Starting phenix.real_space_refine on Sun Dec 10 14:13:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m23_30061/12_2023/6m23_30061_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m23_30061/12_2023/6m23_30061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m23_30061/12_2023/6m23_30061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m23_30061/12_2023/6m23_30061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m23_30061/12_2023/6m23_30061_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m23_30061/12_2023/6m23_30061_updated.pdb" } resolution = 3.2 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= 0.002 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 116 5.16 5 Cl 2 4.86 5 C 9452 2.51 5 N 2480 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A ASP 555": "OD1" <-> "OD2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A ARG 654": "NH1" <-> "NH2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 751": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A GLU 797": "OE1" <-> "OE2" Residue "A ARG 857": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A GLU 889": "OE1" <-> "OE2" Residue "A ASP 897": "OD1" <-> "OD2" Residue "A ARG 1079": "NH1" <-> "NH2" Residue "A ARG 1081": "NH1" <-> "NH2" Residue "A PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1105": "NH1" <-> "NH2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B ASP 555": "OD1" <-> "OD2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 638": "OE1" <-> "OE2" Residue "B ASP 643": "OD1" <-> "OD2" Residue "B ARG 654": "NH1" <-> "NH2" Residue "B ARG 659": "NH1" <-> "NH2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ARG 671": "NH1" <-> "NH2" Residue "B ARG 751": "NH1" <-> "NH2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "B ARG 789": "NH1" <-> "NH2" Residue "B GLU 797": "OE1" <-> "OE2" Residue "B ARG 857": "NH1" <-> "NH2" Residue "B ARG 883": "NH1" <-> "NH2" Residue "B GLU 889": "OE1" <-> "OE2" Residue "B ASP 897": "OD1" <-> "OD2" Residue "B ARG 1079": "NH1" <-> "NH2" Residue "B ARG 1081": "NH1" <-> "NH2" Residue "B PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1105": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14744 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7271 Classifications: {'peptide': 936} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 33, 'TRANS': 902} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TPO:plan-1': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 7271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7271 Classifications: {'peptide': 936} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 33, 'TRANS': 902} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TPO:plan-1': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' K': 1, ' CL': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' K': 1, ' CL': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.24, per 1000 atoms: 0.56 Number of scatterers: 14744 At special positions: 0 Unit cell: (96.743, 114.135, 158.702, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 Cl 2 17.00 S 116 16.00 P 4 15.00 O 2688 8.00 N 2480 7.00 C 9452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 331 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1209 " - " ASN A 310 " " NAG B1209 " - " ASN B 310 " " NAG C 1 " - " ASN A 291 " " NAG D 1 " - " ASN A 328 " " NAG E 1 " - " ASN A 339 " " NAG F 1 " - " ASN B 291 " " NAG G 1 " - " ASN B 328 " " NAG H 1 " - " ASN B 339 " Time building additional restraints: 5.93 Conformation dependent library (CDL) restraints added in 2.9 seconds 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 6 sheets defined 45.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.989A pdb=" N ALA A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU A 82 " --> pdb=" O HIS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.563A pdb=" N GLN A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 140 through 154 removed outlier: 3.635A pdb=" N LEU A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 175 through 178 No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 180 through 205 removed outlier: 3.683A pdb=" N TYR A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 247 removed outlier: 3.870A pdb=" N VAL A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 240 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 276 removed outlier: 3.687A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 275 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.569A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.884A pdb=" N GLY A 417 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 418 " --> pdb=" O MET A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 418' Processing helix chain 'A' and resid 427 through 440 removed outlier: 3.608A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.746A pdb=" N ALA A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 453 removed outlier: 3.713A pdb=" N SER A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 477 through 479 No H-bonds generated for 'chain 'A' and resid 477 through 479' Processing helix chain 'A' and resid 485 through 497 removed