Starting phenix.real_space_refine on Sun Jul 5 09:08:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tfo_25878/07_2026/7tfo_25878.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfo_25878/07_2026/7tfo_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tfo_25878/07_2026/7tfo_25878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfo_25878/07_2026/7tfo_25878.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tfo_25878/07_2026/7tfo_25878.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tfo_25878/07_2026/7tfo_25878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tfo_25878/07_2026/7tfo_25878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfo_25878/07_2026/7tfo_25878.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASP:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 3} 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: {'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 2} 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: {'ASP:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 1} 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: {'ASP:plan': 1, 'ARG: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: {'ASP:plan': 1, 'TYR: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: {'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2} 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 3.64, per 1000 atoms: 0.20 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: 1.34 Conformation dependent library (CDL) restraints added in 781.1 milliseconds 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: 0.49 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: 2.76 Time building geometry restraints manager: 1.76 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 - 17.82: 9644 17.82 - 35.63: 779 35.63 - 53.45: 126 53.45 - 71.27: 37 71.27 - 89.09: 12 Dihedral angle restraints: 10598 sinusoidal: 4066 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 10595 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: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.090 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 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 : 13.260 89.085 6295 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.66 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG B 273 TYR 0.020 0.002 TYR C 217 PHE 0.022 0.002 PHE C 288 TRP 0.079 0.002 TRP Z 628 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.30 (18130) covalent geometry : angle 0.73621 / 0.42 (24624) SS BOND : bond 0.06336 / 5.27 ( 31) SS BOND : angle 5.81015 / 3.61 ( 62) hydrogen bonds : bond 0.28360 / 18.93 ( 526) hydrogen bonds : angle 9.40527 / 6.36 ( 1368) link_ALPHA1-3 : bond 0.00142 / 0.07 ( 1) link_ALPHA1-3 : angle 1.69588 / 0.74 ( 3) link_ALPHA1-6 : bond 0.00525 / 0.28 ( 1) link_ALPHA1-6 : angle 1.33605 / 0.61 ( 3) link_BETA1-4 : bond 0.00519 / 0.27 ( 9) link_BETA1-4 : angle 2.20558 / 1.31 ( 27) link_NAG-ASN : bond 0.10398 / 4.97 ( 10) link_NAG-ASN : angle 7.14730 / 4.31 ( 30) *********************** 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 : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.8279 (t) cc_final: 0.7793 (t) REVERT: B 69 TRP cc_start: 0.5838 (p-90) cc_final: 0.4318 (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: 0.7303 (t70) REVERT: C 260 LEU cc_start: 0.8548 (mp) cc_final: 0.8348 (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: 0.5433 (p) REVERT: I 29 PHE cc_start: 0.4284 (m-10) cc_final: 0.4029 (m-10) 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: 0.7416 (ttp) REVERT: J 45 LYS cc_start: 0.7825 (tptp) cc_final: 0.7512 (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: 0.8277 (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: 0.7951 (mt-10) REVERT: Y 620 SER cc_start: 0.7095 (m) cc_final: 0.6702 (p) REVERT: Y 633 LYS cc_start: 0.8310 (mppt) cc_final: 0.7755 (mtpt) REVERT: Z 622 ILE cc_start: 0.8647 (mt) cc_final: 0.8439 (mt) outliers start: 4 outliers final: 0 residues processed: 296 average time/residue: 0.1355 time to fit residues: 61.4437 Evaluate side-chains 137 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS B 258 GLN B 392 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 289 ASN Q 38 GLN Y 543 ASN Z 607 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.081989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068559 restraints weight = 74276.