Starting phenix.real_space_refine on Sun May 25 14:37:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfo_25878/05_2025/7tfo_25878.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfo_25878/05_2025/7tfo_25878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tfo_25878/05_2025/7tfo_25878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfo_25878/05_2025/7tfo_25878.map" model { file = "/net/cci-nas-00/data/ceres_data/7tfo_25878/05_2025/7tfo_25878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfo_25878/05_2025/7tfo_25878.cif" } resolution = 4.1 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 Anisotropic ADP refinement not supported. Converting 11499 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 11219 2.51 5 N 3040 2.21 5 O 3402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17774 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3245 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 10 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3175 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 20, 'TRANS': 390} Chain breaks: 10 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3110 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 21, 'TRANS': 382} Chain breaks: 8 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 914 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 905 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 828 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 103} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 834 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "X" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "Y" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Z" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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: "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 Time building chain proxies: 10.44, per 1000 atoms: 0.59 Number of scatterers: 17774 At special positions: 0 Unit cell: (128.744, 122.056, 141.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 3402 8.00 N 3040 7.00 C 11219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=1.68 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 601 " - " ASN A 197 " " NAG B 601 " - " ASN B 276 " " NAG B 602 " - " ASN B 363 " " NAG C 601 " - " ASN C 197 " " NAG C 602 " - " ASN C 363 " " NAG D 1 " - " ASN A 386 " " NAG E 1 " - " ASN A 363 " " NAG F 1 " - " ASN A 276 " " NAG G 1 " - " ASN A 262 " " NAG K 1 " - " ASN C 276 " Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 2.3 seconds 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4210 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 39 sheets defined 20.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.579A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.818A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 57 through 61 removed outlier: 4.305A pdb=" N TYR B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.542A pdb=" N HIS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 4.242A pdb=" N THR B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.516A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.649A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.609A pdb=" N LYS C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.904A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 removed outlier: 4.094A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'L' and resid 27 through 31 removed outlier: 3.718A pdb=" N SER L 31 " --> pdb=" O PHE L 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.784A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 100A removed outlier: 3.929A pdb=" N SER P 100A" --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27A through 30 removed outlier: 4.022A pdb=" N GLU Q 29 " --> pdb=" O SER Q 27A" (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'X' and resid 515 through 522 removed outlier: 3.588A pdb=" N PHE X 519 " --> pdb=" O ILE X 515 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU X 520 " --> pdb=" O GLY X 516 " (cutoff:3.500A) Processing helix chain 'X' and resid 529 through 541 removed outlier: 3.784A pdb=" N MET X 535 " --> pdb=" O GLY X 531 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR X 538 " --> pdb=" O SER X 534 " (cutoff:3.500A) Processing helix chain 'X' and resid 564 through 596 removed outlier: 3.522A pdb=" N LYS X 574 " --> pdb=" O VAL X 570 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG X 579 " --> pdb=" O GLN X 575 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP X 596 " --> pdb=" O LEU X 592 " (cutoff:3.500A) Processing helix chain 'X' and resid 620 through 624 removed outlier: 3.741A pdb=" N TRP X 623 " --> pdb=" O SER X 620 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 636 Processing helix chain 'X' and resid 638 through 656 removed outlier: 3.716A pdb=" N GLU X 648 " --> pdb=" O GLY X 644 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER X 649 " --> pdb=" O LEU X 645 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN X 653 " --> pdb=" O SER X 649 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS X 655 " --> pdb=" O ASN X 651 " (cutoff:3.500A) Processing helix chain 'Y' and resid 529 through 536 removed outlier: 3.515A pdb=" N THR Y 536 " --> pdb=" O ALA Y 532 " (cutoff:3.500A) Processing helix chain 'Y' and resid 540 through 545 removed outlier: 4.048A pdb=" N LEU Y 545 " --> pdb=" O ARG Y 542 " (cutoff:3.500A) Processing helix chain 'Y' and resid 564 through 596 removed outlier: 3.744A pdb=" N TRP Y 596 " --> pdb=" O LEU Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 618 through 623 removed outlier: 3.573A pdb=" N TRP Y 623 " --> pdb=" O LEU Y 619 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 636 Processing helix chain 'Y' and resid 637 through 654 removed outlier: 3.928A pdb=" N ILE Y 641 " --> pdb=" O ASN Y 637 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU Y 648 " --> pdb=" O GLY Y 644 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER Y 649 " --> pdb=" O LEU Y 645 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 540 removed outlier: 4.150A pdb=" N MET Z 535 " --> pdb=" O GLY Z 531 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR Z 536 " --> pdb=" O ALA Z 532 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL Z 539 " --> pdb=" O MET Z 535 " (cutoff:3.500A) Processing helix chain 'Z' and resid 564 through 596 Processing helix chain 'Z' and resid 618 through 625 removed outlier: 3.604A pdb=" N ILE Z 622 " --> pdb=" O ASN Z 618 " (cutoff:3.500A) Processing helix chain 'Z' and resid 630 through 635 removed outlier: 3.511A pdb=" N GLU Z 634 " --> pdb=" O GLN Z 630 " (cutoff:3.500A) Processing helix chain 'Z' and resid 638 through 660 removed outlier: 3.826A pdb=" N TYR Z 643 " --> pdb=" O THR Z 639 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 497 removed outlier: 4.414A pdb=" N VAL A 36 " --> pdb=" O THR X 606 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR X 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.550A pdb=" N THR A 244 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 removed outlier: 4.291A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS A 239 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 159 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 307 removed outlier: 6.668A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 317 through 323 current: chain 'A' and resid 381 through 385 removed outlier: 4.756A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 414 through 421 current: chain 'A' and resid 468 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 359 through 361 Processing sheet with id=AB1, first strand: chain 'B' and resid 495 through 499 removed outlier: 5.306A pdb=" N VAL Y 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL B 38 " --> pdb=" O THR Y 606 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR Y 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.701A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 94 removed outlier: 4.143A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B 239 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE B 93 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 131 through 133 removed outlier: 3.611A pdb=" N ASN B 156 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS B 155 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 287 current: chain 'B' and resid 394 through 395 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 394 through 395 current: chain 'B' and resid 465 through 470 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 294 through 297 removed outlier: 4.063A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 374 through 378 Processing sheet with id=AB9, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.534A pdb=" N ALA C 497 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.814A pdb=" N LYS C 490 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC4, first strand: chain 'C' and resid 181 through 182 removed outlier: 3.597A pdb=" N ARG C 192 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.594A pdb=" N GLN C 287 " --> pdb=" O MET C 271 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 331 through 332 removed outlier: 7.327A pdb=" N ARG C 298 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS C 445 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C 300 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE C 443 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 376 through 378 removed outlier: 3.585A pdb=" N ARG C 419 " --> pdb=" O TYR C 384 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.518A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.501A pdb=" N VAL H 95 " --> pdb=" O SER H 33 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL H 56 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.596A pdb=" N VAL I 5 " --> pdb=" O LYS I 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 45 through 52 removed outlier: 3.598A pdb=" N VAL I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 56 through 59 current: chain 'I' and resid 100E through 103 Processing sheet with id=AD3, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AD4, first strand: chain 'J' and resid 9 through 13 Processing sheet with id=AD5, first strand: chain 'J' and resid 44 through 48 removed outlier: 6.832A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE J 32 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL J 97 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 3 through 5 removed outlier: 4.185A pdb=" N ALA L 3 " --> pdb=" O SER L 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.829A pdb=" N THR L 105 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.519A pdb=" N VAL P 5 " --> pdb=" O LYS P 23 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET P 80 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR P 68 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 10 through 11 current: chain 'P' and resid 45 through 51 removed outlier: 4.065A pdb=" N VAL P 50 " --> pdb=" O ASN P 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 100E through 103 Processing sheet with id=AE1, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.558A pdb=" N THR Q 105 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER Q 84 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 19 through 23 Processing sheet with id=AE3, first strand: chain 'Q' and resid 89 through 92 526 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 5.39 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: 5686 1.34 - 1.46: 4246 1.46 - 1.58: 8045 1.58 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 18130 Sorted by residual: bond pdb=" N GLY Q 27 " pdb=" CA GLY Q 27 " ideal model delta sigma weight residual 1.444 1.476 -0.032 9.60e-03 1.09e+04 1.10e+01 bond pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.10e+00 bond pdb=" N ILE Q 21 " pdb=" CA ILE Q 21 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.40e+00 