Starting phenix.real_space_refine on Wed Feb 21 11:21:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/02_2024/6bcl_7082.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/02_2024/6bcl_7082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/02_2024/6bcl_7082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/02_2024/6bcl_7082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/02_2024/6bcl_7082.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/02_2024/6bcl_7082.pdb" } resolution = 3.54 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= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 136 5.16 5 Na 2 4.78 5 C 19628 2.51 5 N 5340 2.21 5 O 5368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 826": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 888": "NH1" <-> "NH2" Residue "B ARG 901": "NH1" <-> "NH2" Residue "B ARG 949": "NH1" <-> "NH2" Residue "B ARG 953": "NH1" <-> "NH2" Residue "B ARG 960": "NH1" <-> "NH2" Residue "B ARG 993": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1118": "NH1" <-> "NH2" Residue "B ARG 1137": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 949": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 1063": "NH1" <-> "NH2" Residue "A ARG 1118": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 611": "NH1" <-> "NH2" Residue "C ARG 637": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 878": "NH1" <-> "NH2" Residue "C ARG 888": "NH1" <-> "NH2" Residue "C ARG 949": "NH1" <-> "NH2" Residue "C ARG 953": "NH1" <-> "NH2" Residue "C ARG 960": "NH1" <-> "NH2" Residue "C ARG 993": "NH1" <-> "NH2" Residue "C ARG 1063": "NH1" <-> "NH2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C ARG 1137": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 611": "NH1" <-> "NH2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 826": "NH1" <-> "NH2" Residue "D ARG 878": "NH1" <-> "NH2" Residue "D ARG 888": "NH1" <-> "NH2" Residue "D ARG 949": "NH1" <-> "NH2" Residue "D ARG 953": "NH1" <-> "NH2" Residue "D ARG 960": "NH1" <-> "NH2" Residue "D ARG 993": "NH1" <-> "NH2" Residue "D ARG 1063": "NH1" <-> "NH2" Residue "D ARG 1118": "NH1" <-> "NH2" Residue "D ARG 1137": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30474 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.94, per 1000 atoms: 0.52 Number of scatterers: 30474 At special positions: 0 Unit cell: (148.73, 148.73, 177.62, 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 136 16.00 Na 2 11.00 O 5368 8.00 N 5340 7.00 C 19628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1007 " distance=2.03 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1007 " distance=2.03 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1007 " distance=2.03 Simple disulfide: pdb=" SG CYS D 989 " - pdb=" SG CYS D1007 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 11.50 Conformation dependent library (CDL) restraints added in 5.6 seconds 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7232 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 12 sheets defined 66.9% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 284 through 295 removed outlier: 4.158A pdb=" N ARG B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.738A pdb=" N LEU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 5.511A pdb=" N GLU B 360 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 362 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.636A pdb=" N ILE B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 406 through 415 removed outlier: 4.122A pdb=" N ALA B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.577A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 449 removed outlier: 3.744A pdb=" N VAL B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 removed outlier: 3.916A pdb=" N TYR B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.678A pdb=" N ASN B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 484 " --> pdb=" O GLN B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 558 through 569 removed outlier: 3.630A pdb=" N LEU B 562 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.574A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.563A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 670 through 681 Processing helix chain 'B' and resid 689 through 698 removed outlier: 3.634A pdb=" N LEU B 693 " --> pdb=" O PRO B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.651A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 772 Processing helix chain 'B' and resid 774 through 799 Processing helix chain 'B' and resid 807 through 830 removed outlier: 3.562A pdb=" N LEU B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 857 Processing helix chain 'B' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR B 880 " --> pdb=" O GLY B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 900 removed outlier: 4.030A pdb=" N CYS B 892 " --> pdb=" O ARG B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 906 removed outlier: 3.509A pdb=" N PHE B 906 " --> pdb=" O LEU B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 948 removed outlier: 3.717A pdb=" N VAL B 926 " --> pdb=" O MET B 922 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 943 " --> pdb=" O ALA B 939 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 964 Processing helix chain 'B' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU B 968 " --> pdb=" O TYR B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 984 Processing helix chain 'B' and resid 1012 through 1029 removed outlier: 3.909A pdb=" N VAL B1016 " --> pdb=" O ALA B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1067 removed outlier: 5.778A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN B1049 " --> pdb=" O LYS B1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1089 Processing helix chain 'B' and resid 1113 through 1141 Processing helix chain 'B' and resid 1142 through 1191 removed outlier: 4.486A pdb=" N GLN B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B1168 " --> pdb=" O ILE B1164 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B1169 " --> pdb=" O ARG B1165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 19 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 284 through 295 removed outlier: 4.157A pdb=" N ARG A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.739A pdb=" N LEU A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 5.510A pdb=" N GLU A 360 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 362 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.637A pdb=" N ILE A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 406 through 415 removed outlier: 4.123A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.576A pdb=" N LEU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 removed outlier: 3.745A pdb=" N VAL A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.915A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.677A pdb=" N ASN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 484 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.629A pdb=" N LEU A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.573A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.562A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 670 through 681 Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.634A pdb=" N LEU A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.650A pdb=" N ILE A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 774 through 799 Processing helix chain 'A' and resid 807 through 830 removed outlier: 3.562A pdb=" N LEU A 811 " --> pdb=" O SER A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 857 Processing helix chain 'A' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 900 removed outlier: 4.030A pdb=" N CYS A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.510A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 removed outlier: 3.717A pdb=" N VAL A 926 " --> pdb=" O MET A 922 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 964 Processing helix chain 'A' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU A 968 " --> pdb=" O TYR A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 984 Processing helix chain 'A' and resid 1012 through 1029 removed outlier: 3.910A pdb=" N VAL A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1067 removed outlier: 5.778A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A1060 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1089 Processing helix chain 'A' and resid 1113 through 1141 Processing helix chain 'A' and resid 1142 through 1191 removed outlier: 4.487A pdb=" N GLN A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A1164 " --> pdb=" O GLN A1160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A1168 " --> pdb=" O ILE A1164 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'C' and