outlier: 3.998A pdb=" N SER A 494 " --> pdb=" O GLY A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 Proline residue: A 507 - end of helix removed outlier: 3.580A pdb=" N GLN A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.676A pdb=" N GLN A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 524 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 546 through 549 No H-bonds generated for 'chain 'A' and resid 546 through 549' Processing helix chain 'A' and resid 558 through 582 removed outlier: 3.517A pdb=" N SER A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 573 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 removed outlier: 3.887A pdb=" N ALA A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 621 removed outlier: 4.337A pdb=" N VAL A 620 " --> pdb=" O TYR A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 640 removed outlier: 3.636A pdb=" N LYS A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 658 removed outlier: 4.351A pdb=" N SER A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.679A pdb=" N SER A 693 " --> pdb=" O GLN A 690 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 694 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 697 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 699 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 718 No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'A' and resid 720 through 733 removed outlier: 3.602A pdb=" N ARG A 724 " --> pdb=" O PRO A 720 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 729 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 removed outlier: 3.598A pdb=" N LEU A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 800 removed outlier: 3.865A pdb=" N ARG A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 792 " --> pdb=" O TRP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 836 through 847 removed outlier: 3.902A pdb=" N LEU A 841 " --> pdb=" O MET A 837 " (cutoff:3.500A) Proline residue: A 842 - end of helix removed outlier: 4.011A pdb=" N HIS A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 880 Processing helix chain 'A' and resid 908 through 917 removed outlier: 3.702A pdb=" N SER A 913 " --> pdb=" O MET A 909 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1064 removed outlier: 3.769A pdb=" N VAL A1059 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A1063 " --> pdb=" O VAL A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1083 No H-bonds generated for 'chain 'A' and resid 1081 through 1083' Processing helix chain 'A' and resid 1088 through 1094 removed outlier: 3.985A pdb=" N VAL A1093 " --> pdb=" O GLU A1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 82 removed outlier: 3.989A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU B 82 " --> pdb=" O HIS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.563A pdb=" N GLN B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 140 through 154 removed outlier: 3.635A pdb=" N LEU B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 175 through 178 No H-bonds generated for 'chain 'B' and resid 175 through 178' Processing helix chain 'B' and resid 180 through 205 removed outlier: 3.683A pdb=" N TYR B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 196 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 247 removed outlier: 3.870A pdb=" N VAL B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 240 " --> pdb=" O CYS B 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 245 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 276 removed outlier: 3.687A pdb=" N ALA B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 257 " --> pdb=" O ASN B 253 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 275 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 321 No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 400 through 410 removed outlier: 3.569A pdb=" N VAL B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.884A pdb=" N GLY B 417 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 418 " --> pdb=" O MET B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 418' Processing helix chain 'B' and resid 427 through 440 removed outlier: 3.608A pdb=" N ILE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.746A pdb=" N ALA B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 453 removed outlier: 3.713A pdb=" N SER B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 462 No H-bonds generated for 'chain 'B' and resid 459 through 462' Processing helix chain 'B' and resid 477 through 479 No H-bonds generated for 'chain 'B' and resid 477 through 479' Processing helix chain 'B' and resid 485 through 497 removed outlier: 3.998A pdb=" N SER B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 516 Proline residue: B 507 - end of helix removed outlier: 3.580A pdb=" N GLN B 511 " --> pdb=" O PRO B 507 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.676A pdb=" N GLN B 523 " --> pdb=" O PRO B 520 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL B 524 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 544 Processing helix chain 'B' and resid 546 through 549 No H-bonds generated for 'chain 'B' and