bond pdb=" N VAL C 371 " pdb=" CA VAL C 371 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.07e+00 bond pdb=" N GLY C 263 " pdb=" CA GLY C 263 " ideal model delta sigma weight residual 1.447 1.476 -0.029 1.03e-02 9.43e+03 8.02e+00 ... (remaining 18125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 23655 1.75 - 3.50: 832 3.50 - 5.25: 112 5.25 - 7.00: 23 7.00 - 8.75: 2 Bond angle restraints: 24624 Sorted by residual: angle pdb=" C VAL C 446 " pdb=" N SER C 447 " pdb=" CA SER C 447 " ideal model delta sigma weight residual 122.17 115.69 6.48 1.54e+00 4.22e-01 1.77e+01 angle pdb=" N GLY Q 25 " pdb=" CA GLY Q 25 " pdb=" C GLY Q 25 " ideal model delta sigma weight residual 115.36 109.98 5.38 1.33e+00 5.65e-01 1.63e+01 angle pdb=" N THR C 387 " pdb=" CA THR C 387 " pdb=" C THR C 387 " ideal model delta sigma weight residual 113.02 108.35 4.67 1.20e+00 6.94e-01 1.51e+01 angle pdb=" N CYS C 196 " pdb=" CA CYS C 196 " pdb=" C CYS C 196 " ideal model delta sigma weight residual 113.43 108.61 4.82 1.26e+00 6.30e-01 1.46e+01 angle pdb=" CA THR A 63 " pdb=" C THR A 63 " pdb=" O THR A 63 " ideal model delta sigma weight residual 122.64 118.14 4.50 1.25e+00 6.40e-01 1.29e+01 ... (remaining 24619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 10267 21.62 - 43.24: 605 43.24 - 64.86: 93 64.86 - 86.49: 44 86.49 - 108.11: 18 Dihedral angle restraints: 11027 sinusoidal: 4495 harmonic: 6532 Sorted by residual: dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual -86.00 -173.81 87.81 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual 93.00 158.90 -65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.27 -55.27 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 11024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 2831 0.153 - 0.307: 25 0.307 - 0.460: 2 0.460 - 0.614: 0 0.614 - 0.767: 1 Chirality restraints: 2859 Sorted by residual: 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 -2.24 -0.16 2.00e-02 2.50e+03 6.60e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.64e+01 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.72e+01 ... (remaining 2856 not shown) Planarity restraints: 3105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 262 " -0.028 2.00e-02 2.50e+03 3.54e-01 1.57e+03 pdb=" CG ASN A 262 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN A 262 " 0.337 2.00e-02 2.50e+03 pdb=" ND2 ASN A 262 " -0.595 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.387 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG A 601 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " -0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG B 601 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " 0.522 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " -0.186 2.00e-02 2.50e+03 ... (remaining 3102 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 481 2.67 - 3.23: 18016 3.23 - 3.79: 26920 3.79 - 4.34: 35728 4.34 - 4.90: 57054 Nonbonded interactions: 138199 Sorted by model distance: nonbonded pdb=" NE2 GLN L 38 " pdb=" O MET L 42 " model vdw 2.118 3.120 nonbonded pdb=" OG SER A 364 " pdb=" O THR A 372 " model vdw 2.165 3.040 nonbonded pdb=" O LEU B 369 " pdb=" OG1 THR B 373 " model vdw 2.173 3.040 nonbonded pdb=" OG SER L 12 " pdb=" OG1 THR L 105 " model vdw 2.188 3.040 nonbonded pdb=" O PRO J 7 " pdb=" OG1 THR J 102 " model vdw 2.190 3.040 ... (remaining 138194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 63 or (resid 72 through 73 and (name N or na \ me CA or name C or name O or name CB )) or resid 75 through 113 or resid 119 or \ (resid 120 through 121 and (name N or name CA or name C or name O or name CB )) \ or resid 122 or (resid 123 and (name N or name CA or name C or name O or name CB \ )) or resid 124 or (resid 125 through 126 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 130 through 131 and (name N or name CA or name C o \ r name O or name CB )) or resid 132 through 138 or (resid 151 through 153 and (n \ ame N or name CA or name C or name O or name CB )) or resid 154 through 162 or r \ esid 172 through 207 or resid 210 or (resid 211 and (name N or name CA or name C \ or name O or name CB )) or resid 212 through 231 or (resid 232 and (name N or n \ ame CA or name C or name O or name CB )) or resid 233 through 306 or resid 315 t \ hrough 352 or resid 356 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 396 or resid 415 through 420 or \ (resid 421 and (name N or name CA or name C or name O or name CB )) or resid 422 \ through 457 or resid 467 through 483 or (resid 484 through 485 and (name N or n \ ame CA or name C or name O or name CB )) or resid 486 through 499 or (resid 500 \ through 503 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 1)) selection = (chain 'B' and (resid 34 through 45 or (resid 46 through 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 56 or (resid 57 through \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 63 and (n \ ame N or name CA or name C or name O or name CB )) or resid 72 through 77 or (re \ sid 78 and (name N or name CA or name C or name O or name CB )) or resid 79 thro \ ugh 119 or (resid 120 through 121 and (name N or name CA or name C or name O or \ name CB )) or resid 122 or (resid 123 and (name N or name CA or name C or name O \ or name CB )) or resid 124 or (resid 125 through 131 and (name N or name CA or \ name C or name O or name CB )) or resid 132 through 194 or (resid 195 and (name \ N or name CA or name C or name O or name CB )) or resid 196 through 231 or (resi \ d 232 and (name N or name CA or name C or name O or name CB )) or resid 233 thro \ ugh 267 or resid 270 through 306 or resid 315 through 324 or resid 326 through 3 \ 52 or resid 356 through 391 or (resid 392 and (name N or name CA or name C or na \ me O or name CB )) or resid 393 through 396 or resid 415 through 420 or (resid 4 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 422 through \ 457 or resid 467 through 483 or (resid 484 through 485 and (name N or name CA o \ r name C or