resid 284 through 295 removed outlier: 4.157A pdb=" N ARG C 288 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.738A pdb=" N LEU C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 5.511A pdb=" N GLU C 360 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 362 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.636A pdb=" N ILE C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 406 through 415 removed outlier: 4.124A pdb=" N ALA C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.577A pdb=" N LEU C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 449 removed outlier: 3.744A pdb=" N VAL C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.917A pdb=" N TYR C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.678A pdb=" N ASN C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 484 " --> pdb=" O GLN C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 558 through 569 removed outlier: 3.629A pdb=" N LEU C 562 " --> pdb=" O PRO C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 582 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.573A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.562A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 670 through 681 Processing helix chain 'C' and resid 689 through 698 removed outlier: 3.634A pdb=" N LEU C 693 " --> pdb=" O PRO C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 703 removed outlier: 3.651A pdb=" N ILE C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 772 Processing helix chain 'C' and resid 774 through 799 Processing helix chain 'C' and resid 807 through 830 removed outlier: 3.561A pdb=" N LEU C 811 " --> pdb=" O SER C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 857 Processing helix chain 'C' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR C 880 " --> pdb=" O GLY C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 900 removed outlier: 4.030A pdb=" N CYS C 892 " --> pdb=" O ARG C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.520A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL C 919 " --> pdb=" O LYS C 915 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 948 removed outlier: 3.718A pdb=" N VAL C 926 " --> pdb=" O MET C 922 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 943 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 948 " --> pdb=" O THR C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 964 Processing helix chain 'C' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU C 968 " --> pdb=" O TYR C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 984 Processing helix chain 'C' and resid 1012 through 1029 removed outlier: 3.911A pdb=" N VAL C1016 " --> pdb=" O ALA C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1067 removed outlier: 5.778A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR C1059 " --> pdb=" O LYS C1055 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1089 Processing helix chain 'C' and resid 1113 through 1141 Processing helix chain 'C' and resid 1142 through 1191 removed outlier: 4.487A pdb=" N GLN C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C1164 " --> pdb=" O GLN C1160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C1168 " --> pdb=" O ILE C1164 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG C1169 " --> pdb=" O ARG C1165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C1170 " --> pdb=" O GLU C1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER D 178 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 284 through 295 removed outlier: 4.158A pdb=" N ARG D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 344 through 356 removed outlier: 3.739A pdb=" N LEU D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 362 removed outlier: 5.511A pdb=" N GLU D 360 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 362 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.636A pdb=" N ILE D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 406 through 415 removed outlier: 4.124A pdb=" N ALA D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.578A pdb=" N LEU D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 449 removed outlier: 3.744A pdb=" N VAL D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 465 removed outlier: 3.916A pdb=" N TYR D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.677A pdb=" N ASN D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 484 " --> pdb=" O GLN D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 558 through 569 removed outlier: 3.629A pdb=" N LEU D 562 " --> pdb=" O PRO D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 582 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.573A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.562A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 670 through 681 Processing helix chain 'D' and resid 689 through 698 removed outlier: 3.633A pdb=" N LEU D 693 " --> pdb=" O PRO D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 703 removed outlier: 3.651A pdb=" N ILE D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 772 Processing helix chain 'D' and resid 774 through 799 Processing helix chain 'D' and resid 807 through 830 removed outlier: 3.562A pdb=" N LEU D 811 " --> pdb=" O SER D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 857 Processing helix chain 'D' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR D 880 " --> pdb=" O GLY D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 900 removed outlier: 4.029A pdb=" N CYS D 892 " --> pdb=" O ARG D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 906 Processing helix chain 'D' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL D 919 " --> pdb=" O LYS D 915 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 948 removed outlier: 3.717A pdb=" N VAL D 926 " --> pdb=" O MET D 922 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 948 " --> pdb=" O THR D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 964 Processing helix chain 'D' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU D 968 " --> pdb=" O TYR D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 984 Processing helix chain 'D' and resid 1012 through 1029 removed outlier: 3.911A pdb=" N VAL D1016 " --> pdb=" O ALA D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1029 through 1067 removed outlier: 5.778A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1089 Processing helix chain 'D' and resid 1113 through 1141 Processing helix chain 'D' and resid 1142 through 1191 removed outlier: 4.487A pdb=" N GLN D1163 " --> pdb=" O LYS D1159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D1164 " --> pdb=" O GLN D1160 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP D1168 " --> pdb=" O ILE D1164 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG D1169 " --> pdb=" O ARG D1165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D1170 " --> pdb=" O GLU D1166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.525A pdb=" N GLY B 77 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 90 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 235 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 92 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP B 237 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 94 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 186 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE B 234 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 188 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL B 236 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA B 190 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY B 157 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU B 300 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU B 276 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 302 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 278 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR B 365 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 301 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 985 through 986 removed outlier: 3.957A pdb=" N ILE B 985 " --> pdb=" O HIS B 998 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA5, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.526A pdb=" N GLY A 77 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN A 90 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 235 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 92 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP A 237 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 94 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 186 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE A 234 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY A 188 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL A 236 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA A 190 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY A 157 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU A 300 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A 276 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 302 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU A 278 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N TYR A 365 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 301 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 986 removed outlier: 3.956A pdb=" N ILE A 985 " --> pdb=" O HIS A 998 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.526A pdb=" N GLY C 77 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN C 90 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU C 235 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU C 92 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP C 237 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU C 94 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA C 186 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE C 234 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 188 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 236 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA C 190 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY C 157 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU C 300 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 276 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL C 302 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU C 278 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N TYR C 365 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU C 301 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 985 through 986 removed outlier: 3.956A pdb=" N ILE C 985 " --> pdb=" O HIS C 998 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.526A pdb=" N GLY D 77 " --> pdb=" O PHE D 91 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN D 90 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 235 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU D 92 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP D 237 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 94 " --> pdb=" O ASP D 237 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA D 186 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE D 234 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY D 188 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL D 236 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA D 190 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY D 157 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU D 300 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU D 276 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL D 302 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 278 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR D 365 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU D 301 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 985 through 986 removed outlier: 3.957A pdb=" N ILE D 985 " --> pdb=" O HIS D 998 " (cutoff:3.500A) 1779 hydrogen bonds defined for protein. 5265 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: 14.94 Time building geometry restraints manager: 12.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9880 1.34 - 1.46: 7411 1.46 - 1.58: 13649 1.58 - 1.71: 0 1.71 - 1.83: 204 Bond restraints: 31144 Sorted by residual: bond pdb=" C PRO C1073 " pdb=" N PRO C1074 " ideal model delta sigma weight residual 1.337 1.371 -0.034 1.11e-02 8.12e+03 9.52e+00 bond pdb=" C PRO A1073 " pdb=" N PRO A1074 " ideal model delta sigma weight residual 1.337 1.370 -0.034 1.11e-02 8.12e+03 9.20e+00 bond pdb=" C PRO D1073 " pdb=" N PRO D1074 " ideal model delta sigma weight residual 1.337 1.370 -0.034 1.11e-02 8.12e+03 9.13e+00 bond pdb=" C PRO B1073 " pdb=" N PRO B1074 " ideal model delta sigma weight residual 1.337 1.370 -0.033 1.11e-02 8.12e+03 8.88e+00 bond pdb=" C PHE C 340 " pdb=" N PRO C 341 " ideal model delta sigma weight residual 1.334 1.381 -0.048 2.34e-02 1.83e+03 4.13e+00 ... (remaining 31139 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.98: 611 105.98 - 113.00: 16976 113.00 - 120.02: 11803 120.02 - 127.05: 12422 127.05 - 134.07: 420 Bond angle restraints: 42232 Sorted by residual: angle pdb=" N LEU B1030 " pdb=" CA LEU B1030 " pdb=" C LEU B1030 " ideal model delta sigma weight residual 111.36 118.54 -7.18 1.09e+00 8.42e-01 4.34e+01 angle pdb=" N ILE B1029 " pdb=" CA ILE B1029 " pdb=" C ILE B1029 " ideal model delta sigma weight residual 111.67 116.63 -4.96 9.50e-01 1.11e+00 2.72e+01 angle pdb=" N LEU C 948 " pdb=" CA LEU C 948 " pdb=" C LEU C 948 " ideal model delta sigma weight residual 108.41 100.41 8.00 1.63e+00 3.76e-01 2.41e+01 angle pdb=" N LEU A 948 " pdb=" CA LEU A 948 " pdb=" C LEU A 948 " ideal model delta sigma weight residual 108.41 100.44 7.97 1.63e+00 3.76e-01 2.39e+01 angle pdb=" N LEU B 948 " pdb=" CA LEU B 948 " pdb=" C LEU B 948 " ideal model delta sigma weight residual 108.41 100.47 7.94 1.63e+00 3.76e-01 2.37e+01 ... (remaining 42227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 17790 17.64 - 35.28: 588 35.28 - 52.93: 74 52.93 - 70.57: 8 70.57 - 88.21: 20 Dihedral angle restraints: 18480 sinusoidal: 7320 harmonic: 11160 Sorted by residual: dihedral pdb=" CB CYS D 989 " pdb=" SG CYS D 989 " pdb=" SG CYS D1007 " pdb=" CB CYS D1007 " ideal model delta sinusoidal sigma weight residual 93.00 -178.79 -88.21 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS A 989 " pdb=" SG CYS A 989 " pdb=" SG CYS A1007 " pdb=" CB CYS A1007 " ideal model delta sinusoidal sigma weight residual 93.00 -178.82 -88.18 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C 989 " pdb=" SG CYS C 989 " pdb=" SG CYS C1007 " pdb=" CB CYS C1007 " ideal model delta sinusoidal sigma weight residual 93.00 -178.84 -88.16 1 1.00e+01 1.00e-02 9.29e+01 ... (remaining 18477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3508 0.057 - 0.113: 1152 0.113 - 0.170: 129 0.170 - 0.226: 2 0.226 - 0.283: 5 Chirality restraints: 4796 Sorted by residual: chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE D 279 " pdb=" CA ILE D 279 " pdb=" CG1 ILE D 279 " pdb=" CG2 ILE D 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE B 279 " pdb=" CA ILE B 279 " pdb=" CG1 ILE B 279 " pdb=" CG2 ILE B 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4793 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 816 " 0.024 2.00e-02 2.50e+03 2.03e-02 1.03e+01 pdb=" CG TRP D 816 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP D 816 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 816 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 816 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 816 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 816 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 816 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 816 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 816 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.025 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP A 816 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 816 " -0.024 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP B 816 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 816 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 816 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 816 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 816 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 816 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 816 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 816 " -0.002 2.00e-02 2.50e+03 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9732 2.84 - 3.35: 27498 3.35 - 3.87: 47502 3.87 - 4.38: 53447 4.38 - 4.90: 92626 Nonbonded interactions: 230805 Sorted by model distance: nonbonded pdb=" O ARG D 354 " pdb=" OG1 THR D 357 " model vdw 2.324 2.440 nonbonded pdb=" O ARG B 354 " pdb=" OG1 THR B 357 " model vdw 2.324 2.440 nonbonded pdb=" O ARG C 354 " pdb=" OG1 THR C 357 " model vdw 2.324 2.440 nonbonded pdb=" O ARG A 354 " pdb=" OG1 THR A 357 " model vdw 2.325 2.440 nonbonded pdb=" O VAL C 506 " pdb=" OG1 THR C 509 " model vdw 2.341 2.440 ... (remaining 230800 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 1193) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.690 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 85.280 Find NCS groups from input model: 3.140 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 0.008 0.055 31144 Z= 0.481 Angle : 0.964 10.380 42232 Z= 0.532 Chirality : 0.052 0.283 4796 Planarity : 0.006 0.064 5332 Dihedral : 9.609 76.901 11236 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.38 % Allowed : 2.00 