resid 546 through 549' Processing helix chain 'B' and resid 558 through 582 removed outlier: 3.517A pdb=" N SER B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B 563 " --> pdb=" O PRO B 559 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 564 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN B 573 " --> pdb=" O TYR B 569 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR B 580 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 611 removed outlier: 3.887A pdb=" N ALA B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 621 removed outlier: 4.337A pdb=" N VAL B 620 " --> pdb=" O TYR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 640 removed outlier: 3.636A pdb=" N LYS B 630 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 658 removed outlier: 4.351A pdb=" N SER B 649 " --> pdb=" O ILE B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.679A pdb=" N SER B 693 " --> pdb=" O GLN B 690 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 694 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 697 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 699 " --> pdb=" O SER B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 718 No H-bonds generated for 'chain 'B' and resid 715 through 718' Processing helix chain 'B' and resid 720 through 733 removed outlier: 3.602A pdb=" N ARG B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 725 " --> pdb=" O GLN B 721 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE B 729 " --> pdb=" O ALA B 725 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 removed outlier: 3.598A pdb=" N LEU B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 800 removed outlier: 3.865A pdb=" N ARG B 789 " --> pdb=" O HIS B 785 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 790 " --> pdb=" O GLN B 786 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 792 " --> pdb=" O TRP B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 813 No H-bonds generated for 'chain 'B' and resid 811 through 813' Processing helix chain 'B' and resid 836 through 847 removed outlier: 3.902A pdb=" N LEU B 841 " --> pdb=" O MET B 837 " (cutoff:3.500A) Proline residue: B 842 - end of helix removed outlier: 4.011A pdb=" N HIS B 847 " --> pdb=" O PHE B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 880 Processing helix chain 'B' and resid 908 through 917 removed outlier: 3.702A pdb=" N SER B 913 " --> pdb=" O MET B 909 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 914 " --> pdb=" O GLU B 910 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1064 removed outlier: 3.769A pdb=" N VAL B1059 " --> pdb=" O ARG B1055 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS B1063 " --> pdb=" O VAL B1059 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1083 No H-bonds generated for 'chain 'B' and resid 1081 through 1083' Processing helix chain 'B' and resid 1088 through 1094 removed outlier: 3.985A pdb=" N VAL B1093 " --> pdb=" O GLU B1089 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 285 through 288 Processing sheet with id= B, first strand: chain 'A' and resid 675 through 677 removed outlier: 6.579A pdb=" N ILE A 706 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE A 741 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N SER A 709 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN A 743 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU A 711 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 745 " --> pdb=" O LEU A 711 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 770 through 773 removed outlier: 6.509A pdb=" N ALA A 804 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL A 773 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A 806 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A1101 " --> pdb=" O LYS A 809 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL A1070 " --> pdb=" O MET A1102 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A1104 " --> pdb=" O VAL A1070 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A1072 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP A 827 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN A1073 " --> pdb=" O ASP A 827 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N TRP A 829 " --> pdb=" O ASN A1073 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG A 857 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU A 887 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR A 860 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A 889 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA A 862 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 891 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 285 through 288 Processing sheet with id= E, first strand: chain 'B' and resid 675 through 677 removed outlier: 6.579A pdb=" N ILE B 706 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE B 741 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N SER B 709 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN B 743 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 711 " --> pdb=" O GLN B 743 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 745 " --> pdb=" O LEU