name O or name CB )) or resid 486 through 503 or resid 602)) selection = (chain 'C' and ((resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 45 or (resid 46 through 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 58 or (resid 71 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 75 through 113 or re \ sid 119 through 125 or (resid 126 and (name N or name CA or name C or name O or \ name CB )) or (resid 130 through 131 and (name N or name CA or name C or name O \ or name CB )) or resid 132 through 138 or (resid 151 through 153 and (name N or \ name CA or name C or name O or name CB )) or resid 154 through 162 or resid 172 \ through 194 or (resid 195 and (name N or name CA or name C or name O or name CB \ )) or resid 196 through 207 or resid 210 or (resid 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 267 or resid 270 through 30 \ 6 or resid 315 through 324 or resid 326 through 499 or (resid 500 through 503 an \ d (name N or name CA or name C or name O or name CB )) or resid 601)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' } ncs_group { reference = (chain 'H' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 71 or (resid 72 and (n \ ame N or name CA or name C or name O or name CB )) or resid 73 or resid 76 throu \ gh 96 or (resid 97 through 98 and (name N or name CA or name C or name O or name \ CB )) or resid 99 through 111)) selection = (chain 'I' and (resid 2 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB )) or resid 65 through 71 or (resid 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 or resid 76 through 111)) selection = (chain 'P' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 96 or (resid 97 through 98 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 111)) } ncs_group { reference = (chain 'J' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 95A through 106)) selection = (chain 'L' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 95A or (resid 95B and (name N or \ name CA or name C or name O or name CB )) or resid 96 through 106)) selection = (chain 'Q' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 59 or (resid 60 and (name N or name \ CA or name C or name O or name CB )) or resid 61 through 106)) } ncs_group { reference = (chain 'X' and (resid 522 through 534 or (resid 535 through 536 and (name N or n \ ame CA or name C or name O or name CB )) or resid 537 through 540 or (resid 563 \ through 564 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 5 through 570 or (resid 571 and (name N or name CA or name C or name O or name C \ B )) or resid 572 through 647 or (resid 648 and (name N or name CA or name C or \ name O or name CB )) or resid 649 through 654)) selection = (chain 'Y' and (resid 522 through 537 or (resid 538 through 539 and (name N or n \ ame CA or name C or name O or name CB )) or resid 540 or (resid 563 through 564 \ and (name N or name CA or name C or name O or name CB )) or resid 565 through 58 \ 7 or (resid 588 and (name N or name CA or name C or name O or name CB )) or resi \ d 589 through 594 or (resid 595 and (name N or name CA or name C or name O or na \ me CB )) or resid 596 through 615 or (resid 616 and (name N or name CA or name C \ or name O or name CB )) or resid 617 through 646 or (resid 647 through 648 and \ (name N or name CA or name C or name O or name CB )) or resid 649 through 654)) selection = (chain 'Z' and (resid 522 through 535 or (resid 536 and (name N or name CA or na \ me C or name O or name CB )) or resid 537 or (resid 538 through 539 and (name N \ or name CA or name C or name O or name CB )) or resid 540 or (resid 563 through \ 564 and (name N or name CA or name C or name O or name CB )) or resid 565 throug \ h 566 or (resid 567 and (name N or name CA or name C or name O or name CB )) or \ resid 568 through 570 or (resid 571 and (name N or name CA or name C or name O o \ r name CB )) or resid 572 through 587 or (resid 588 and (name N or name CA or na \ me C or name O or name CB )) or resid 589 through 594 or (resid 595 and (name N \ or name CA or name C or name O or name CB )) or resid 596 through 615 or (resid \ 616 and (name N or name CA or name C or name O or name CB )) or resid 617 throug \ h 654)) } 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.710 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 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 : 0.007 0.352 18182 Z= 0.347 Angle : 0.832 44.934 24749 Z= 0.448 Chirality : 0.053 0.767 2859 Planarity : 0.011 0.299 3095 Dihedral : 14.987 108.107 6724 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.88 % Favored : 91.07 % Rotamer: Outliers : 0.21 % Allowed : 0.64 % Favored : 99.15 % 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: -1.50 (0.18), residues: 2195 helix: 0.18 (0.27), residues: 367 sheet: -0.44 (0.22), residues: 572 loop : -1.67 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP Z 628 HIS 0.006 0.001 HIS C 216 PHE 0.022 0.002 PHE C 288 TYR 0.020 0.002 TYR C 217 ARG 0.004 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.10398 ( 10) link_NAG-ASN : angle 7.14730 ( 30) link_ALPHA1-6 : bond 0.00525 ( 1) link_ALPHA1-6 : angle 1.33605 ( 3) link_BETA1-4 : bond 0.00519 ( 9) link_BETA1-4 : angle 2.20558 ( 27) link_ALPHA1-3 : bond 0.00142 ( 1) link_ALPHA1-3 : angle 1.69588 ( 3) hydrogen bonds : bond 0.28360 ( 526) hydrogen bonds : angle 9.40527 ( 1368) SS BOND : bond 0.06336 ( 31) SS BOND : angle 5.81015 ( 62) covalent geometry : bond 0.00562 (18130) covalent geometry : angle 0.73621 (24624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 293 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.8279 (t) cc_final: 0.7792 (t) REVERT: B 69 TRP cc_start: 0.5838 (p-90) cc_final: 0.4313 (m100) REVERT: B 216 HIS cc_start: 0.5961 (m170) cc_final: 0.5738 (m170) REVERT: B 352 HIS cc_start: 0.7707 (t-90) cc_final: 0.7302 (t70) REVERT: C 260 LEU cc_start: 0.8548 (mp) cc_final: 0.8347 (mp) REVERT: H 10 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8245 (mp0) REVERT: H 105 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7083 (mtm-85) REVERT: I 28 THR cc_start: 0.6013 (p) cc_final: 0.5435 (p) REVERT: I 80 MET cc_start: 0.3141 (ptt) cc_final: 0.2861 (ptt) REVERT: J 42 MET cc_start: 0.7653 (mpp) cc_final: 0.7419 (ttp) REVERT: J 45 LYS cc_start: 0.7825 (tptp) cc_final: 0.7510 (mttp) REVERT: P 62 LYS cc_start: 0.8187 (pptt) cc_final: 0.7065 (ptpt) REVERT: Q 39 VAL cc_start: 0.8657 (t) cc_final: 0.8278 (t) REVERT: X 535 MET cc_start: 0.8413 (mpp) cc_final: 0.8155 (mpp) REVERT: Y 584 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7954 (mt-10) REVERT: Y 618 ASN cc_start: 0.6576 (t0) cc_final: 0.6347 (m110) REVERT: Y 620 SER cc_start: 0.7095 (m) cc_final: 0.6698 (p) REVERT: Y 633 LYS cc_start: 0.8310 (mppt) cc_final: 0.7749 (mtpt) REVERT: Z 622 ILE cc_start: 0.8647 (mt) cc_final: 0.8445 (mt) outliers start: 4 outliers final: 0 residues processed: 296 average time/residue: 0.2940 time to fit residues: 131.5081 Evaluate side-chains 139 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 203 optimal weight: 0.0010 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 392 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 289 ASN ** X 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 543 ASN Z 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.083447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.070335 restraints weight = 74348.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.070238 restraints weight = 61509.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.070837 restraints weight = 51761.857| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18182 Z= 0.147 Angle : 0.673 16.228 24749 Z= 0.338 Chirality : 0.046 0.196 2859 Planarity : 0.005 0.070 3095 Dihedral : 9.447 76.218 2847 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.06 % Favored : 93.90 % Rotamer: Outliers : 0.27 % Allowed : 4.67 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2195 helix: 0.80 (0.26), residues: 387 sheet: -0.28 (0.21), residues: 601 loop : -1.61 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Z 628 HIS 0.007 0.001 HIS B 105 PHE 0.022 0.002 PHE J 98 TYR 0.020 0.001 TYR C 191 ARG 0.005 0.001 ARG Z 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 10) link_NAG-ASN : angle 5.76608 ( 30) link_ALPHA1-6 : bond 0.00770 ( 1) link_ALPHA1-6 : angle 1.94242 ( 3) link_BETA1-4 : bond 0.00607 ( 9) link_BETA1-4 : angle 2.26736 ( 27) link_ALPHA1-3 : bond 0.00928 ( 1) link_ALPHA1-3 : angle 2.71122 ( 3) hydrogen bonds : bond 0.05507 ( 526) hydrogen bonds : angle 6.41773 ( 1368) SS BOND : bond 0.00381 ( 31) SS BOND : angle 1.51336 ( 62) covalent geometry : bond 0.00322 (18130) covalent geometry : angle 0.63369 (24624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 222 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5922 (p-90) cc_final: 0.4388 (m100) REVERT: B 216 HIS cc_start: 0.6061 (m170) cc_final: 0.5840 (m170) REVERT: B 248 THR cc_start: 0.7740 (p) cc_final: 0.7314 (t) REVERT: C 203 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7035 (pt0) REVERT: H 105 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7045 (mtm-85) REVERT: I 28 THR cc_start: 0.6120 (p) cc_final: 0.5321 (p) REVERT: J 45 LYS cc_start: 0.7786 (tptp) cc_final: 0.7431 (pttt) REVERT: P 62 LYS cc_start: 0.8060 (pptt) cc_final: 0.7050 (ptpt) REVERT: Q 39 VAL cc_start: 0.8495 (t) cc_final: 0.8062 (t) REVERT: Q 104 LEU cc_start: 0.8624 (tp) cc_final: 0.8316 (tp) REVERT: X 535 MET cc_start: 0.8310 (mpp) cc_final: 0.7778 (mpp) REVERT: Y 573 ILE cc_start: 0.8921 (mm) cc_final: 0.7645 (mm) REVERT: Y 620 SER cc_start: 0.6988 (m) cc_final: 0.6656 (p) REVERT: Y 633 LYS cc_start: 0.8311 (mppt) cc_final: 0.7936 (mtpt) outliers start: 5 outliers final: 0 residues processed: 226 average time/residue: 0.2644 time to fit residues: 94.6573 Evaluate side-chains 136 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 192 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 136 optimal weight: 0.0670 chunk 212 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 448 ASN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN X 563 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.079999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.065914 restraints weight = 74643.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065572 restraints weight = 58216.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065815 restraints weight = 50686.969| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 18182 Z= 0.247 Angle : 0.751 15.397 24749 Z= 0.381 Chirality : 0.049 0.257 2859 Planarity : 0.005 0.091 3095 Dihedral : 7.289 57.890 2847 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.93 % Favored : 91.94 % Rotamer: Outliers : 0.11 % Allowed : 6.10 % Favored : 93.80 % 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: -1.39 (0.17), residues: 2195 helix: 0.58 (0.26), residues: 386 sheet: -0.40 (0.21), residues: 609 loop : -1.76 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 35 HIS 0.016 0.002 HIS B 374 PHE 0.042 0.003 PHE P 99 TYR 0.018 0.002 TYR C 191 ARG 0.007 0.001 ARG X 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 10) link_NAG-ASN : angle 4.64279 ( 30) link_ALPHA1-6 : bond 0.01869 ( 1) link_ALPHA1-6 : angle 1.74879 ( 3) link_BETA1-4 : bond 0.00499 ( 9) link_BETA1-4 : angle 2.46740 ( 27) link_ALPHA1-3 : bond 0.00956 ( 1) link_ALPHA1-3 : angle 2.01361 ( 3) hydrogen bonds : bond 0.04856 ( 526) hydrogen bonds : angle 6.22172 ( 1368) SS BOND : bond 0.00955 ( 31) SS BOND : angle 1.76072 ( 62) covalent geometry : bond 0.00562 (18130) covalent geometry : angle 0.72443 (24624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6050 (p-90) cc_final: 0.4283 (m100) REVERT: B 216 HIS cc_start: 0.6487 (m170) cc_final: 0.6243 (m170) REVERT: B 248 THR cc_start: 0.7684 (p) cc_final: 0.7012 (t) REVERT: B 390 LEU cc_start: 0.8034 (mt) cc_final: 0.7371 (mt) REVERT: C 203 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6779 (pp30) REVERT: H 105 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7028 (mtm-85) REVERT: P 62 LYS cc_start: 0.8343 (pptt) cc_final: 0.7376 (ptpt) REVERT: Q 79 GLN cc_start: 0.8133 (mp10) cc_final: 0.7906 (mp10) REVERT: Q 104 LEU cc_start: 0.8735 (tp) cc_final: 0.8503 (tp) REVERT: X 535 MET cc_start: 0.8458 (mpp) cc_final: 0.7831 (mpp) REVERT: Y 633 LYS cc_start: 0.8383 (mppt) cc_final: 0.8076 (mtpt) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.2570 time to fit residues: 76.7119 Evaluate side-chains 132 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 49 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 101 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS B 258 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.079854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066140 restraints weight = 74351.