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.09), residues: 3796 helix: -3.23 (0.06), residues: 2408 sheet: -0.81 (0.37), residues: 208 loop : -3.13 (0.14), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP D 816 HIS 0.007 0.003 HIS A1127 PHE 0.024 0.003 PHE A 23 TYR 0.022 0.003 TYR B 339 ARG 0.008 0.001 ARG A 767 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 641 time to evaluate : 3.674 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: B 13 LYS cc_start: 0.2334 (OUTLIER) cc_final: 0.2098 (pmmt) REVERT: B 17 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7743 (tptt) REVERT: B 173 ASP cc_start: 0.7735 (m-30) cc_final: 0.7130 (m-30) REVERT: B 197 ASN cc_start: 0.7270 (m-40) cc_final: 0.6541 (t0) REVERT: B 224 PHE cc_start: 0.6899 (m-10) cc_final: 0.6667 (m-10) REVERT: B 228 TYR cc_start: 0.7066 (p90) cc_final: 0.6673 (p90) REVERT: B 310 ASP cc_start: 0.7504 (t0) cc_final: 0.6867 (t0) REVERT: B 355 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.6034 (mp) REVERT: B 356 MET cc_start: 0.7092 (mmm) cc_final: 0.6235 (tpp) REVERT: B 413 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7577 (mt-10) REVERT: B 430 LEU cc_start: 0.8523 (tp) cc_final: 0.8194 (mt) REVERT: B 432 ASP cc_start: 0.7675 (m-30) cc_final: 0.7315 (m-30) REVERT: B 613 LYS cc_start: 0.8509 (mttt) cc_final: 0.8290 (mmmt) REVERT: B 675 LEU cc_start: 0.8717 (mt) cc_final: 0.8498 (tp) REVERT: B 695 LEU cc_start: 0.8805 (mt) cc_final: 0.8601 (mt) REVERT: B 825 LEU cc_start: 0.8228 (mp) cc_final: 0.7920 (pp) REVERT: B 873 LEU cc_start: 0.9172 (tp) cc_final: 0.8818 (tt) REVERT: B 979 MET cc_start: 0.9484 (ptt) cc_final: 0.9095 (ptm) REVERT: B 1145 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8077 (tm-30) REVERT: A 13 LYS cc_start: 0.2188 (OUTLIER) cc_final: 0.1943 (pmmt) REVERT: A 17 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7721 (tptt) REVERT: A 173 ASP cc_start: 0.7616 (m-30) cc_final: 0.7022 (m-30) REVERT: A 197 ASN cc_start: 0.7352 (m-40) cc_final: 0.7010 (t0) REVERT: A 224 PHE cc_start: 0.6915 (m-10) cc_final: 0.6674 (m-10) REVERT: A 228 TYR cc_start: 0.7045 (p90) cc_final: 0.6682 (p90) REVERT: A 310 ASP cc_start: 0.7508 (t0) cc_final: 0.6891 (t0) REVERT: A 355 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.5845 (mp) REVERT: A 356 MET cc_start: 0.7124 (mmm) cc_final: 0.6800 (tpp) REVERT: A 427 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7872 (mp0) REVERT: A 430 LEU cc_start: 0.8491 (tp) cc_final: 0.8122 (mt) REVERT: A 432 ASP cc_start: 0.7640 (m-30) cc_final: 0.7288 (m-30) REVERT: A 675 LEU cc_start: 0.8717 (mt) cc_final: 0.8440 (tp) REVERT: A 684 MET cc_start: 0.8659 (mtt) cc_final: 0.8442 (mtm) REVERT: A 695 LEU cc_start: 0.8895 (mt) cc_final: 0.8647 (mt) REVERT: A 823 GLU cc_start: 0.8212 (tp30) cc_final: 0.7865 (tp30) REVERT: A 825 LEU cc_start: 0.8296 (mp) cc_final: 0.7963 (pp) REVERT: A 873 LEU cc_start: 0.9186 (tp) cc_final: 0.8789 (tt) REVERT: A 1145 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8068 (tm-30) REVERT: C 13 LYS cc_start: 0.2301 (OUTLIER) cc_final: 0.2072 (pmmt) REVERT: C 17 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7724 (tptt) REVERT: C 173 ASP cc_start: 0.7594 (m-30) cc_final: 0.7015 (m-30) REVERT: C 197 ASN cc_start: 0.7348 (m-40) cc_final: 0.7019 (t0) REVERT: C 224 PHE cc_start: 0.6935 (m-10) cc_final: 0.6691 (m-10) REVERT: C 228 TYR cc_start: 0.7021 (p90) cc_final: 0.6668 (p90) REVERT: C 310 ASP cc_start: 0.7507 (t0) cc_final: 0.6867 (t0) REVERT: C 355 ILE cc_start: 0.6348 (OUTLIER) cc_final: 0.5964 (mp) REVERT: C 356 MET cc_start: 0.7175 (mmm) cc_final: 0.6761 (tpp) REVERT: C 413 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 427 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7890 (mp0) REVERT: C 430 LEU cc_start: 0.8502 (tp) cc_final: 0.8119 (mt) REVERT: C 432 ASP cc_start: 0.7653 (m-30) cc_final: 0.7309 (m-30) REVERT: C 675 LEU cc_start: 0.8752 (mt) cc_final: 0.8507 (tp) REVERT: C 695 LEU cc_start: 0.8803 (mt) cc_final: 0.8565 (mt) REVERT: C 823 GLU cc_start: 0.8273 (tp30) cc_final: 0.7975 (tp30) REVERT: C 825 LEU cc_start: 0.8292 (mp) cc_final: 0.7966 (pp) REVERT: C 873 LEU cc_start: 0.9203 (tp) cc_final: 0.8815 (tt) REVERT: C 979 MET cc_start: 0.9397 (ptt) cc_final: 0.8864 (ptm) REVERT: C 1145 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8112 (tm-30) REVERT: D 16 ARG cc_start: 0.7513 (ptp-170) cc_final: 0.6870 (ptp-170) REVERT: D 17 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7881 (tptt) REVERT: D 163 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.6123 (pp) REVERT: D 169 VAL cc_start: 0.7215 (t) cc_final: 0.6821 (m) REVERT: D 173 ASP cc_start: 0.7608 (m-30) cc_final: 0.7191 (m-30) REVERT: D 197 ASN cc_start: 0.6730 (m-40) cc_final: 0.5995 (t0) REVERT: D 228 TYR cc_start: 0.7088 (p90) cc_final: 0.6649 (p90) REVERT: D 355 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.6147 (mp) REVERT: D 356 MET cc_start: 0.7075 (mmm) cc_final: 0.6552 (tpp) REVERT: D 413 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7486 (mt-10) REVERT: D 430 LEU cc_start: 0.8638 (tp) cc_final: 0.8243 (mt) REVERT: D 825 LEU cc_start: 0.8245 (mp) cc_final: 0.7951 (pp) REVERT: D 873 LEU cc_start: 0.9184 (tp) cc_final: 0.8829 (tt) REVERT: D 979 MET cc_start: 0.9440 (ptt) cc_final: 0.8962 (ptm) REVERT: D 1038 MET cc_start: 0.8864 (mtm) cc_final: 0.8633 (mtp) REVERT: D 1145 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8182 (tm-30) REVERT: D 1159 LYS cc_start: 0.8229 (mttt) cc_final: 0.7936 (tppt) outliers start: 12 outliers final: 0 residues processed: 653 average time/residue: 0.5213 time to fit residues: 496.6038 Evaluate side-chains 292 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 284 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 355 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN B 229 ASN B 248 ASN B 261 GLN B 436 ASN B 476 ASN B1080 HIS A 136 GLN A 229 ASN A 248 ASN A 261 GLN A 436 ASN A 476 ASN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 HIS C 136 GLN C 229 ASN C 248 ASN C 261 GLN C 436 ASN C 476 ASN C1080 HIS D 136 GLN D 229 ASN D 261 GLN D 436 ASN D1080 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 31144 Z= 0.250 Angle : 0.625 7.806 42232 Z= 0.325 Chirality : 0.040 0.157 4796 Planarity : 0.005 0.050 5332 Dihedral : 5.348 54.993 4238 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.84 % Allowed : 7.03 % Favored : 91.12 % 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: -1.66 (0.12), residues: 3796 helix: -0.32 (0.09), residues: 2464 sheet: -1.07 (0.35), residues: 236 loop : -2.76 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 214 HIS 0.005 0.001 HIS B 425 PHE 0.027 0.002 PHE B 415 TYR 0.018 0.001 TYR C 339 ARG 0.005 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 357 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7691 (tptt) REVERT: B 93 ARG cc_start: 0.7481 (ttt180) cc_final: 0.7146 (ttt180) REVERT: B 173 ASP cc_start: 0.7561 (m-30) cc_final: 0.7204 (m-30) REVERT: B 197 ASN cc_start: 0.7044 (m-40) cc_final: 0.6627 (m-40) REVERT: B 224 PHE cc_start: 0.6980 (m-10) cc_final: 0.6733 (m-10) REVERT: B 228 TYR cc_start: 0.7051 (p90) cc_final: 0.6704 (p90) REVERT: B 351 GLN cc_start: 0.4845 (mm-40) cc_final: 0.4639 (mm-40) REVERT: B 427 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: B 430 LEU cc_start: 0.8380 (tp) cc_final: 0.8063 (tp) REVERT: B 645 ARG cc_start: 0.7293 (ttp-170) cc_final: 0.7071 (mpt180) REVERT: B 649 TRP cc_start: 0.6104 (OUTLIER) cc_final: 0.5713 (m-90) REVERT: B 825 LEU cc_start: 0.7964 (mp) cc_final: 0.7702 (pp) REVERT: B 977 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: B 979 MET cc_start: 0.9454 (ptt) cc_final: 0.9023 (ptm) REVERT: B 1119 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7478 (mtmt) REVERT: A 17 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7687 (tptt) REVERT: A 93 ARG cc_start: 0.7458 (ttt180) cc_final: 0.7137 (ttt180) REVERT: A 173 ASP cc_start: 0.7561 (m-30) cc_final: 0.7210 (m-30) REVERT: A 197 ASN cc_start: 0.7111 (m-40) cc_final: 0.6326 (t0) REVERT: A 224 PHE cc_start: 0.6981 (m-10) cc_final: 0.6744 (m-10) REVERT: A 228 TYR cc_start: 0.7184 (p90) cc_final: 0.6778 (p90) REVERT: A 351 GLN cc_start: 0.4682 (mm-40) cc_final: 0.4316 (mm-40) REVERT: A 355 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5872 (mp) REVERT: A 415 PHE cc_start: 0.7114 (m-80) cc_final: 0.6908 (m-80) REVERT: A 427 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7683 (mp0) REVERT: A 683 GLU cc_start: 0.7225 (pm20) cc_final: 0.6993 (pm20) REVERT: A 823 GLU cc_start: 0.8095 (tp30) cc_final: 0.7595 (tm-30) REVERT: A 825 LEU cc_start: 0.7957 (mp) cc_final: 0.7671 (pp) REVERT: A 1119 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7567 (mtmt) REVERT: C 17 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7673 (tptt) REVERT: C 93 ARG cc_start: 0.7488 (ttt180) cc_final: 0.7140 (ttt180) REVERT: C 173 ASP cc_start: 0.7487 (m-30) cc_final: 0.7121 (m-30) REVERT: C 197 ASN cc_start: 0.7164 (m-40) cc_final: 0.6437 (t0) REVERT: C 224 PHE cc_start: 0.7008 (m-10) cc_final: 0.6785 (m-10) REVERT: C 228 TYR cc_start: 0.7162 (p90) cc_final: 0.6762 (p90) REVERT: C 351 GLN cc_start: 0.4650 (mm-40) cc_final: 0.4003 (mm-40) REVERT: C 355 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5634 (mp) REVERT: C 427 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7653 (mp0) REVERT: C 601 ARG cc_start: 0.7223 (mtm110) cc_final: 0.7020 (mtt180) REVERT: C 683 GLU cc_start: 0.7184 (pm20) cc_final: 0.6759 (pm20) REVERT: C 823 GLU cc_start: 0.8157 (tp30) cc_final: 0.7629 (tm-30) REVERT: C 825 LEU cc_start: 0.7984 (mp) cc_final: 0.7700 (pp) REVERT: C 979 MET cc_start: 0.9415 (ptt) cc_final: 0.8939 (ptm) REVERT: C 1119 LYS cc_start: 0.7773 (mtmt) cc_final: 0.7548 (mtmt) REVERT: D 16 ARG cc_start: 0.7540 (ptp-170) cc_final: 0.6654 (ptp-170) REVERT: D 17 LYS cc_start: 0.8308 (ttpp) cc_final: 0.7837 (tptt) REVERT: D 93 ARG cc_start: 0.7519 (ttt180) cc_final: 0.7293 (ttt90) REVERT: D 169 VAL cc_start: 0.7224 (t) cc_final: 0.6786 (m) REVERT: D 173 ASP cc_start: 0.7511 (m-30) cc_final: 0.7263 (m-30) REVERT: D 197 ASN cc_start: 0.6653 (m-40) cc_final: 0.6114 (t0) REVERT: D 228 TYR cc_start: 0.7032 (p90) cc_final: 0.6604 (p90) REVERT: D 355 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.5854 (mp) REVERT: D 415 PHE cc_start: 0.6968 (m-80) cc_final: 0.6733 (m-80) REVERT: D 422 ARG cc_start: 0.5412 (tpp-160) cc_final: 0.5102 (tpp-160) REVERT: D 432 ASP cc_start: 0.7614 (m-30) cc_final: 0.7402 (t0) REVERT: D 825 LEU cc_start: 0.7980 (mp) cc_final: 0.7710 (pp) REVERT: D 979 MET cc_start: 0.9422 (ptt) cc_final: 0.8959 (ptm) REVERT: D 1119 LYS cc_start: 0.7740 (mtmt) cc_final: 0.7490 (mtmt) outliers start: 59 outliers final: 28 residues processed: 407 average time/residue: 0.4759 time to fit residues: 295.5324 Evaluate side-chains 311 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 457 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 290 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 9.9990 chunk 377 optimal weight: 6.9990 chunk 311 optimal weight: 0.0020 chunk 346 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 280 optimal weight: 0.0770 overall best weight: 2.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 GLN ** C1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 969 GLN ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31144 Z= 0.189 Angle : 0.547 8.422 42232 Z= 0.280 Chirality : 0.038 0.165 4796 Planarity : 0.004 0.049 5332 Dihedral : 4.700 55.193 4234 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.00 % Allowed : 8.88 % Favored : 89.12 % 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: -0.12 (0.14), residues: 3796 helix: 1.07 (0.10), residues: 2484 sheet: -0.72 (0.37), residues: 212 loop : -2.68 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1054 HIS 0.003 0.001 HIS D 174 PHE 0.030 0.002 PHE C 415 TYR 0.016 0.001 TYR A 339 ARG 0.004 0.000 ARG C 637 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 327 time to evaluate : 3.360 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: B 173 ASP cc_start: 0.7547 (m-30) cc_final: 0.7277 (m-30) REVERT: B 197 ASN cc_start: 0.6371 (m-40) cc_final: 0.5819 (t0) REVERT: B 228 TYR cc_start: 0.6946 (p90) cc_final: 0.6582 (p90) REVERT: B 351 GLN cc_start: 0.4719 (mm-40) cc_final: 0.4501 (mm-40) REVERT: B 649 TRP cc_start: 0.6200 (OUTLIER) cc_final: 0.5894 (m-90) REVERT: B 683 GLU cc_start: 0.7370 (pm20) cc_final: 0.7048 (pm20) REVERT: B 825 LEU cc_start: 0.7900 (mp) cc_final: 0.7627 (pp) REVERT: B 977 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: B 979 MET cc_start: 0.9429 (ptt) cc_final: 0.9013 (ptm) REVERT: B 1119 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7408 (mtmt) REVERT: A 173 ASP cc_start: 0.7530 (m-30) cc_final: 0.7205 (m-30) REVERT: A 197 ASN cc_start: 0.7101 (m-40) cc_final: 0.6449 (t0) REVERT: A 228 TYR cc_start: 0.7161 (p90) cc_final: 0.6744 (p90) REVERT: A 351 GLN cc_start: 0.4737 (mm-40) cc_final: 0.4522 (mm-40) REVERT: A 427 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7526 (mp0) REVERT: A 430 LEU cc_start: 0.8389 (tp) cc_final: 0.8104 (tp) REVERT: A 823 GLU cc_start: 0.7914 (tp30) cc_final: 0.7458 (tm-30) REVERT: A 825 LEU cc_start: 0.7774 (mp) cc_final: 0.7541 (pp) REVERT: A 1119 LYS cc_start: 0.7603 (mtmt) cc_final: 0.7361 (mtmt) REVERT: C 17 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7642 (tptt) REVERT: C 88 HIS cc_start: 0.6343 (m-70) cc_final: 0.6142 (m170) REVERT: C 173 ASP cc_start: 0.7440 (m-30) cc_final: 0.7113 (m-30) REVERT: C 197 ASN cc_start: 0.7094 (m-40) cc_final: 0.6451 (t0) REVERT: C 228 TYR cc_start: 0.7143 (p90) cc_final: 0.6734 (p90) REVERT: C 351 GLN cc_start: 0.4384 (mm-40) cc_final: 0.3979 (mm-40) REVERT: C 355 ILE cc_start: 0.6475 (OUTLIER) cc_final: 0.6248 (mt) REVERT: C 427 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7551 (mp0) REVERT: C 430 LEU cc_start: 0.8373 (tp) cc_final: 0.8074 (tp) REVERT: C 823 GLU cc_start: 0.7860 (tp30) cc_final: 0.7369 (tm-30) REVERT: C 825 LEU cc_start: 0.7789 (mp) cc_final: 0.7557 (pp) REVERT: C 979 MET cc_start: 0.9433 (ptt) cc_final: 0.9020 (ptm) REVERT: C 1119 LYS cc_start: 0.7595 (mtmt) cc_final: 0.7337 (mtmt) REVERT: D 16 ARG cc_start: 0.7419 (ptp-170) cc_final: 0.6621 (ptp-170) REVERT: D 17 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7739 (tptt) REVERT: D 169 VAL cc_start: 0.7144 (t) cc_final: 0.6745 (m) REVERT: D 173 ASP cc_start: 0.7481 (m-30) cc_final: 0.7249 (m-30) REVERT: D 197 ASN cc_start: 0.6538 (m-40) cc_final: 0.5980 (t0) REVERT: D 228 TYR cc_start: 0.7100 (p90) cc_final: 0.6663 (p90) REVERT: D 355 ILE cc_start: 0.6369 (OUTLIER) cc_final: 0.6090 (mp) REVERT: D 464 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8531 (mt) REVERT: D 825 LEU cc_start: 0.7918 (mp) cc_final: 0.7641 (pp) REVERT: D 979 MET cc_start: 0.9399 (ptt) cc_final: 0.8988 (ptm) REVERT: D 1119 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7330 (mtmt) outliers start: 64 outliers final: 37 residues processed: 375 average time/residue: 0.4594 time to fit residues: 265.4556 Evaluate side-chains 312 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 270 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain B residue 1144 SER Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1144 SER Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 649 TRP Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 937 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 332 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1013 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31144 Z= 0.202 Angle : 0.537 7.200 42232 Z= 0.274 Chirality : 0.038 0.173 4796 Planarity : 0.004 0.048 5332 Dihedral : 4.331 28.711 4232 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.44 % Allowed : 10.56 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.52 (0.14), residues: 3796 helix: 1.63 (0.10), residues: 2468 sheet: -0.65 (0.37), residues: 212 loop : -2.52 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1054 HIS 0.004 0.001 HIS D1127 PHE 0.023 0.002 PHE D 91 TYR 0.012 0.001 TYR D 339 ARG 0.003 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 272 time to evaluate : 3.423 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: B 173 ASP cc_start: 0.7550 (m-30) cc_final: 0.7289 (m-30) REVERT: B 197 ASN cc_start: 0.6306 (m-40) cc_final: 0.5763 (t0) REVERT: B 228 TYR cc_start: 0.7073 (p90) cc_final: 0.6675 (p90) REVERT: B 351 GLN cc_start: 0.4757 (mm-40) cc_final: 0.4478 (mm-40) REVERT: B 430 LEU cc_start: 0.8360 (tp) cc_final: 0.8159 (tp) REVERT: B 649 TRP cc_start: 0.6468 (OUTLIER) cc_final: 0.6083 (m-90) REVERT: B 683 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: B 684 MET cc_start: 0.8986 (mtt) cc_final: 0.8660 (mtt) REVERT: B 825 LEU cc_start: 0.7822 (mp) cc_final: 0.7532 (pp) REVERT: B 977 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: B 1119 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7462 (mtmt) REVERT: A 173 ASP cc_start: 0.7536 (m-30) cc_final: 0.7196 (m-30) REVERT: A 197 ASN cc_start: 0.7096 (m-40) cc_final: 0.6438 (t0) REVERT: A 228 TYR cc_start: 0.7093 (p90) cc_final: 0.6703 (p90) REVERT: A 351 GLN cc_start: 0.4703 (mm-40) cc_final: 0.4416 (mm-40) REVERT: A 427 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7468 (mp0) REVERT: A 1119 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7557 (mtmt) REVERT: C 173 ASP cc_start: 0.7440 (m-30) cc_final: 0.7109 (m-30) REVERT: C 197 ASN cc_start: 0.7103 (m-40) cc_final: 0.6458 (t0) REVERT: C 228 TYR cc_start: 0.7083 (p90) cc_final: 0.6695 (p90) REVERT: C 351 GLN cc_start: 0.4671 (mm-40) cc_final: 0.4365 (mm-40) REVERT: C 427 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7462 (mp0) REVERT: C 979 MET cc_start: 0.9458 (ptt) cc_final: 0.8959 (ptm) REVERT: C 1119 LYS cc_start: 0.7735 (mtmt) cc_final: 0.7521 (mtmt) REVERT: D 16 ARG cc_start: 0.7403 (ptp-170) cc_final: 0.6530 (ptp-170) REVERT: D 17 LYS cc_start: 0.8277 (ttpp) cc_final: 0.7707 (tptt) REVERT: D 156 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8174 (p) REVERT: D 169 VAL cc_start: 0.7077 (t) cc_final: 0.6643 (m) REVERT: D 173 ASP cc_start: 0.7472 (m-30) cc_final: 0.7238 (m-30) REVERT: D 197 ASN cc_start: 0.6544 (m-40) cc_final: 0.5983 (t0) REVERT: D 228 TYR cc_start: 0.7125 (p90) cc_final: 0.6695 (p90) REVERT: D 464 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8419 (mt) REVERT: D 825 LEU cc_start: 0.7898 (mp) cc_final: 0.7585 (pp) REVERT: D 1087 TRP cc_start: 0.5866 (t-100) cc_final: 0.5254 (t60) REVERT: D 1119 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7379 (mtmt) outliers start: 78 outliers final: 46 residues processed: 330 average time/residue: 0.4436 time to fit residues: 230.2293 Evaluate side-chains 302 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 251 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1083 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 316 optimal weight: 7.9990 chunk 256 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1047 HIS A1013 ASN A1047 HIS ** C 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 HIS ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN D1047 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 31144 Z= 0.468 Angle : 0.751 6.799 42232 Z= 0.381 Chirality : 0.045 0.167 4796 Planarity : 0.005 0.053 5332 Dihedral : 4.919 20.137 4228 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.97 % Allowed : 11.12 % Favored : 85.91 % 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: 0.16 (0.14), residues: 3796 helix: 1.31 (0.10), residues: 2460 sheet: -0.64 (0.37), residues: 208 loop : -2.54 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 860 HIS 0.007 0.002 HIS A1127 PHE 0.025 0.003 PHE D 91 TYR 0.016 0.002 TYR B 967 ARG 0.005 0.001 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 238 time to evaluate : 3.268 Fit side-chains revert: symmetry clash REVERT: B 173 ASP cc_start: 0.7367 (m-30) cc_final: 0.6957 (m-30) REVERT: B 197 ASN cc_start: 0.6251 (m-40) cc_final: 0.5735 (t0) REVERT: B 228 TYR cc_start: 0.7087 (p90) cc_final: 0.6807 (p90) REVERT: B 351 GLN cc_start: 0.5004 (mm-40) cc_final: 0.4467 (mm-40) REVERT: B 415 PHE cc_start: 0.7184 (m-80) cc_final: 0.6952 (m-80) REVERT: B 427 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 649 TRP cc_start: 0.6766 (OUTLIER) cc_final: 0.5786 (t-100) REVERT: B 825 LEU cc_start: 0.8056 (mp) cc_final: 0.7652 (pp) REVERT: B 1087 TRP cc_start: 0.5797 (t-100) cc_final: 0.5291 (t60) REVERT: A 173 ASP cc_start: 0.7377 (m-30) cc_final: 0.6963 (m-30) REVERT: A 197 ASN cc_start: 0.7110 (m-40) cc_final: 0.6640 (m-40) REVERT: A 228 TYR cc_start: 0.7170 (p90) cc_final: 0.6824 (p90) REVERT: A 427 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7580 (mp0) REVERT: A 430 LEU cc_start: 0.8408 (tp) cc_final: 0.8206 (tp) REVERT: A 649 TRP cc_start: 0.6406 (OUTLIER) cc_final: 0.5793 (t-100) REVERT: C 173 ASP cc_start: 0.7358 (m-30) cc_final: 0.6944 (m-30) REVERT: C 197 ASN cc_start: 0.7086 (m-40) cc_final: 0.6585 (m-40) REVERT: C 228 TYR cc_start: 0.7158 (p90) cc_final: 0.6821 (p90) REVERT: C 427 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7569 (mp0) REVERT: C 649 TRP cc_start: 0.6413 (OUTLIER) cc_final: 0.5802 (t-100) REVERT: C 979 MET cc_start: 0.9493 (ptt) cc_final: 0.9041 (ptt) REVERT: C 1148 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8680 (mtpp) REVERT: D 163 ILE cc_start: 0.5861 (OUTLIER) cc_final: 0.5563 (pp) REVERT: D 173 ASP cc_start: 0.7403 (m-30) cc_final: 0.6970 (m-30) REVERT: D 197 ASN cc_start: 0.6569 (m-40) cc_final: 0.6307 (m-40) REVERT: D 228 TYR cc_start: 0.7148 (p90) cc_final: 0.6782 (p90) REVERT: D 649 TRP cc_start: 0.6388 (OUTLIER) cc_final: 0.5910 (t-100) REVERT: D 825 LEU cc_start: 0.8072 (mp) cc_final: 0.7663 (pp) REVERT: D 1087 TRP cc_start: 0.5969 (t-100) cc_final: 0.5447 (t60) outliers start: 95 outliers final: 57 residues processed: 322 average time/residue: 0.4133 time to fit residues: 211.6696 Evaluate side-chains 277 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 213 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 649 TRP Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 649 TRP Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1148 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 649 TRP Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1083 LEU Chi-restraints excluded: chain D residue 1144 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 371 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 122 optimal weight: 0.0020 chunk 195 optimal weight: 20.0000 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1013 ASN B1033 ASN A 229 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31144 Z= 0.159 Angle : 0.516 7.913 42232 Z= 0.266 Chirality : 0.037 0.185 4796 Planarity : 0.003 0.047 5332 Dihedral : 4.235 20.961 4228 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.06 % Allowed : 12.56 % Favored : 85.38 % 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: 0.90 (0.14), residues: 3796 helix: 1.96 (0.10), residues: 2468 sheet: -0.73 (0.36), residues: 212 loop : -2.41 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1123 HIS 0.004 0.001 HIS A 174 PHE 0.027 0.001 PHE D 415 TYR 0.011 0.001 TYR D 339 ARG 0.007 0.000 ARG B1118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 270 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 ASP cc_start: 0.7501 (m-30) cc_final: 0.7164 (m-30) REVERT: B 197 ASN cc_start: 0.6306 (m-40) cc_final: 0.5833 (t0) REVERT: B 228 TYR cc_start: 0.7019 (p90) cc_final: 0.6735 (p90) REVERT: B 351 GLN cc_start: 0.4940 (mm-40) cc_final: 0.4481 (mm-40) REVERT: B 427 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: B 430 LEU cc_start: 0.8273 (tp) cc_final: 0.7872 (mt) REVERT: B 649 TRP cc_start: 0.6624 (OUTLIER) cc_final: 0.6225 (m-90) REVERT: B 812 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8022 (tt) REVERT: B 825 LEU cc_start: 0.7939 (mp) cc_final: 0.7568 (pp) REVERT: B 1119 LYS cc_start: 0.7485 (mtmt) cc_final: 0.7247 (mtmt) REVERT: A 15 PHE cc_start: 0.5705 (p90) cc_final: 0.5460 (p90) REVERT: A 16 ARG cc_start: 0.7141 (ptp-170) cc_final: 0.6750 (ptp-170) REVERT: A 173 ASP cc_start: 0.7522 (m-30) cc_final: 0.7186 (m-30) REVERT: A 197 ASN cc_start: 0.6421 (m-40) cc_final: 0.5903 (t0) REVERT: A 228 TYR cc_start: 0.7206 (p90) cc_final: 0.6861 (p90) REVERT: A 351 GLN cc_start: 0.5494 (mm-40) cc_final: 0.4674 (mm-40) REVERT: A 427 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7344 (mp0) REVERT: A 430 LEU cc_start: 0.8258 (tp) cc_final: 0.7836 (mt) REVERT: A 431 MET cc_start: 0.8637 (tpp) cc_final: 0.8436 (tpp) REVERT: A 812 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8071 (tt) REVERT: A 825 LEU cc_start: 0.7452 (mt) cc_final: 0.7126 (pp) REVERT: A 1119 LYS cc_start: 0.7581 (mtmt) cc_final: 0.7340 (mtmt) REVERT: C 15 PHE cc_start: 0.5728 (p90) cc_final: 0.5472 (p90) REVERT: C 16 ARG cc_start: 0.7108 (ptp-170) cc_final: 0.6708 (ptp-170) REVERT: C 173 ASP cc_start: 0.7426 (m-30) cc_final: 0.7080 (m-30) REVERT: C 197 ASN cc_start: 0.6448 (m-40) cc_final: 0.6008 (t0) REVERT: C 228 TYR cc_start: 0.7200 (p90) cc_final: 0.6872 (p90) REVERT: C 351 GLN cc_start: 0.5365 (mm-40) cc_final: 0.4502 (mm-40) REVERT: C 427 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7305 (mp0) REVERT: C 812 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8071 (tt) REVERT: C 825 LEU cc_start: 0.7474 (mt) cc_final: 0.7150 (pp) REVERT: C 979 MET cc_start: 0.9433 (ptt) cc_final: 0.8966 (ptm) REVERT: C 1119 LYS cc_start: 0.7594 (mtmt) cc_final: 0.7317 (mtmt) REVERT: D 17 LYS cc_start: 0.8314 (ttpp) cc_final: 0.7718 (tptt) REVERT: D 173 ASP cc_start: 0.7408 (m-30) cc_final: 0.7073 (m-30) REVERT: D 197 ASN cc_start: 0.6537 (m-40) cc_final: 0.6021 (t0) REVERT: D 228 TYR cc_start: 0.6982 (p90) cc_final: 0.6669 (p90) REVERT: D 464 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8439 (mt) REVERT: D 649 TRP cc_start: 0.6163 (OUTLIER) cc_final: 0.5730 (t-100) REVERT: D 812 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8021 (tt) REVERT: D 825 LEU cc_start: 0.7951 (mp) cc_final: 0.7579 (pp) REVERT: D 1087 TRP cc_start: 0.5750 (t-100) cc_final: 0.5173 (t60) outliers start: 66 outliers final: 29 residues processed: 323 average time/residue: 0.4306 time to fit residues: 220.7252 Evaluate side-chains 290 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 