B 711 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 770 through 773 removed outlier: 6.509A pdb=" N ALA B 804 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL B 773 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU B 806 " --> pdb=" O VAL B 773 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B1101 " --> pdb=" O LYS B 809 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B1070 " --> pdb=" O MET B1102 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B1104 " --> pdb=" O VAL B1070 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B1072 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP B 827 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN B1073 " --> pdb=" O ASP B 827 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N TRP B 829 " --> pdb=" O ASN B1073 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG B 857 " --> pdb=" O VAL B 828 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU B 887 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR B 860 " --> pdb=" O GLU B 887 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU B 889 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA B 862 " --> pdb=" O GLU B 889 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL B 891 " --> pdb=" O ALA B 862 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1116 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: 4.50 Time building geometry restraints manager: 6.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4016 1.33 - 1.45: 2756 1.45 - 1.57: 8082 1.57 - 1.69: 16 1.69 - 1.81: 186 Bond restraints: 15056 Sorted by residual: bond pdb=" OG1 TPO A 906 " pdb=" P TPO A 906 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" OG1 TPO B 906 " pdb=" P TPO B 906 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C ARG B 671 " pdb=" N PRO B 672 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.12e-02 7.97e+03 2.55e+01 bond pdb=" C ARG A 671 " pdb=" N PRO A 672 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.12e-02 7.97e+03 2.55e+01 bond pdb=" OG1 TPO A1007 " pdb=" P TPO A1007 " ideal model delta sigma weight residual 1.717 1.618 0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 15051 not shown) Histogram of bond angle deviations from ideal: 98.31 - 106.30: 396 106.30 - 114.29: 8780 114.29 - 122.29: 8942 122.29 - 130.28: 2216 130.28 - 138.28: 100 Bond angle restraints: 20434 Sorted by residual: angle pdb=" C ARG B 671 " pdb=" N PRO B 672 " pdb=" CA PRO B 672 " ideal model delta sigma weight residual 119.98 114.21 5.77 1.16e+00 7.43e-01 2.48e+01 angle pdb=" C ARG A 671 " pdb=" N PRO A 672 " pdb=" CA PRO A 672 " ideal model delta sigma weight residual 119.98 114.21 5.77 1.16e+00 7.43e-01 2.48e+01 angle pdb=" C ALA A 329 " pdb=" N THR A 330 " pdb=" CA THR A 330 " ideal model delta sigma weight residual 122.82 129.73 -6.91 1.42e+00 4.96e-01 2.37e+01 angle pdb=" C ALA B 329 " pdb=" N THR B 330 " pdb=" CA THR B 330 " ideal model delta sigma weight residual 122.82 129.73 -6.91 1.42e+00 4.96e-01 2.37e+01 angle pdb=" N VAL A1054 " pdb=" CA VAL A1054 " pdb=" C VAL A1054 " ideal model delta sigma weight residual 112.12 108.06 4.06 8.40e-01 1.42e+00 2.33e+01 ... (remaining 20429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 8014 17.36 - 34.73: 804 34.73 - 52.09: 182 52.09 - 69.46: 24 69.46 - 86.82: 14 Dihedral angle restraints: 9038 sinusoidal: 3690 harmonic: 5348 Sorted by residual: dihedral pdb=" CA ILE B 612 " pdb=" C ILE B 612 " pdb=" N CYS B 613 " pdb=" CA CYS B 613 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ILE A 612 " pdb=" C ILE A 612 " pdb=" N CYS A 613 " pdb=" CA CYS A 613 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA CYS B 302 " pdb=" C CYS B 302 " pdb=" N ALA B 303 " pdb=" CA ALA B 303 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 9035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1950 0.081 - 0.162: 378 0.162 - 0.243: 42 0.243 - 0.325: 8 0.325 - 0.406: 2 Chirality restraints: 2380 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" CB TPO B1007 " pdb=" CA TPO B1007 " pdb=" OG1 TPO B1007 " pdb=" CG2 TPO B1007 " both_signs ideal model delta sigma weight residual False 2.48 2.08 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 2377 not shown) Planarity restraints: 2554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 291 " -0.030 2.00e-02 2.50e+03 3.91e-02 1.91e+01 pdb=" CG ASN A 291 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 291 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 291 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 291 " 0.030 2.00e-02 2.50e+03 3.91e-02 1.91e+01 pdb=" CG ASN B 291 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN B 291 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 291 " -0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 663 " -0.051 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO A 664 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 664 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 664 " -0.042 5.00e-02 4.00e+02 ... (remaining 2551 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 4288 2.80 - 3.39: 14699 3.39 - 3.97: 25575 3.97 - 4.56: 37672 