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068594 restraints weight = 63811.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069187 restraints weight = 53566.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.069551 restraints weight = 45927.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.069600 restraints weight = 43662.311| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18182 Z= 0.205 Angle : 0.701 16.592 24749 Z= 0.356 Chirality : 0.046 0.199 2859 Planarity : 0.005 0.079 3095 Dihedral : 4.754 24.202 2418 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.32 % Allowed : 5.14 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 2195 helix: 0.72 (0.26), residues: 387 sheet: -0.34 (0.21), residues: 601 loop : -1.65 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Z 617 TYR 0.020 0.002 TYR C 191 PHE 0.021 0.002 PHE I 99 TRP 0.029 0.002 TRP B 479 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (18130) covalent geometry : angle 0.66398 / 0.35 (24624) SS BOND : bond 0.00339 / 0.19 ( 31) SS BOND : angle 1.63624 / 0.99 ( 62) hydrogen bonds : bond 0.05804 / 3.89 ( 526) hydrogen bonds : angle 6.52431 / 4.45 ( 1368) link_ALPHA1-3 : bond 0.00495 / 0.26 ( 1) link_ALPHA1-3 : angle 1.79205 / 0.90 ( 3) link_ALPHA1-6 : bond 0.01315 / 0.69 ( 1) link_ALPHA1-6 : angle 1.81325 / 0.93 ( 3) link_BETA1-4 : bond 0.00750 / 0.43 ( 9) link_BETA1-4 : angle 1.96280 / 1.38 ( 27) link_NAG-ASN : bond 0.00710 / 0.38 ( 10) link_NAG-ASN : angle 5.78013 / 3.48 ( 30) *********************** 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 211 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 205 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5949 (p-90) cc_final: 0.4342 (m100) REVERT: B 216 HIS cc_start: 0.6198 (m170) cc_final: 0.5992 (m170) REVERT: B 248 THR cc_start: 0.7730 (p) cc_final: 0.7286 (t) REVERT: C 203 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7157 (pt0) REVERT: H 105 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7140 (mtm-85) REVERT: I 28 THR cc_start: 0.6132 (p) cc_final: 0.5382 (p) REVERT: J 45 LYS cc_start: 0.7845 (tptp) cc_final: 0.7455 (pttt) REVERT: P 62 LYS cc_start: 0.8127 (pptt) cc_final: 0.7129 (ptpt) REVERT: Q 39 VAL cc_start: 0.8554 (t) cc_final: 0.8071 (t) REVERT: Q 104 LEU cc_start: 0.8667 (tp) cc_final: 0.8346 (tp) REVERT: X 535 MET cc_start: 0.8284 (mpp) cc_final: 0.7751 (mpp) REVERT: Y 573 ILE cc_start: 0.8946 (mm) cc_final: 0.7680 (mm) REVERT: Y 620 SER cc_start: 0.7057 (m) cc_final: 0.6595 (p) REVERT: Y 633 LYS cc_start: 0.8337 (mppt) cc_final: 0.7973 (mtpt) outliers start: 6 outliers final: 1 residues processed: 210 average time/residue: 0.1163 time to fit residues: 38.6554 Evaluate side-chains 134 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 215 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.082756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.068628 restraints weight = 74770.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.068892 restraints weight = 49304.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069343 restraints weight = 43464.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.069550 restraints weight = 37788.