649 TRP Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 1083 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 271 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 312 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 370 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 170 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D 294 GLN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 31144 Z= 0.161 Angle : 0.521 12.553 42232 Z= 0.263 Chirality : 0.037 0.168 4796 Planarity : 0.003 0.047 5332 Dihedral : 4.039 20.443 4228 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.56 % Allowed : 13.56 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.14), residues: 3796 helix: 2.14 (0.10), residues: 2488 sheet: -0.63 (0.36), residues: 212 loop : -2.44 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 214 HIS 0.004 0.001 HIS A1127 PHE 0.027 0.001 PHE D 91 TYR 0.010 0.001 TYR B 339 ARG 0.006 0.000 ARG B1118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 255 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 ASP cc_start: 0.7512 (m-30) cc_final: 0.7257 (m-30) REVERT: B 197 ASN cc_start: 0.6319 (m-40) cc_final: 0.5828 (t0) REVERT: B 228 TYR cc_start: 0.6866 (p90) cc_final: 0.6595 (p90) REVERT: B 351 GLN cc_start: 0.4857 (mm-40) cc_final: 0.4393 (mm-40) REVERT: B 430 LEU cc_start: 0.8333 (tp) cc_final: 0.7921 (mt) REVERT: B 432 ASP cc_start: 0.8324 (t70) cc_final: 0.7836 (t0) REVERT: B 649 TRP cc_start: 0.6715 (OUTLIER) cc_final: 0.6320 (m-90) REVERT: B 812 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8132 (tt) REVERT: B 825 LEU cc_start: 0.7990 (mp) cc_final: 0.7603 (pp) REVERT: B 979 MET cc_start: 0.9276 (ptt) cc_final: 0.8921 (ptt) REVERT: B 1087 TRP cc_start: 0.5656 (t-100) cc_final: 0.5068 (t60) REVERT: A 173 ASP cc_start: 0.7415 (m-30) cc_final: 0.7057 (m-30) REVERT: A 197 ASN cc_start: 0.6337 (m-40) cc_final: 0.5841 (t0) REVERT: A 228 TYR cc_start: 0.7127 (p90) cc_final: 0.6791 (p90) REVERT: A 351 GLN cc_start: 0.5431 (mm-40) cc_final: 0.4605 (mm-40) REVERT: A 427 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7399 (mp0) REVERT: A 430 LEU cc_start: 0.8344 (tp) cc_final: 0.7917 (mt) REVERT: A 812 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8161 (tt) REVERT: A 825 LEU cc_start: 0.7495 (mt) cc_final: 0.7167 (pp) REVERT: A 1119 LYS cc_start: 0.7485 (mtmt) cc_final: 0.7184 (mtmt) REVERT: C 173 ASP cc_start: 0.7406 (m-30) cc_final: 0.7046 (m-30) REVERT: C 197 ASN cc_start: 0.6350 (m-40) cc_final: 0.5884 (t0) REVERT: C 228 TYR cc_start: 0.6918 (p90) cc_final: 0.6661 (p90) REVERT: C 351 GLN cc_start: 0.5296 (mm-40) cc_final: 0.4410 (mm-40) REVERT: C 427 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7344 (mp0) REVERT: C 812 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8151 (tt) REVERT: C 825 LEU cc_start: 0.7515 (mt) cc_final: 0.7190 (pp) REVERT: C 979 MET cc_start: 0.9411 (ptt) cc_final: 0.8923 (ptt) REVERT: C 1119 LYS cc_start: 0.7547 (mtmt) cc_final: 0.7282 (mtmt) REVERT: D 16 ARG cc_start: 0.7439 (ptp-170) cc_final: 0.7056 (ptp-170) REVERT: D 163 ILE cc_start: 0.5776 (OUTLIER) cc_final: 0.5546 (pp) REVERT: D 173 ASP cc_start: 0.7451 (m-30) cc_final: 0.7172 (m-30) REVERT: D 197 ASN cc_start: 0.6436 (m-40) cc_final: 0.5938 (t0) REVERT: D 228 TYR cc_start: 0.6843 (p90) cc_final: 0.6558 (p90) REVERT: D 430 LEU cc_start: 0.8280 (tp) cc_final: 0.7858 (mt) REVERT: D 812 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8132 (tt) REVERT: D 825 LEU cc_start: 0.8004 (mp) cc_final: 0.7609 (pp) REVERT: D 1087 TRP cc_start: 0.5787 (t-100) cc_final: 0.5220 (t60) outliers start: 50 outliers final: 33 residues processed: 293 average time/residue: 0.4472 time to fit residues: 207.2058 Evaluate side-chains 280 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 241 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 770 ASP Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1083 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 221 optimal weight: 30.0000 chunk 111 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1013 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 31144 Z= 0.258 Angle : 0.579 12.948 42232 Z= 0.292 Chirality : 0.040 0.166 4796 Planarity : 0.004 0.047 5332 Dihedral : 4.176 19.965 4228 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.78 % Allowed : 13.94 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.14), residues: 3796 helix: 2.09 (0.10), residues: 2480 sheet: -0.62 (0.36), residues: 212 loop : -2.39 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 214 HIS 0.005 0.001 HIS D1127 PHE 0.027 0.002 PHE D 91 TYR 0.011 0.001 TYR A 967 ARG 0.004 0.000 ARG B1118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 243 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 173 ASP cc_start: 0.7427 (m-30) cc_final: 0.7076 (m-30) REVERT: B 197 ASN cc_start: 0.6307 (m-40) cc_final: 0.5819 (t0) REVERT: B 228 TYR cc_start: 0.6900 (p90) cc_final: 0.6644 (p90) REVERT: B 351 GLN cc_start: 0.5063 (mm-40) cc_final: 0.4550 (mm-40) REVERT: B 415 PHE cc_start: 0.7128 (m-80) cc_final: 0.6918 (m-80) REVERT: B 427 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: B 430 LEU cc_start: 0.8280 (tp) cc_final: 0.7880 (mt) REVERT: B 649 TRP cc_start: 0.6695 (OUTLIER) cc_final: 0.6364 (m-90) REVERT: B 662 ASP cc_start: 0.8065 (t0) cc_final: 0.7760 (t0) REVERT: B 812 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8187 (tt) REVERT: B 825 LEU cc_start: 0.7998 (mp) cc_final: 0.7609 (pp) REVERT: B 1087 TRP cc_start: 0.5733 (t-100) cc_final: 0.5173 (t60) REVERT: B 1119 LYS cc_start: 0.7632 (mtmt) cc_final: 0.7378 (mtmt) REVERT: A 173 ASP cc_start: 0.7417 (m-30) cc_final: 0.7056 (m-30) REVERT: A 197 ASN cc_start: 0.6336 (m-40) cc_final: 0.5855 (t0) REVERT: A 228 TYR cc_start: 0.6954 (p90) cc_final: 0.6686 (p90) REVERT: A 351 GLN cc_start: 0.5627 (mm-40) cc_final: 0.4700 (mm-40) REVERT: A 415 PHE cc_start: 0.7160 (m-80) cc_final: 0.6904 (m-80) REVERT: A 427 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7496 (mp0) REVERT: A 430 LEU cc_start: 0.8315 (tp) cc_final: 0.7862 (mt) REVERT: A 662 ASP cc_start: 0.8083 (t0) cc_final: 0.7776 (t0) REVERT: A 812 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8214 (tt) REVERT: A 825 LEU cc_start: 0.7566 (mt) cc_final: 0.7187 (pp) REVERT: C 173 ASP cc_start: 0.7421 (m-30) cc_final: 0.7059 (m-30) REVERT: C 197 ASN cc_start: 0.6316 (m-40) cc_final: 0.5858 (t0) REVERT: C 228 TYR cc_start: 0.6882 (p90) cc_final: 0.6635 (p90) REVERT: C 351 GLN cc_start: 0.5391 (mm-40) cc_final: 0.4486 (mm-40) REVERT: C 427 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7403 (mp0) REVERT: C 662 ASP cc_start: 0.8078 (t0) cc_final: 0.7773 (t0) REVERT: C 812 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8216 (tt) REVERT: C 825 LEU cc_start: 0.7600 (mt) cc_final: 0.7226 (pp) REVERT: C 979 MET cc_start: 0.9468 (ptt) cc_final: 0.8963 (ptt) REVERT: D 173 ASP cc_start: 0.7415 (m-30) cc_final: 0.7060 (m-30) REVERT: D 197 ASN cc_start: 0.6413 (m-40) cc_final: 0.5870 (t0) REVERT: D 228 TYR cc_start: 0.6865 (p90) cc_final: 0.6608 (p90) REVERT: D 662 ASP cc_start: 0.8052 (t0) cc_final: 0.7740 (t0) REVERT: D 812 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8185 (tt) REVERT: D 825 LEU cc_start: 0.8023 (mp) cc_final: 0.7617 (pp) REVERT: D 1087 TRP cc_start: 0.5824 (t-100) cc_final: 0.5288 (t60) outliers start: 57 outliers final: 45 residues processed: 285 average time/residue: 0.4274 time to fit residues: 194.6203 Evaluate side-chains 289 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 238 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1018 LEU Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain B residue 1144 SER Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 770 ASP Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 1018 LEU Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1083 LEU Chi-restraints excluded: chain D residue 1084 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 6.9990 chunk 354 optimal weight: 8.9990 chunk 323 optimal weight: 2.9990 chunk 344 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 311 optimal weight: 7.9990 chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1013 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 31144 Z= 0.248 Angle : 0.576 13.426 42232 Z= 0.291 Chirality : 0.040 0.208 4796 Planarity : 0.004 0.047 5332 Dihedral : 4.211 20.405 4228 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.06 % Allowed : 13.81 % Favored : 84.12 % 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: 1.06 (0.14), residues: 3796 helix: 2.07 (0.10), residues: 2484 sheet: -0.66 (0.35), residues: 212 loop : -2.38 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 214 HIS 0.004 0.001 HIS D1127 PHE 0.027 0.002 PHE D 91 TYR 0.010 0.001 TYR A 