4.56 - 5.14: 54647 Nonbonded interactions: 136881 Sorted by model distance: nonbonded pdb=" O GLN A 673 " pdb=" O LEU A 704 " model vdw 2.216 3.040 nonbonded pdb=" O GLN B 673 " pdb=" O LEU B 704 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 151 " pdb=" CE2 PHE A 591 " model vdw 2.245 3.340 nonbonded pdb=" OG SER B 151 " pdb=" CE2 PHE B 591 " model vdw 2.245 3.340 nonbonded pdb=" O THR B 934 " pdb=" N GLU B 936 " model vdw 2.253 2.520 ... (remaining 136876 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.010 Extract box with map and model: 7.710 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 41.610 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.010 0.112 15056 Z= 0.639 Angle : 1.124 13.275 20434 Z= 0.604 Chirality : 0.067 0.406 2380 Planarity : 0.007 0.076 2546 Dihedral : 14.890 86.819 5608 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 1.52 % Allowed : 10.73 % Favored : 87.76 % Rotamer: Outliers : 2.32 % Allowed : 9.52 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.36 (0.12), residues: 1846 helix: -4.62 (0.07), residues: 938 sheet: -2.30 (0.38), residues: 160 loop : -3.92 (0.16), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 318 HIS 0.008 0.002 HIS B 756 PHE 0.028 0.003 PHE B1090 TYR 0.023 0.003 TYR A 407 ARG 0.006 0.001 ARG B1105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 306 time to evaluate : 1.682 Fit side-chains outliers start: 36 outliers final: 12 residues processed: 334 average time/residue: 0.2722 time to fit residues: 132.9818 Evaluate side-chains 196 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1434 time to fit residues: 5.3869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 344 GLN A 419 ASN A 573 ASN A 579 GLN A 673 GLN A 688 HIS A 723 GLN A 778 ASN A 790 ASN A 848 HIS ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 HIS B 73 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN B 344 GLN B 419 ASN B 573 ASN B 579 GLN B 673 GLN B 688 HIS B 723 GLN B 778 ASN B 790 ASN B 848 HIS ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15056 Z= 0.279 Angle : 0.745 12.468 20434 Z= 0.386 Chirality : 0.045 0.170 2380 Planarity : 0.005 0.054 2546 Dihedral : 7.474 53.246 2322 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.27 % Favored : 87.97 % Rotamer: Outliers : 1.93 % Allowed : 16.28 % Favored : 81.79 % 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: -4.74 (0.16), residues: 1846 helix: -2.99 (0.13), residues: 936 sheet: -1.72 (0.40), residues: 156 loop : -3.56 (0.18), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 596 HIS 0.007 0.001 HIS B 756 PHE 0.021 0.002 PHE A 591 TYR 0.022 0.002 TYR A 593 ARG 0.005 0.001 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 220 average time/residue: 0.2344 time to fit residues: 80.6197 Evaluate side-chains 200 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.749 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1407 time to fit residues: 7.6593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 182 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 135 optimal weight: 0.0060 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN A 870 GLN A 931 GLN A1057 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN B1057 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15056 Z= 0.231 Angle : 0.675 11.678 20434 Z= 0.344 Chirality : 0.044 0.160 2380 Planarity : 0.004 0.054 2546 Dihedral : 6.727 55.802 2322 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.81 % Favored : 87.54 % Rotamer: Outliers : 2.45 % Allowed : 17.89 % Favored : 79.67 % 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: -3.66 (0.18), residues: 1846 helix: -1.96 (0.15), residues: 922 sheet: -1.42 (0.42), residues: 160 loop : -3.19 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 122 HIS 0.006 0.001 HIS B 756 PHE 0.014 0.001 PHE B 591 TYR 0.013 0.001 TYR B 593 ARG 0.006 0.001 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 192 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 218 average time/residue: 0.2242 time to fit residues: 77.0218 Evaluate side-chains 188 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.666 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1319 time to fit residues: 6.2221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 0.0010 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN A 931 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15056 Z= 0.233 Angle : 0.677 11.268 20434 Z= 0.336 Chirality : 0.043 0.159 2380 Planarity : 0.004 0.051 2546 Dihedral : 6.403 55.854 2322 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.73 % Favored : 88.73 % Rotamer: Outliers : 2.06 % Allowed : 18.47 % Favored : 79.47 % 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: -3.18 (0.18), residues: 1846 helix: -1.50 (0.16), residues: 918 sheet: -1.21 (0.44), residues: 160 loop : -3.04 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 596 HIS 0.004 0.001 HIS B 756 PHE 0.012 0.001 PHE B 184 TYR 0.017 0.001 TYR B 880 ARG 0.003 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.754 Fit side-chains outliers start: 32 outliers final: 20 residues processed: 215 average time/residue: 