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.069699 restraints weight = 34532.516| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18182 Z= 0.132 Angle : 0.623 13.159 24749 Z= 0.315 Chirality : 0.045 0.264 2859 Planarity : 0.004 0.066 3095 Dihedral : 4.576 22.334 2418 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.97 % Favored : 93.99 % Rotamer: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.18), residues: 2195 helix: 0.91 (0.27), residues: 388 sheet: -0.32 (0.21), residues: 620 loop : -1.57 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 18 TYR 0.013 0.001 TYR C 191 PHE 0.021 0.001 PHE P 99 TRP 0.029 0.001 TRP B 35 HIS 0.008 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (18130) covalent geometry : angle 0.59425 / 0.31 (24624) SS BOND : bond 0.00337 / 0.17 ( 31) SS BOND : angle 1.42964 / 0.92 ( 62) hydrogen bonds : bond 0.04542 / 3.01 ( 526) hydrogen bonds : angle 5.91435 / 4.01 ( 1368) link_ALPHA1-3 : bond 0.00656 / 0.35 ( 1) link_ALPHA1-3 : angle 1.41060 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00953 / 0.50 ( 1) link_ALPHA1-6 : angle 1.22820 / 0.56 ( 3) link_BETA1-4 : bond 0.00487 / 0.28 ( 9) link_BETA1-4 : angle 1.69066 / 1.09 ( 27) link_NAG-ASN : bond 0.00729 / 0.53 ( 10) link_NAG-ASN : angle 4.84616 / 2.70 ( 30) *********************** 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 201 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.4959 (ppp) cc_final: 0.4714 (ppp) REVERT: B 69 TRP cc_start: 0.5986 (p-90) cc_final: 0.4309 (m100) REVERT: B 216 HIS cc_start: 0.6196 (m170) cc_final: 0.5942 (m170) REVERT: B 248 THR cc_start: 0.7682 (p) cc_final: 0.7062 (t) REVERT: C 203 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6688 (pp30) REVERT: H 105 ARG cc_start: 0.8134 (mmm160) cc_final: 0.6969 (mtm-85) REVERT: I 29 PHE cc_start: 0.4146 (m-10) cc_final: 0.3597 (m-10) REVERT: Q 104 LEU cc_start: 0.8610 (tp) cc_final: 0.8282 (tp) REVERT: X 535 MET cc_start: 0.8381 (mpp) cc_final: 0.8131 (mpp) REVERT: Y 620 SER cc_start: 0.7197 (m) cc_final: 0.6755 (p) REVERT: Y 633 LYS cc_start: 0.8431 (mppt) cc_final: 0.8083 (mtpt) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1133 time to fit residues: 36.2951 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 : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 102 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 180 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 332 ASN C 203 GLN C 301 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.082990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.069553 restraints weight = 74235.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069114 restraints weight = 54801.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.069664 restraints weight = 46026.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.069934 restraints weight = 39721.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.070027 restraints weight = 37012.970| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18182 Z= 0.120 Angle : 0.599 19.491 24749 Z= 0.300 Chirality : 0.044 0.263 2859 Planarity : 0.004 0.059 3095 Dihedral : 4.401 22.200 2418 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 2195 helix: 1.15 (0.27), residues: 383 sheet: -0.22 (0.21), residues: 625 loop : -1.53 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 18 TYR 0.021 0.001 TYR J 30 PHE 0.021 0.001 PHE C 288 TRP 0.023 0.001 TRP Z 628 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (18130) covalent geometry : angle 0.56813 / 0.29 (24624) SS BOND : bond 0.00256 / 0.13 ( 31) SS BOND : angle 1.12404 / 0.72 ( 62) hydrogen bonds : bond 0.03883 / 2.57 ( 526) hydrogen bonds : angle 5.57255 / 3.78 ( 1368) link_ALPHA1-3 : bond 0.00656 / 0.35 ( 1) link_ALPHA1-3 : angle 1.40937 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00837 / 0.44 ( 1) link_ALPHA1-6 : angle 1.36604 / 0.63 ( 3) link_BETA1-4 : bond 0.00460 / 0.26 ( 9) link_BETA1-4 : angle 1.71725 / 1.13 ( 27) link_NAG-ASN : bond 0.00468 / 0.25 ( 10) link_NAG-ASN : angle 5.02764 / 2.78 ( 30) *********************** 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 203 