339 ARG 0.005 0.000 ARG B1118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 241 time to evaluate : 3.480 Fit side-chains revert: symmetry clash REVERT: B 173 ASP cc_start: 0.7418 (m-30) cc_final: 0.7073 (m-30) REVERT: B 197 ASN cc_start: 0.6311 (m-40) cc_final: 0.5833 (t0) REVERT: B 228 TYR cc_start: 0.6913 (p90) cc_final: 0.6671 (p90) REVERT: B 351 GLN cc_start: 0.4989 (mm-40) cc_final: 0.4504 (mm-40) REVERT: B 427 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: B 649 TRP cc_start: 0.6637 (OUTLIER) cc_final: 0.6265 (m-90) REVERT: B 662 ASP cc_start: 0.8077 (t0) cc_final: 0.7770 (t0) REVERT: B 812 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8192 (tt) REVERT: B 825 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7590 (pp) REVERT: B 1119 LYS cc_start: 0.7610 (mtmt) cc_final: 0.7334 (mtmt) REVERT: A 173 ASP cc_start: 0.7378 (m-30) cc_final: 0.7009 (m-30) REVERT: A 197 ASN cc_start: 0.6330 (m-40) cc_final: 0.5841 (t0) REVERT: A 228 TYR cc_start: 0.6952 (p90) cc_final: 0.6681 (p90) REVERT: A 351 GLN cc_start: 0.5576 (mm-40) cc_final: 0.4715 (mm-40) REVERT: A 427 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7475 (mp0) REVERT: A 430 LEU cc_start: 0.8335 (tp) cc_final: 0.8070 (mt) REVERT: A 662 ASP cc_start: 0.8097 (t0) cc_final: 0.7694 (t0) REVERT: A 812 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 825 LEU cc_start: 0.7481 (mt) cc_final: 0.7140 (pp) REVERT: A 1119 LYS cc_start: 0.7618 (mtmt) cc_final: 0.7385 (mtmt) REVERT: C 173 ASP cc_start: 0.7370 (m-30) cc_final: 0.6999 (m-30) REVERT: C 197 ASN cc_start: 0.6317 (m-40) cc_final: 0.5849 (t0) REVERT: C 228 TYR cc_start: 0.6901 (p90) cc_final: 0.6676 (p90) REVERT: C 351 GLN cc_start: 0.5491 (mm-40) cc_final: 0.4565 (mm-40) REVERT: C 427 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7367 (mp0) REVERT: C 431 MET cc_start: 0.8479 (tpp) cc_final: 0.8247 (tpp) REVERT: C 662 ASP cc_start: 0.8093 (t0) cc_final: 0.7693 (t0) REVERT: C 812 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8215 (tt) REVERT: C 825 LEU cc_start: 0.7515 (mt) cc_final: 0.7182 (pp) REVERT: C 979 MET cc_start: 0.9461 (ptt) cc_final: 0.8970 (ptt) REVERT: C 1119 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7379 (mtmt) REVERT: D 173 ASP cc_start: 0.7417 (m-30) cc_final: 0.7070 (m-30) REVERT: D 197 ASN cc_start: 0.6418 (m-40) cc_final: 0.5865 (t0) REVERT: D 228 TYR cc_start: 0.6896 (p90) cc_final: 0.6677 (p90) REVERT: D 415 PHE cc_start: 0.7282 (m-80) cc_final: 0.7023 (m-80) REVERT: D 430 LEU cc_start: 0.8320 (tp) cc_final: 0.8100 (tp) REVERT: D 649 TRP cc_start: 0.6364 (OUTLIER) cc_final: 0.5636 (t-100) REVERT: D 662 ASP cc_start: 0.8067 (t0) cc_final: 0.7656 (t0) REVERT: D 812 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8192 (tt) REVERT: D 825 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7555 (pp) REVERT: D 1087 TRP cc_start: 0.5782 (t-100) cc_final: 0.5252 (t60) outliers start: 66 outliers final: 49 residues processed: 289 average time/residue: 0.4673 time to fit residues: 215.0237 Evaluate side-chains 296 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 238 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1018 LEU Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1144 SER Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1144 SER Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 649 TRP Chi-restraints excluded: chain D residue 770 ASP Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 1018 LEU Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1083 LEU Chi-restraints excluded: chain D residue 1084 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 9.9990 chunk 364 optimal weight: 0.6980 chunk 222 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 382 optimal weight: 10.0000 chunk 352 optimal weight: 30.0000 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 chunk 186 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN B1013 ASN B1033 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31144 Z= 0.341 Angle : 0.642 13.054 42232 Z= 0.324 Chirality : 0.042 0.226 4796 Planarity : 0.004 0.048 5332 Dihedral : 4.425 20.225 4228 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.94 % Allowed : 14.28 % Favored : 83.78 % 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: 0.85 (0.14), residues: 3796 helix: 1.90 (0.10), residues: 2480 sheet: -0.68 (0.36), residues: 212 loop : -2.43 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 214 HIS 0.005 0.001 HIS D1127 PHE 0.030 0.002 PHE B 415 TYR 0.013 0.001 TYR A 967 ARG 0.004 0.000 ARG D 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 229 time to evaluate : 3.845 Fit side-chains revert: symmetry clash REVERT: B 173 ASP cc_start: 0.7378 (m-30) cc_final: 0.7014 (m-30) REVERT: B 197 ASN cc_start: 0.6299 (m-40) cc_final: 0.5823 (t0) REVERT: B 351 GLN cc_start: 0.5054 (mm-40) cc_final: 0.4491 (mm-40) REVERT: B 427 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: B 662 ASP cc_start: 0.8173 (t0) cc_final: 0.7865 (t0) REVERT: B 812 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8234 (tt) REVERT: B 825 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7596 (pp) REVERT: B 1119 LYS cc_start: 0.7624 (mtmt) cc_final: 0.7349 (mtmt) REVERT: A 173 ASP cc_start: 0.7406 (m-30) cc_final: 0.7017 (m-30) REVERT: A 197 ASN cc_start: 0.6340 (m-40) cc_final: 0.5833 (t0) REVERT: A 351 GLN cc_start: 0.5522 (mm-40) cc_final: 0.5115 (mm-40) REVERT: A 427 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7476 (mp0) REVERT: A 430 LEU cc_start: 0.8297 (tp) cc_final: 0.8072 (mt) REVERT: A 662 ASP cc_start: 0.8134 (t0) cc_final: 0.7814 (t0) REVERT: A 825 LEU cc_start: 0.7569 (mt) cc_final: 0.7190 (pp) REVERT: C 173 ASP cc_start: 0.7398 (m-30) cc_final: 0.7008 (m-30) REVERT: C 197 ASN cc_start: 0.6297 (m-40) cc_final: 0.5829 (t0) REVERT: C 228 TYR cc_start: 0.6979 (p90) cc_final: 0.6717 (p90) REVERT: C 427 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7399 (mp0) REVERT: C 431 MET cc_start: 0.8502 (tpp) cc_final: 0.8301 (tpp) REVERT: C 662 ASP cc_start: 0.8136 (t0) cc_final: 0.7816 (t0) REVERT: C 825 LEU cc_start: 0.7583 (mt) cc_final: 0.7208 (pp) REVERT: C 979 MET cc_start: 0.9490 (ptt) cc_final: 0.9001 (ptt) REVERT: D 173 ASP cc_start: 0.7398 (m-30) cc_final: 0.7008 (m-30) REVERT: D 197 ASN cc_start: 0.6428 (m-40) cc_final: 0.5881 (t0) REVERT: D 228 TYR cc_start: 0.6871 (p90) cc_final: 0.6662 (p90) REVERT: D 415 PHE cc_start: 0.7370 (m-80) cc_final: 0.7093 (m-80) REVERT: D 649 TRP cc_start: 0.6426 (OUTLIER) cc_final: 0.5530 (t-100) REVERT: D 662 ASP cc_start: 0.8187 (t0) cc_final: 0.7875 (t0) REVERT: D 812 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8228 (tt) REVERT: D 825 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7609 (pp) REVERT: D 1087 TRP cc_start: 0.5803 (t-100) cc_final: 0.5233 (t60) outliers start: 62 outliers final: 54 residues processed: 279 average time/residue: 0.4514 time to fit residues: 199.7026 Evaluate side-chains 284 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 224 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1018 LEU Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1144 SER Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1144 SER Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 649 TRP Chi-restraints excluded: chain D residue 770 ASP Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1018 LEU Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1083 LEU Chi-restraints excluded: chain D residue 1084 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 280 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 305 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 313 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1013 ASN A 229 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.127707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.099149 restraints weight = 66202.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097703 restraints weight = 46082.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098312 restraints weight = 44302.358| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 31144 Z= 0.331 Angle : 0.638 13.154 42232 Z= 0.322 Chirality : 0.042 0.213 4796 Planarity : 0.004 0.047 5332 Dihedral : 4.472 20.457 4228 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.12 % Allowed : 14.38 % Favored : 83.50 % 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: 0.78 (0.14), residues: 3796 helix: 1.86 (0.10), residues: 2472 sheet: -0.76 (0.35), residues: 212 loop : -2.44 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 680 HIS 0.005 0.001 HIS A1127 PHE 0.033 0.002 PHE B 415 TYR 0.011 0.001 TYR A 365 ARG 0.004 0.000 ARG B1118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5638.71 seconds wall clock time: 103 minutes 23.08 seconds (6203.08 seconds total)