0.2333 time to fit residues: 79.3977 Evaluate side-chains 188 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1378 time to fit residues: 7.5037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 124 optimal weight: 0.0070 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 0.0370 chunk 161 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN B 870 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15056 Z= 0.148 Angle : 0.625 11.060 20434 Z= 0.311 Chirality : 0.041 0.156 2380 Planarity : 0.004 0.055 2546 Dihedral : 6.018 53.569 2322 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.86 % Favored : 89.60 % Rotamer: Outliers : 1.22 % Allowed : 18.79 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.74 (0.19), residues: 1846 helix: -1.12 (0.17), residues: 924 sheet: -1.06 (0.44), residues: 160 loop : -2.83 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 596 HIS 0.004 0.000 HIS B 756 PHE 0.009 0.001 PHE B 184 TYR 0.012 0.001 TYR A 593 ARG 0.003 0.000 ARG A 912 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 1.749 Fit side-chains outliers start: 19 outliers final: 6 residues processed: 218 average time/residue: 0.2235 time to fit residues: 78.0354 Evaluate side-chains 186 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1735 time to fit residues: 4.0477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15056 Z= 0.301 Angle : 0.679 9.929 20434 Z= 0.339 Chirality : 0.045 0.162 2380 Planarity : 0.004 0.050 2546 Dihedral : 6.085 55.138 2322 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.16 % Favored : 88.30 % Rotamer: Outliers : 1.93 % Allowed : 18.34 % Favored : 79.73 % 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: -2.44 (0.19), residues: 1846 helix: -0.80 (0.17), residues: 914 sheet: -0.92 (0.44), residues: 160 loop : -2.78 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 596 HIS 0.003 0.001 HIS A 719 PHE 0.014 0.002 PHE B 611 TYR 0.012 0.001 TYR A 629 ARG 0.003 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 1.891 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 201 average time/residue: 0.2412 time to fit residues: 76.7448 Evaluate side-chains 184 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1382 time to fit residues: 6.4142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 0.0570 chunk 112 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15056 Z= 0.166 Angle : 0.621 10.559 20434 Z= 0.308 Chirality : 0.042 0.158 2380 Planarity : 0.004 0.053 2546 Dihedral : 5.869 52.620 2322 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.83 % Favored : 88.62 % Rotamer: Outliers : 1.54 % Allowed : 18.92 % Favored : 79.54 % 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: -2.18 (0.20), residues: 1846 helix: -0.46 (0.17), residues: 918 sheet: -0.86 (0.45), residues: 160 loop : -2.83 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 596 HIS 0.002 0.000 HIS B 756 PHE 0.010 0.001 PHE B 611 TYR 0.011 0.001 TYR B 593 ARG 0.007 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 1.803 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 199 average time/residue: 0.2333 time to fit residues: 74.0761 Evaluate side-chains 181 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1487 time to fit residues: 4.2924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.25 > 50: distance: 65 - 84: 25.384 distance: 70 - 90: 31.622 distance: 81 - 84: 22.523 distance: 84 - 85: 33.268 distance: 85 - 86: 20.669 distance: 85 - 88: 28.001 distance: 86 - 87: 27.849 distance: 86 - 90: 25.363 distance: 88 - 89: 41.074 distance: 90 - 91: 30.870 distance: 91 - 92: 39.822 distance: 91 - 94: 17.147 distance: 92 - 93: 39.785 distance: 92 - 98: 34.728 distance: 94 - 95: 21.717 distance: 95 - 97: 23.355 distance: 98 - 99: 28.831 distance: 99 - 100: 53.419 distance: 99 - 102: 17.148 distance: 100 - 101: 39.361 distance: 100 - 104: 16.783 distance: 102 - 103: 42.142 distance: 104 - 105: 19.754 distance: 105 - 106: 39.277 distance: 105 - 108: 42.622 distance: 106 - 107: 32.282 distance: 106 - 113: 36.340 distance: 108 - 109: 17.171 distance: 109 - 110: 24.659 distance: 110 - 112: 40.442 distance: 113 - 114: 39.232 distance: 114 - 115: 57.607 distance: 114 - 117: 44.246 distance: 117 - 118: 44.878 distance: 117 - 119: 37.654 distance: 121 - 122: 39.530 distance: 122 - 123: 56.183 distance: 123 - 124: 40.270 distance: 123 - 125: 40.958 distance: 125 - 126: 55.680 distance: 126 - 127: 68.158 distance: 126 - 129: 33.547 distance: 127 - 128: 63.133 distance: 127 - 133: 41.238 distance: 129 - 130: 39.708 distance: 129 - 131: 35.693 distance: 130 - 132: 55.195 distance: 133 - 134: 29.231 distance: 134 - 135: 30.620 distance: 134 - 137: 58.521 distance: 135 - 136: 24.154 distance: 135 - 141: 39.473 distance: 137 - 138: 5.737 distance: 138 - 139: 39.162 distance: 138 - 140: 13.324 distance: 141 - 142: 33.841 distance: 142 - 143: 4.111 distance: 142 - 145: 33.137 distance: 143 - 149: 39.936 distance: 145 - 146: 40.622 distance: 145 - 147: 38.493 distance: 146 - 148: 50.940 distance: 149 - 150: 40.695 distance: 150 - 151: 40.027 distance: 150 - 153: 7.511 distance: 151 - 152: 35.746 distance: 151 - 154: 34.581