliers start: 21 outliers final: 17 residues processed: 94 average time/residue: 0.4703 time to fit residues: 61.2564 Evaluate side-chains 95 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 370 THR Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 414 GLN Chi-restraints excluded: chain H residue 429 SER 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 399 THR 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 93 CYS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 174 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 50.0000 chunk 27 optimal weight: 3.9990 chunk 88 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 69 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 127 optimal weight: 40.0000 chunk 133 optimal weight: 50.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10029 Z= 0.248 Angle : 0.519 6.606 13763 Z= 0.275 Chirality : 0.043 0.166 1671 Planarity : 0.004 0.066 1838 Dihedral : 5.290 56.652 1736 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.72 % Favored : 94.01 % Rotamer: Outliers : 3.46 % Allowed : 21.16 % Favored : 75.38 % 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: 1.09 (0.23), residues: 1470 helix: 3.25 (0.31), residues: 296 sheet: 0.91 (0.22), residues: 556 loop : -0.73 (0.26), residues: 618 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 466 TYR 0.015 0.002 TYR A 174 ARG 0.008 0.000 ARG H 405 *********************** 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 99 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.219 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: 0.8224 (OUTLIER) cc_final: 0.7967 (m) REVERT: H 414 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.5851 (tp40) REVERT: H 507 GLU cc_start: 0.5581 (tp30) cc_final: 0.4701 (tp30) REVERT: X 305 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7903 (mpp80) REVERT: X 456 LYS cc_start: 0.7085 (tmmt) cc_final: 0.6780 (tmmt) REVERT: X 512 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6225 (tt0) outliers start: 25 outliers final: 18 residues processed: 94 average time/residue: 0.4572 time to fit residues: 59.5361 Evaluate side-chains 94 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 414 GLN Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 399 THR Chi-restraints excluded: chain X residue 461 CYS Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 VAL 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 122 optimal weight: 50.0000 chunk 130 optimal weight: 50.0000 chunk 133 optimal weight: 50.0000 chunk 78 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 129 optimal weight: 40.0000 chunk 85 optimal weight: 5.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10029 Z= 0.424 Angle : 0.627 6.443 13763 Z= 0.333 Chirality : 0.045 0.203 1671 Planarity : 0.005 0.070 1838 Dihedral : 5.808 54.154 1736 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.95 % Favored : 92.85 % Rotamer: Outliers : 4.01 % Allowed : 20.89 % Favored : 75.10 % 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: 0.74 (0.23), residues: 1470 helix: 3.04 (0.31), residues: 296 sheet: 0.56 (0.22), residues: 564 loop : -0.86 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP X 407 HIS 0.010 0.002 HIS X 419 PHE 0.026 0.002 PHE H 466 TYR 0.024 0.003 TYR A 174 ARG 0.005 0.001 ARG A 40 *********************** 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 104 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 1.553 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: 0.8262 (OUTLIER) cc_final: 0.8030 (m) REVERT: H 414 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.5811 (tp40) REVERT: X 500 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.6481 (m-10) REVERT: X 512 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6309 (tt0) outliers start: 29 outliers final: 23 residues processed: 98 average time/residue: 0.4354 time to fit residues: 59.1648 Evaluate side-chains 101 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 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 398 SER Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 414 GLN Chi-restraints excluded: chain H residue 429 SER 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 399 THR Chi-restraints excluded: chain X residue 413 TYR Chi-restraints excluded: chain X residue 461 CYS Chi-restraints excluded: chain X residue 500 PHE Chi-restraints excluded: chain X residue 506 LEU Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 174 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 40.0000 chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 50.0000 chunk 144 optimal weight: 30.0000 chunk 132 optimal weight: 50.0000 chunk 115 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 88 optimal weight: 50.0000 chunk 70 optimal weight: 0.9980 chunk 91 optimal weight: 40.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10029 Z= 0.169 Angle : 0.492 5.710 13763 Z= 0.261 Chirality : 0.042 0.168 1671 Planarity : 0.004 0.058 1838 Dihedral : 5.175 54.951 1736 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 2.90 % Allowed : 22.27 % Favored : 74.83 % 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: 1.13 (0.23), residues: 1470 helix: 3.38 (0.31), residues: 293 sheet: 0.91 (0.22), residues: 556 loop : -0.73 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 513 HIS 0.004 0.001 HIS A 66 PHE 0.007 0.001 PHE H 500 TYR 0.012 0.001 TYR A 174 ARG 0.006 0.001 ARG H 405 ********************** 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 99 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.322 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: 0.8198 (OUTLIER) cc_final: 0.7957 (m) REVERT: H 414 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.5676 (tp40) REVERT: H 507 GLU cc_start: 0.5429 (tp30) cc_final: 0.4683 (tp30) REVERT: X 456 LYS cc_start: 0.6999 (tmmt) cc_final: 0.6711 (tmmt) REVERT: X 512 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6264 (tt0) outliers start: 21 outliers final: 16 residues processed: 95 average time/residue: 0.4532 time to fit residues: 60.4448 Evaluate side-chains 93 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 HIS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 414 GLN Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain X residue 370 THR Chi-restraints excluded: chain X residue 399 THR Chi-restraints excluded: chain X residue 461 CYS Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 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 122 optimal weight: 50.0000 chunk 35 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 30.0000 chunk 118 optimal weight: 0.0670 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 0.1980 chunk 101 optimal weight: 20.0000 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.255972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.222498 restraints weight = 30513.536| |-----------------------------------------------------------------------------| r_work (start): 0.4641 rms_B_bonded: 1.92 r_work: 0.4319 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4279 r_free = 0.4279 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4279 r_free = 0.4279 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10029 Z= 0.155 Angle : 0.471 5.164 13763 Z= 0.250 Chirality : 0.042 0.164 1671 Planarity : 0.004 0.052 1838 Dihedral : 4.833 56.769 1736 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 2.49 % Allowed : 22.82 % Favored : 74.69 % 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: 1.37 (0.23), residues: 1470 helix: 3.57 (0.31), residues: 293 sheet: 1.08 (0.22), residues: 554 loop : -0.59 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 513 HIS 0.003 0.001 HIS A 66 PHE 0.007 0.001 PHE X 501 TYR 0.010 0.001 TYR A 175 ARG 0.004 0.000 ARG X 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3512.49 seconds wall clock time: 63 minutes 27.95 seconds (3807.95 seconds total)