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5997 (p-90) cc_final: 0.4313 (m100) REVERT: B 216 HIS cc_start: 0.6229 (m170) cc_final: 0.5935 (m170) REVERT: B 248 THR cc_start: 0.7623 (p) cc_final: 0.7010 (t) REVERT: C 203 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6668 (pp30) REVERT: C 287 GLN cc_start: 0.7847 (mt0) cc_final: 0.7643 (mt0) REVERT: H 105 ARG cc_start: 0.8056 (mmm160) cc_final: 0.6880 (mtm-85) REVERT: J 27 ASN cc_start: 0.6040 (m-40) cc_final: 0.5385 (p0) REVERT: J 42 MET cc_start: 0.7834 (mpp) cc_final: 0.7547 (ttm) REVERT: P 62 LYS cc_start: 0.8206 (pptt) cc_final: 0.7092 (ptpt) REVERT: P 81 ASP cc_start: 0.7521 (p0) cc_final: 0.7321 (p0) REVERT: Q 104 LEU cc_start: 0.8637 (tp) cc_final: 0.8403 (tp) REVERT: X 535 MET cc_start: 0.8342 (mpp) cc_final: 0.7738 (mpp) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.1284 time to fit residues: 41.1485 Evaluate side-chains 134 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 179 optimal weight: 0.0670 chunk 169 optimal weight: 6.9990 chunk 29 optimal weight: 0.0870 chunk 32 optimal weight: 10.0000 overall best weight: 1.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 332 ASN C 203 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.082007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068289 restraints weight = 74192.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.068334 restraints weight = 65084.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.068857 restraints weight = 53329.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.069067 restraints weight = 46802.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069170 restraints weight = 41724.823| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18182 Z= 0.152 Angle : 0.608 14.557 24749 Z= 0.308 Chirality : 0.045 0.254 2859 Planarity : 0.004 0.054 3095 Dihedral : 4.496 22.468 2418 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.97 % Favored : 93.94 % Rotamer: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2195 helix: 1.18 (0.27), residues: 383 sheet: -0.20 (0.21), residues: 611 loop : -1.56 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 94 TYR 0.012 0.001 TYR L 95B PHE 0.020 0.002 PHE C 288 TRP 0.035 0.002 TRP X 571 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (18130) covalent geometry : angle 0.58268 / 0.30 (24624) SS BOND : bond 0.00396 / 0.21 ( 31) SS BOND : angle 1.34114 / 0.85 ( 62) hydrogen bonds : bond 0.03665 / 2.40 ( 526) hydrogen bonds : angle 5.50846 / 3.74 ( 1368) link_ALPHA1-3 : bond 0.00610 / 0.32 ( 1) link_ALPHA1-3 : angle 1.44196 / 0.74 ( 3) link_ALPHA1-6 : bond 0.01275 / 0.67 ( 1) link_ALPHA1-6 : angle 1.47329 / 0.67 ( 3) link_BETA1-4 : bond 0.00587 / 0.32 ( 9) link_BETA1-4 : angle 1.58863 / 1.05 ( 27) link_NAG-ASN : bond 0.00509 / 0.28 ( 10) link_NAG-ASN : angle 4.45099 / 2.51 ( 30) *********************** 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 192 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5961 (p-90) cc_final: 0.4279 (m100) REVERT: B 216 HIS cc_start: 0.6477 (m170) cc_final: 0.6191 (m170) REVERT: B 248 THR cc_start: 0.7572 (p) cc_final: 0.6931 (t) REVERT: C 203 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6557 (pp30) REVERT: C 475 MET cc_start: 0.8492 (mmm) cc_final: 0.8090 (mmm) REVERT: H 105 ARG cc_start: 0.8059 (mmm160) cc_final: 0.6898 (mtm-85) REVERT: L 48 ILE cc_start: 0.9647 (tt) cc_final: 0.9270 (pt) REVERT: P 62 LYS cc_start: 0.8088 (pptt) cc_final: 0.7871 (ttpp) REVERT: Q 104 LEU cc_start: 0.8760 (tp) cc_final: 0.8525 (tp) REVERT: X 535 MET cc_start: 0.8233 (mpp) cc_final: 0.7657 (mpp) REVERT: Y 542 ARG cc_start: 0.7132 (tmt-80) cc_final: 0.6824 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.1255 time to fit residues: 38.0533 Evaluate side-chains 124 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 2.9990 chunk 181 optimal weight: 0.0010 chunk 140 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 180 optimal weight: 0.0980 chunk 113 optimal weight: 6.