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066290 restraints weight = 64935.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066855 restraints weight = 56560.829| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18182 Z= 0.218 Angle : 0.689 18.643 24749 Z= 0.349 Chirality : 0.047 0.276 2859 Planarity : 0.005 0.081 3095 Dihedral : 6.672 58.629 2847 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 0.11 % Allowed : 4.19 % Favored : 95.71 % 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: -1.46 (0.18), residues: 2195 helix: 0.63 (0.27), residues: 386 sheet: -0.47 (0.21), residues: 604 loop : -1.83 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Z 628 HIS 0.007 0.001 HIS A 330 PHE 0.023 0.002 PHE I 29 TYR 0.024 0.002 TYR J 30 ARG 0.007 0.001 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 10) link_NAG-ASN : angle 5.09194 ( 30) link_ALPHA1-6 : bond 0.01215 ( 1) link_ALPHA1-6 : angle 1.28495 ( 3) link_BETA1-4 : bond 0.00550 ( 9) link_BETA1-4 : angle 2.28500 ( 27) link_ALPHA1-3 : bond 0.00975 ( 1) link_ALPHA1-3 : angle 1.88652 ( 3) hydrogen bonds : bond 0.04254 ( 526) hydrogen bonds : angle 5.94862 ( 1368) SS BOND : bond 0.00403 ( 31) SS BOND : angle 1.52916 ( 62) covalent geometry : bond 0.00504 (18130) covalent geometry : angle 0.65873 (24624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6062 (p-90) cc_final: 0.4284 (m100) REVERT: B 216 HIS cc_start: 0.6685 (m170) cc_final: 0.6433 (m170) REVERT: B 248 THR cc_start: 0.7679 (p) cc_final: 0.7067 (t) REVERT: J 27 ASN cc_start: 0.6017 (m-40) cc_final: 0.5545 (p0) REVERT: X 535 MET cc_start: 0.8309 (mpp) cc_final: 0.7745 (mpp) REVERT: Y 573 ILE cc_start: 0.8792 (mm) cc_final: 0.8050 (mm) REVERT: Y 577 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7305 (mp10) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.2543 time to fit residues: 76.0516 Evaluate side-chains 132 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 53 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 125 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 0.0060 chunk 59 optimal weight: 0.8980 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 287 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.080948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.067282 restraints weight = 74840.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067232 restraints weight = 65503.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.067577 restraints weight = 55239.176| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18182 Z= 0.142 Angle : 0.635 14.623 24749 Z= 0.321 Chirality : 0.046 0.353 2859 Planarity : 0.004 0.062 3095 Dihedral : 6.323 58.680 2847 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.30 (0.18), residues: 2195 helix: 0.70 (0.27), residues: 392 sheet: -0.34 (0.21), residues: 601 loop : -1.73 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Z 628 HIS 0.006 0.001 HIS A 249 PHE 0.020 0.001 PHE C 288 TYR 0.018 0.001 TYR L 95B ARG 0.005 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 10) link_NAG-ASN : angle 4.60807 ( 30) link_ALPHA1-6 : bond 0.00971 ( 1) link_ALPHA1-6 : angle 1.31421 ( 3) link_BETA1-4 : bond 0.00537 ( 9) link_BETA1-4 : angle 1.93305 ( 27) link_ALPHA1-3 : bond 0.00982 ( 1) link_ALPHA1-3 : angle 1.69881 ( 3) hydrogen bonds : bond 0.03877 ( 526) hydrogen bonds : angle 5.63970 ( 1368) SS BOND : bond 0.00559 ( 31) SS BOND : angle 2.23001 ( 62) covalent geometry : bond 0.00324 (18130) covalent geometry : angle 0.60141 (24624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5547 (ppp) cc_final: 0.5164 (ppp) REVERT: B 69 TRP cc_start: 0.6040 (p-90) cc_final: 0.4201 (m100) REVERT: B 216 HIS cc_start: 0.6633 (m170) cc_final: 0.6306 (m170) REVERT: B 248 THR cc_start: 0.7483 (p) cc_final: 0.6790 (t) REVERT: L 48 ILE cc_start: 0.9656 (tt) cc_final: 0.9339 (pt) REVERT: P 62 LYS cc_start: 0.8311 (pptt) cc_final: 0.8075 (ttpp) REVERT: X 535 MET cc_start: 0.8269 (mpp) cc_final: 0.7687 (mpp) REVERT: Y 573 ILE cc_start: 0.8914 (mm) cc_final: 0.8197 (mm) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.2581 time to fit residues: 79.9629 Evaluate side-chains 128 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 143 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 129 optimal weight: 0.0070 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 301 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.080324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066702 restraints weight = 74616.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.066582 restraints weight = 65956.