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS B 332 ASN C 203 GLN C 287 GLN C 301 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.083216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.069359 restraints weight = 73032.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.069539 restraints weight = 59054.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.070168 restraints weight = 47619.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.070382 restraints weight = 40524.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.070448 restraints weight = 37541.993| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18182 Z= 0.108 Angle : 0.578 11.724 24749 Z= 0.291 Chirality : 0.044 0.252 2859 Planarity : 0.004 0.053 3095 Dihedral : 4.334 21.541 2418 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 0.11 % Allowed : 2.23 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.18), residues: 2195 helix: 1.38 (0.28), residues: 377 sheet: -0.29 (0.21), residues: 637 loop : -1.49 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.017 0.001 TYR C 191 PHE 0.025 0.001 PHE C 288 TRP 0.018 0.001 TRP Z 628 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (18130) covalent geometry : angle 0.55780 / 0.29 (24624) SS BOND : bond 0.00204 / 0.10 ( 31) SS BOND : angle 1.14466 / 0.73 ( 62) hydrogen bonds : bond 0.03375 / 2.23 ( 526) hydrogen bonds : angle 5.25284 / 3.56 ( 1368) link_ALPHA1-3 : bond 0.00681 / 0.36 ( 1) link_ALPHA1-3 : angle 1.39040 / 0.67 ( 3) link_ALPHA1-6 : bond 0.00865 / 0.46 ( 1) link_ALPHA1-6 : angle 1.32525 / 0.61 ( 3) link_BETA1-4 : bond 0.00486 / 0.27 ( 9) link_BETA1-4 : angle 1.48007 / 0.96 ( 27) link_NAG-ASN : bond 0.00427 / 0.20 ( 10) link_NAG-ASN : angle 3.87049 / 2.32 ( 30) *********************** 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 188 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5985 (p-90) cc_final: 0.4366 (m100) REVERT: B 216 HIS cc_start: 0.6419 (m170) cc_final: 0.6117 (m170) REVERT: B 248 THR cc_start: 0.7444 (p) cc_final: 0.6730 (t) REVERT: C 203 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6572 (pp30) REVERT: C 318 TYR cc_start: 0.7330 (m-10) cc_final: 0.6937 (m-80) REVERT: H 105 ARG cc_start: 0.7980 (mmm160) cc_final: 0.6882 (mtm-85) REVERT: L 48 ILE cc_start: 0.9609 (tt) cc_final: 0.9310 (pt) REVERT: P 62 LYS cc_start: 0.8049 (pptt) cc_final: 0.7833 (ttpp) REVERT: P 80 MET cc_start: 0.7739 (tmm) cc_final: 0.7510 (tmm) REVERT: P 81 ASP cc_start: 0.7682 (p0) cc_final: 0.7301 (p0) REVERT: Q 104 LEU cc_start: 0.8717 (tp) cc_final: 0.8496 (tp) REVERT: X 535 MET cc_start: 0.8123 (mpp) cc_final: 0.7582 (mpp) REVERT: Y 632 ASP cc_start: 0.6716 (t70) cc_final: 0.6466 (t0) outliers start: 2 outliers final: 1 residues processed: 188 average time/residue: 0.1318 time to fit residues: 39.0416 Evaluate side-chains 131 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 75 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 448 ASN B 258 GLN B 332 ASN C 203 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.081643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.068253 restraints weight = 74422.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067793 restraints weight = 66334.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068091 restraints weight = 61784.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.068430 restraints weight = 54251.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.068513 restraints weight = 46205.114| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18182 Z= 0.155 Angle : 0.613 9.835 24749 Z= 0.310 Chirality : 0.045 0.249 2859 Planarity : 0.004 0.060 3095 Dihedral : 4.454 20.983 2418 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 0.05 % Allowed : 1.80 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2195 helix: 1.20 (0.28), residues: 375 sheet: -0.28 (0.21), residues: 649 loop : -1.54 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 94 TYR 0.017 0.001 TYR L 95B PHE 0.025 0.002 PHE I 29 TRP 0.029 0.002 TRP Z 628 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (18130) covalent geometry : angle 0.59438 / 0.31 (24624) SS BOND : bond 0.00324 / 0.14 ( 31) SS BOND : angle 1.30084 / 0.83 ( 62) hydrogen bonds : bond 0.03454 / 2.27 ( 526) hydrogen bonds : angle 5.36331 / 3.65 ( 1368) link_ALPHA1-3 : bond 0.00597 / 0.31 ( 1) link_ALPHA1-3 : angle 1.46642 / 0.75 ( 3) link_ALPHA1-6 : bond 0.00913 / 0.48 ( 1) link_ALPHA1-6 : angle 1.26699 / 0.54 ( 3) link_BETA1-4 : bond 0.00472 / 0.27 ( 9) link_BETA1-4 : angle 1.55817 / 1.03 ( 27) link_NAG-ASN : bond 0.00445 / 0.24 ( 10) link_NAG-ASN : angle 3.68111 / 2.26 ( 30) *********************** 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 173 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6009 (p-90) cc_final: 0.4317 (m100) REVERT: B 216 HIS cc_start: 0.6617 (m170) cc_final: 0.6254 (m170) REVERT: B 248 THR cc_start: 0.7458 (p) cc_final: 0.6667 (t) REVERT: C 203 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6579 (pp30) REVERT: H 105 ARG cc_start: 0.8094 (mmm160) cc_final: 0.6864 (mtm-85) REVERT: I 100 MET cc_start: 0.6697 (ppp) cc_final: 0.5971 (ppp) REVERT: P 81 ASP cc_start: 0.7802 (p0) cc_final: 0.7535 (p0) REVERT: Q 60 ASP cc_start: 0.7906 (t0) cc_final: 0.7705 (t0) REVERT: Q 104 LEU cc_start: 0.8803 (tp) cc_final: 0.8592 (tp) REVERT: X 535 MET cc_start: 0.8200 (mpp) cc_final: 0.7638 (mpp) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1205 time to fit residues: 34.0649 Evaluate side-chains 116 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 115 optimal weight: 0.0370 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 147 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 148 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 332 ASN C 203 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.082933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069601 restraints weight = 73631.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.069281 restraints weight = 60699.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.069784 restraints weight = 51342.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.070100 restraints weight = 45736.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070224 restraints weight = 42559.562| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18182 Z= 0.104 Angle : 0.569 9.497 24749 Z= 0.287 Chirality : 0.044 0.253 2859 Planarity : 0.004 0.055 3095 Dihedral : 4.287 22.243 2418 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.76 % Rotamer: Outliers : 0.05 % Allowed : 0.64 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.18), residues: 2195 helix: 1.26 (0.28), residues: 383 sheet: -0.22 (0.21), residues: 635 loop : -1.51 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 18 TYR 0.012 0.001 TYR J 87 PHE 0.024 0.001 PHE C 288 TRP 0.029 0.001 TRP Z 628 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (18130) covalent geometry : angle 0.54982 / 0.28 (24624) SS BOND : bond 0.00224 / 0.11 ( 31) SS BOND : angle 1.55438 / 1.03 ( 62) hydrogen bonds : bond 0.03221 / 2.10 ( 526) hydrogen bonds : angle 5.15009 / 3.49 ( 1368) link_ALPHA1-3 : bond 0.00696 / 0.37 ( 1) link_ALPHA1-3 : angle 1.41305 / 0.67 ( 3) link_ALPHA1-6 : bond 0.00802 / 0.42 ( 1) link_ALPHA1-6 : angle 1.31371 / 0.60 ( 3) link_BETA1-4 : bond 0.00471 / 0.26 ( 9) link_BETA1-4 : angle 1.44242 / 0.93 ( 27) link_NAG-ASN : bond 0.00413 / 0.19 ( 10) link_NAG-ASN : angle 3.43279 / 2.14 ( 30) *********************** 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 189 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5998 (p-90) cc_final: 0.4356 (m100) REVERT: B 216 HIS cc_start: 0.6488 (m170) cc_final: 0.6108 (m170) REVERT: B 248 THR cc_start: 0.7407 (p) cc_final: 