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066826 restraints weight = 56428.118| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18182 Z= 0.174 Angle : 0.662 12.092 24749 Z= 0.334 Chirality : 0.046 0.263 2859 Planarity : 0.005 0.085 3095 Dihedral : 6.231 56.403 2847 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.03 % Rotamer: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.31 (0.18), residues: 2195 helix: 0.72 (0.27), residues: 386 sheet: -0.36 (0.21), residues: 607 loop : -1.72 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP X 571 HIS 0.010 0.001 HIS B 85 PHE 0.024 0.002 PHE C 288 TYR 0.016 0.002 TYR C 191 ARG 0.007 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 10) link_NAG-ASN : angle 4.21143 ( 30) link_ALPHA1-6 : bond 0.00994 ( 1) link_ALPHA1-6 : angle 1.28621 ( 3) link_BETA1-4 : bond 0.00520 ( 9) link_BETA1-4 : angle 1.87032 ( 27) link_ALPHA1-3 : bond 0.01031 ( 1) link_ALPHA1-3 : angle 1.74464 ( 3) hydrogen bonds : bond 0.03813 ( 526) hydrogen bonds : angle 5.60636 ( 1368) SS BOND : bond 0.00330 ( 31) SS BOND : angle 1.98866 ( 62) covalent geometry : bond 0.00408 (18130) covalent geometry : angle 0.63593 (24624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6101 (p-90) cc_final: 0.4205 (m100) REVERT: B 216 HIS cc_start: 0.6794 (m170) cc_final: 0.6454 (m170) REVERT: B 248 THR cc_start: 0.7547 (p) cc_final: 0.6751 (t) REVERT: I 100 MET cc_start: 0.6795 (ppp) cc_final: 0.6074 (ppp) REVERT: J 45 LYS cc_start: 0.7596 (pttt) cc_final: 0.7333 (mttp) REVERT: X 535 MET cc_start: 0.8297 (mpp) cc_final: 0.7678 (mpp) REVERT: Y 573 ILE cc_start: 0.8875 (mm) cc_final: 0.8247 (mm) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2393 time to fit residues: 70.6581 Evaluate side-chains 124 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 166 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 203 optimal weight: 10.0000 chunk 100 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN B 302 ASN B 332 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN X 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.081535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.068016 restraints weight = 73692.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067956 restraints weight = 66648.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.068640 restraints weight = 53187.847| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18182 Z= 0.119 Angle : 0.603 10.617 24749 Z= 0.306 Chirality : 0.045 0.253 2859 Planarity : 0.004 0.051 3095 Dihedral : 5.856 56.211 2847 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.21 (0.18), residues: 2195 helix: 0.73 (0.27), residues: 395 sheet: -0.36 (0.21), residues: 613 loop : -1.61 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 45 HIS 0.006 0.001 HIS A 249 PHE 0.026 0.001 PHE B 53 TYR 0.014 0.001 TYR C 191 ARG 0.005 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 10) link_NAG-ASN : angle 3.84860 ( 30) link_ALPHA1-6 : bond 0.00727 ( 1) link_ALPHA1-6 : angle 1.27173 ( 3) link_BETA1-4 : bond 0.00524 ( 9) link_BETA1-4 : angle 1.70142 ( 27) link_ALPHA1-3 : bond 0.01097 ( 1) link_ALPHA1-3 : angle 1.56205 ( 3) hydrogen bonds : bond 0.03533 ( 526) hydrogen bonds : angle 5.40973 ( 1368) SS BOND : bond 0.00325 ( 31) SS BOND : angle 1.49236 ( 62) covalent geometry : bond 0.00273 (18130) covalent geometry : angle 0.58177 (24624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6176 (p-90) cc_final: 0.4247 (m100) REVERT: B 216 HIS cc_start: 0.6682 (m170) cc_final: 0.6321 (m170) REVERT: B 248 THR cc_start: 0.7446 (p) cc_final: 0.6618 (t) REVERT: J 45 LYS cc_start: 0.7633 (pttt) cc_final: 0.7313 (mttp) REVERT: J 85 ASP cc_start: 0.7160 (t0) cc_final: 0.6934 (t0) REVERT: L 48 ILE cc_start: 0.9624 (tt) cc_final: 0.9328 (pt) REVERT: Q 104 LEU cc_start: 0.8901 (tp) cc_final: 0.8691 (tp) REVERT: X 535 MET cc_start: 0.8183 (mpp) cc_final: 0.7611 (mpp) REVERT: Y 573 ILE cc_start: 0.8866 (mm) cc_final: 0.8282 (mt) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2639 time to fit residues: 82.0680 Evaluate side-chains 126 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 160 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 chunk 172 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.081729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068433 restraints weight = 73339.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.068209 restraints weight = 69303.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.068799 restraints weight = 55555.184| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18182 Z= 0.116 Angle : 0.601 9.706 24749 Z= 0.304 Chirality : 0.045 0.253 2859 Planarity : 0.004 0.048 3095 Dihedral : 5.640 56.608 2847 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.11 (0.18), residues: 2195 helix: 0.91 (0.28), residues: 387 sheet: -0.28 (0.21), residues: 622 loop : -1.59 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Z 628 HIS 0.005 0.001 HIS A 249 PHE 0.022 0.001 PHE C 288 TYR 0.015 0.001 TYR A 217 ARG 0.008 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 10) link_NAG-ASN : angle 3.71942 ( 30) link_ALPHA1-6 : bond 0.00715 ( 1) link_ALPHA1-6 : angle 1.36038 ( 3) link_BETA1-4 : bond 0.00523 ( 9) link_BETA1-4 : angle 1.63042 ( 27) link_ALPHA1-3 : bond 0.00954 ( 1) link_ALPHA1-3 : angle 1.47609 ( 3) hydrogen bonds : bond 0.03378 ( 526) hydrogen bonds : angle 5.28820 ( 1368) SS BOND : bond 0.00345 ( 31) SS BOND : angle 1.21514 ( 62) covalent geometry : bond 0.00268 (18130) covalent geometry : angle 0.58219 (24624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6157 (p-90) cc_final: 0.4242 (m100) REVERT: B 216 HIS cc_start: 0.6753 (m170) cc_final: 0.6397 (m170) REVERT: B 248 THR cc_start: 0.7493 (p) cc_final: 0.6653 (t) REVERT: I 100 MET cc_start: 0.6526 (ppp) cc_final: 0.5648 (ppp) REVERT: J 45 LYS cc_start: 0.7593 (pttt) cc_final: 0.7303 (mttp) REVERT: L 48 ILE cc_start: 0.9617 (tt) cc_final: 0.9335 (pt) REVERT: Q 104 LEU cc_start: 0.8893 (tp) cc_final: 0.8661 (tp) REVERT: X 535 MET cc_start: 0.8184 (mpp) cc_final: 0.7618 (mpp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2647 time to fit residues: 78.5647 Evaluate side-chains 128 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 70 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.079964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.066501 restraints weight = 73865.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.066548 restraints weight = 60262.