0.6526 (t) REVERT: C 203 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6575 (pp30) REVERT: H 105 ARG cc_start: 0.7751 (mmm160) cc_final: 0.6597 (mtm-85) REVERT: I 100 MET cc_start: 0.6549 (ppp) cc_final: 0.5764 (ppp) REVERT: P 81 ASP cc_start: 0.7906 (p0) cc_final: 0.7514 (p0) REVERT: Q 60 ASP cc_start: 0.7880 (t0) cc_final: 0.7668 (t0) REVERT: Q 104 LEU cc_start: 0.8783 (tp) cc_final: 0.8551 (tp) REVERT: X 535 MET cc_start: 0.8144 (mpp) cc_final: 0.7619 (mpp) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1162 time to fit residues: 35.8163 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 : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 7.9990 chunk 214 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 203 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.081242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.067803 restraints weight = 74103.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067906 restraints weight = 64314.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.068163 restraints weight = 54068.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068556 restraints weight = 51596.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.068529 restraints weight = 44909.491| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4029 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= 0.155 Angle : 0.637 16.158 24749 Z= 0.317 Chirality : 0.045 0.286 2859 Planarity : 0.004 0.056 3095 Dihedral : 4.438 22.475 2418 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.61 % Favored : 93.35 % Rotamer: Outliers : 0.05 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 2195 helix: 1.19 (0.28), residues: 383 sheet: -0.26 (0.21), residues: 628 loop : -1.53 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 94 TYR 0.016 0.001 TYR L 95B PHE 0.020 0.002 PHE C 288 TRP 0.036 0.002 TRP Z 628 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (18130) covalent geometry : angle 0.60544 / 0.31 (24624) SS BOND : bond 0.00290 / 0.14 ( 31) SS BOND : angle 1.56541 / 1.02 ( 62) hydrogen bonds : bond 0.03365 / 2.21 ( 526) hydrogen bonds : angle 5.28802 / 3.60 ( 1368) link_ALPHA1-3 : bond 0.00625 / 0.33 ( 1) link_ALPHA1-3 : angle 1.47993 / 0.74 ( 3) link_ALPHA1-6 : bond 0.00916 / 0.48 ( 1) link_ALPHA1-6 : angle 1.28342 / 0.55 ( 3) link_BETA1-4 : bond 0.00428 / 0.25 ( 9) link_BETA1-4 : angle 2.04773 / 1.37 ( 27) link_NAG-ASN : bond 0.00892 / 0.70 ( 10) link_NAG-ASN : angle 4.93814 / 2.60 ( 30) *********************** 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: 1 poor density : 165 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5944 (p-90) cc_final: 0.4272 (m100) REVERT: B 216 HIS cc_start: 0.6694 (m170) cc_final: 0.6311 (m170) REVERT: B 248 THR cc_start: 0.7524 (p) cc_final: 0.6650 (t) REVERT: C 203 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6527 (pp30) REVERT: Q 60 ASP cc_start: 0.7990 (t0) cc_final: 0.7781 (t0) REVERT: Q 104 LEU cc_start: 0.8787 (tp) cc_final: 0.8577 (tp) REVERT: X 535 MET cc_start: 0.8185 (mpp) cc_final: 0.7608 (mpp) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1087 time to fit residues: 30.4288 Evaluate side-chains 114 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 45 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 175 optimal weight: 0.1980 chunk 131 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 203 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.080327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066637 restraints weight = 73792.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066843 restraints weight = 65088.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.066959 restraints weight = 57879.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067239 restraints weight = 53943.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067359 restraints weight = 48736.234| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18182 Z= 0.182 Angle : 0.653 13.752 24749 Z= 0.328 Chirality : 0.046 0.286 2859 Planarity : 0.004 0.055 3095 Dihedral : 4.673 22.552 2418 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.05 % Allowed : 0.48 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2195 helix: 0.88 (0.27), residues: 385 sheet: -0.34 (0.21), residues: 634 loop : -1.66 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 94 TYR 0.018 0.002 TYR L 95B PHE 0.022 0.002 PHE C 288 TRP 0.051 0.002 TRP Z 628 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (18130) covalent geometry : angle 0.62911 / 0.32 (24624) SS BOND : bond 0.00319 / 0.16 ( 31) SS BOND : angle 1.49291 / 0.95 ( 62) hydrogen bonds : bond 0.03547 / 2.33 ( 526) hydrogen bonds : angle 5.47027 / 3.73 ( 1368) link_ALPHA1-3 : bond 0.00593 / 0.31 ( 1) link_ALPHA1-3 : angle 1.45745 / 0.74 ( 3) link_ALPHA1-6 : bond 0.01032 / 0.54 ( 1) link_ALPHA1-6 : angle 1.21077 / 0.50 ( 3) link_BETA1-4 : bond 0.00491 / 0.28 ( 9) link_BETA1-4 : angle 1.63276 / 1.08 ( 27) link_NAG-ASN : bond 0.00529 / 0.34 ( 10) link_NAG-ASN : angle 4.44107 / 2.53 ( 30) ********************** 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 160 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5551 (ppp) cc_final: 0.5154 (ppp) REVERT: B 69 TRP cc_start: 0.5915 (p-90) cc_final: 0.4178 (m100) REVERT: B 248 THR cc_start: 0.7539 (p) cc_final: 0.6936 (t) REVERT: C 203 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6483 (pp30) REVERT: C 318 TYR cc_start: 0.7416 (m-10) cc_final: 0.7068 (m-80) REVERT: I 100 MET cc_start: 0.6335 (ppp) cc_final: 0.5441 (ppp) REVERT: P 81 ASP cc_start: 0.7857 (p0) cc_final: 0.7633 (p0) REVERT: Q 60 ASP cc_start: 0.8085 (t0) cc_final: 0.7879 (t0) REVERT: Q 104 LEU cc_start: 0.8838 (tp) cc_final: 0.8636 (tp) REVERT: X 535 MET cc_start: 0.8197 (mpp) cc_final: 0.7612 (mpp) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1114 time to fit residues: 29.8813 Evaluate side-chains 117 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 190 optimal weight: 6.9990 chunk 85 optimal weight: 0.0010 chunk 116 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 203 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.081805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.068312 restraints weight = 73490.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.068311 restraints weight = 62008.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.068548 restraints weight = 51761.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.068839 restraints weight = 47929.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068905 restraints weight = 44635.616| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18182 Z= 0.114 Angle : 0.609 13.030 24749 Z= 0.303 Chirality : 0.045 0.278 2859 Planarity : 0.004 0.053 3095 Dihedral : 4.427 21.914 2418 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.53 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2195 helix: 1.10 (0.27), residues: 383 sheet: -0.33 (0.21), residues: 620 loop : -1.52 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 94 TYR 0.015 0.001 TYR C 191 PHE 0.028 0.001 PHE C 288 TRP 0.050 0.002 TRP Z 628 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (18130) covalent geometry : angle 0.58697 / 0.30 (24624) SS BOND : bond 0.00282 / 0.13 ( 31) SS BOND : angle 1.27996 / 0.84 ( 62) hydrogen bonds : bond 0.03204 / 2.11 ( 526) hydrogen bonds : angle 5.19686 / 3.55 ( 1368) link_ALPHA1-3 : bond 0.00684 / 0.36 ( 1) link_ALPHA1-3 : angle 1.45799 / 0.70 ( 3) link_ALPHA1-6 : bond 0.00823 / 0.43 ( 1) link_ALPHA1-6 : angle 1.26352 / 0.57 ( 3) link_BETA1-4 : bond 0.00468 / 0.26 ( 9) link_BETA1-4 : angle 1.47019 / 0.96 ( 27) link_NAG-ASN : bond 0.00442 / 0.23 ( 10) link_NAG-ASN : angle 4.15183 / 2.38 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2482.06 seconds wall clock time: 59 minutes 38.80 seconds (3578.80 seconds total)