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.066819 restraints weight = 52321.664| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18182 Z= 0.196 Angle : 0.671 10.167 24749 Z= 0.342 Chirality : 0.047 0.258 2859 Planarity : 0.005 0.057 3095 Dihedral : 5.815 56.710 2847 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.56 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.29 (0.18), residues: 2195 helix: 0.65 (0.27), residues: 394 sheet: -0.43 (0.21), residues: 635 loop : -1.67 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP Z 628 HIS 0.006 0.001 HIS A 330 PHE 0.035 0.002 PHE P 99 TYR 0.024 0.002 TYR C 191 ARG 0.005 0.001 ARG C 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 10) link_NAG-ASN : angle 3.86970 ( 30) link_ALPHA1-6 : bond 0.00885 ( 1) link_ALPHA1-6 : angle 1.28122 ( 3) link_BETA1-4 : bond 0.00513 ( 9) link_BETA1-4 : angle 1.80434 ( 27) link_ALPHA1-3 : bond 0.00749 ( 1) link_ALPHA1-3 : angle 1.60631 ( 3) hydrogen bonds : bond 0.03655 ( 526) hydrogen bonds : angle 5.56081 ( 1368) SS BOND : bond 0.00428 ( 31) SS BOND : angle 1.43949 ( 62) covalent geometry : bond 0.00458 (18130) covalent geometry : angle 0.65141 (24624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6146 (p-90) cc_final: 0.4159 (m100) REVERT: B 248 THR cc_start: 0.7542 (p) cc_final: 0.6976 (t) REVERT: J 85 ASP cc_start: 0.7143 (t0) cc_final: 0.6814 (t0) REVERT: P 62 LYS cc_start: 0.8318 (pptt) cc_final: 0.7209 (ptpt) REVERT: Q 104 LEU cc_start: 0.8957 (tp) cc_final: 0.8752 (tp) REVERT: X 535 MET cc_start: 0.8250 (mpp) cc_final: 0.7619 (mpp) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2409 time to fit residues: 65.7015 Evaluate side-chains 121 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 209 optimal weight: 0.0070 chunk 52 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 75 optimal weight: 0.0570 overall best weight: 1.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.080592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067317 restraints weight = 73129.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067238 restraints weight = 60115.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.067466 restraints weight = 52424.452| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18182 Z= 0.146 Angle : 0.640 17.734 24749 Z= 0.322 Chirality : 0.046 0.338 2859 Planarity : 0.004 0.051 3095 Dihedral : 5.798 56.016 2847 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.23 (0.18), residues: 2195 helix: 0.74 (0.27), residues: 389 sheet: -0.39 (0.21), residues: 628 loop : -1.62 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP Z 628 HIS 0.005 0.001 HIS A 249 PHE 0.026 0.002 PHE C 288 TYR 0.018 0.001 TYR C 191 ARG 0.003 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 10) link_NAG-ASN : angle 5.14866 ( 30) link_ALPHA1-6 : bond 0.00769 ( 1) link_ALPHA1-6 : angle 1.24439 ( 3) link_BETA1-4 : bond 0.00499 ( 9) link_BETA1-4 : angle 1.86618 ( 27) link_ALPHA1-3 : bond 0.00851 ( 1) link_ALPHA1-3 : angle 1.48444 ( 3) hydrogen bonds : bond 0.03492 ( 526) hydrogen bonds : angle 5.42563 ( 1368) SS BOND : bond 0.00364 ( 31) SS BOND : angle 1.48621 ( 62) covalent geometry : bond 0.00340 (18130) covalent geometry : angle 0.60803 (24624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6181 (p-90) cc_final: 0.4156 (m100) REVERT: B 216 HIS cc_start: 0.7111 (m170) cc_final: 0.6723 (m170) REVERT: B 248 THR cc_start: 0.7446 (p) cc_final: 0.6678 (t) REVERT: C 377 ASN cc_start: 0.8334 (t0) cc_final: 0.8080 (t0) REVERT: J 42 MET cc_start: 0.7982 (mpp) cc_final: 0.7556 (ttm) REVERT: J 45 LYS cc_start: 0.7732 (pttt) cc_final: 0.7399 (mttp) REVERT: J 85 ASP cc_start: 0.7172 (t0) cc_final: 0.6884 (t0) REVERT: L 48 ILE cc_start: 0.9641 (tt) cc_final: 0.9327 (pt) REVERT: P 62 LYS cc_start: 0.8240 (pptt) cc_final: 0.7106 (ptpt) REVERT: Q 104 LEU cc_start: 0.8928 (tp) cc_final: 0.8723 (tp) REVERT: X 535 MET cc_start: 0.8241 (mpp) cc_final: 0.7614 (mpp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2409 time to fit residues: 65.6470 Evaluate side-chains 123 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.9888 > 50: distance: 48 - 53: 3.592 distance: 53 - 54: 13.330 distance: 54 - 55: 6.050 distance: 54 - 57: 9.562 distance: 55 - 56: 9.023 distance: 55 - 63: 13.118 distance: 57 - 58: 11.084 distance: 58 - 59: 16.333 distance: 58 - 60: 11.945 distance: 59 - 61: 11.524 distance: 60 - 62: 14.666 distance: 61 - 62: 11.107 distance: 64 - 65: 7.969 distance: 65 - 66: 13.560 distance: 65 - 67: 16.079 distance: 67 - 68: 6.465 distance: 68 - 69: 16.609 distance: 69 - 70: 9.485 distance: 69 - 75: 18.592 distance: 71 - 72: 24.078 distance: 71 - 73: 39.154 distance: 72 - 74: 11.353 distance: 75 - 76: 21.120 distance: 76 - 77: 12.725 distance: 76 - 79: 15.844 distance: 77 - 78: 15.571 distance: 77 - 84: 10.920 distance: 79 - 80: 18.493 distance: 80 - 81: 15.755 distance: 81 - 82: 22.508 distance: 82 - 83: 34.444 distance: 84 - 85: 9.322 distance: 84 - 90: 12.495 distance: 85 - 86: 11.718 distance: 85 - 88: 15.655 distance: 86 - 87: 30.051 distance: 86 - 91: 11.289 distance: 88 - 89: 5.006 distance: 89 - 90: 12.863 distance: 91 - 92: 23.845 distance: 92 - 93: 14.689 distance: 92 - 95: 12.813 distance: 93 - 94: 5.799 distance: 93 - 98: 6.677 distance: 95 - 96: 21.625 distance: 95 - 97: 11.483 distance: 98 - 99: 13.608 distance: 99 - 100: 17.687 distance: 99 - 102: 17.757 distance: 100 - 101: 23.907 distance: 100 - 105: 14.705 distance: 102 - 103: 9.347 distance: 102 - 104: 6.220 distance: 105 - 106: 12.382 distance: 106 - 107: 9.319 distance: 106 - 109: 13.179 distance: 107 - 108: 9.980 distance: 107 - 111: 7.254 distance: 109 - 110: 9.568 distance: 111 - 112: 12.961 distance: 112 - 113: 17.721 distance: 112 - 115: 7.817 distance: 113 - 114: 4.160 distance: 113 - 118: 8.409 distance: 115 - 116: 13.635 distance: 115 - 117: 14.871 distance: 118 - 119: 6.653 distance: 119 - 120: 6.427 distance: 119 - 122: 8.138 distance: 120 - 121: 4.962 distance: 120 - 127: 11.177 distance: 122 - 123: 6.097 distance: 123 - 124: 5.273 distance: 124 - 125: 6.891 distance: 124 - 126: 3.957