Starting phenix.real_space_refine on Fri Mar 6 01:25:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfo_25878/03_2026/7tfo_25878.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfo_25878/03_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_25878/03_2026/7tfo_25878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfo_25878/03_2026/7tfo_25878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tfo_25878/03_2026/7tfo_25878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfo_25878/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.98, per 1000 atoms: 0.22 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: 1.53 Conformation dependent library (CDL) restraints added in 754.5 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: 0.64 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: 2.85 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5686 1.34 - 1.46: 4246 1.46 - 1.58: 8045 1.58 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 18130 Sorted by residual: bond pdb=" N GLY Q 27 " pdb=" CA GLY Q 27 " ideal model delta sigma weight residual 1.444 1.476 -0.032 9.60e-03 1.09e+04 1.10e+01 bond pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.10e+00 bond pdb=" N ILE Q 21 " pdb=" CA ILE Q 21 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.40e+00 bond pdb=" N VAL C 371 " pdb=" CA VAL C 371 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.07e+00 bond pdb=" N GLY C 263 " pdb=" CA GLY C 263 " ideal model delta sigma weight residual 1.447 1.476 -0.029 1.03e-02 9.43e+03 8.02e+00 ... (remaining 18125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 23655 1.75 - 3.50: 832 3.50 - 5.25: 112 5.25 - 7.00: 23 7.00 - 8.75: 2 Bond angle restraints: 24624 Sorted by residual: angle pdb=" C VAL C 446 " pdb=" N SER C 447 " pdb=" CA SER C 447 " ideal model delta sigma weight residual 122.17 115.69 6.48 1.54e+00 4.22e-01 1.77e+01 angle pdb=" N GLY Q 25 " pdb=" CA GLY Q 25 " pdb=" C GLY Q 25 " ideal model delta sigma weight residual 115.36 109.98 5.38 1.33e+00 5.65e-01 1.63e+01 angle pdb=" N THR C 387 " pdb=" CA THR C 387 " pdb=" C THR C 387 " ideal model delta sigma weight residual 113.02 108.35 4.67 1.20e+00 6.94e-01 1.51e+01 angle pdb=" N CYS C 196 " pdb=" CA CYS C 196 " pdb=" C CYS C 196 " ideal model delta sigma weight residual 113.43 108.61 4.82 1.26e+00 6.30e-01 1.46e+01 angle pdb=" CA THR A 63 " pdb=" C THR A 63 " pdb=" O THR A 63 " ideal model delta sigma weight residual 122.64 118.14 4.50 1.25e+00 6.40e-01 1.29e+01 ... (remaining 24619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 10267 21.62 - 43.24: 605 43.24 - 64.86: 93 64.86 - 86.49: 44 86.49 - 108.11: 18 Dihedral angle restraints: 11027 sinusoidal: 4495 harmonic: 6532 Sorted by residual: dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual -86.00 -173.81 87.81 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual 93.00 158.90 -65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.27 -55.27 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 11024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 2831 0.153 - 0.307: 25 0.307 - 0.460: 2 0.460 - 0.614: 0 0.614 - 0.767: 1 Chirality restraints: 2859 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.60e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.64e+01 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.72e+01 ... (remaining 2856 not shown) Planarity restraints: 3105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 262 " -0.028 2.00e-02 2.50e+03 3.54e-01 1.57e+03 pdb=" CG ASN A 262 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN A 262 " 0.337 2.00e-02 2.50e+03 pdb=" ND2 ASN A 262 " -0.595 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.387 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG A 601 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " -0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG B 601 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " 0.522 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " -0.186 2.00e-02 2.50e+03 ... (remaining 3102 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 481 2.67 - 3.23: 18016 3.23 - 3.79: 26920 3.79 - 4.34: 35728 4.34 - 4.90: 57054 Nonbonded interactions: 138199 Sorted by model distance: nonbonded pdb=" NE2 GLN L 38 " pdb=" O MET L 42 " model vdw 2.118 3.120 nonbonded pdb=" OG SER A 364 " pdb=" O THR A 372 " model vdw 2.165 3.040 nonbonded pdb=" O LEU B 369 " pdb=" OG1 THR B 373 " model vdw 2.173 3.040 nonbonded pdb=" OG SER L 12 " pdb=" OG1 THR L 105 " model vdw 2.188 3.040 nonbonded pdb=" O PRO J 7 " pdb=" OG1 THR J 102 " model vdw 2.190 3.040 ... (remaining 138194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 63 or (resid 72 through 73 and (name N or na \ me CA or name C or name O or name CB )) or resid 75 through 113 or resid 119 or \ (resid 120 through 121 and (name N or name CA or name C or name O or name CB )) \ or resid 122 or (resid 123 and (name N or name CA or name C or name O or name CB \ )) or resid 124 or (resid 125 through 126 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 130 through 131 and (name N or name CA or name C o \ r name O or name CB )) or resid 132 through 138 or (resid 151 through 153 and (n \ ame N or name CA or name C or name O or name CB )) or resid 154 through 162 or r \ esid 172 through 207 or resid 210 or (resid 211 and (name N or name CA or name C \ or name O or name CB )) or resid 212 through 231 or (resid 232 and (name N or n \ ame CA or name C or name O or name CB )) or resid 233 through 306 or resid 315 t \ hrough 352 or resid 356 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 396 or resid 415 through 420 or \ (resid 421 and (name N or name CA or name C or name O or name CB )) or resid 422 \ through 457 or resid 467 through 483 or (resid 484 through 485 and (name N or n \ ame CA or name C or name O or name CB )) or resid 486 through 499 or (resid 500 \ through 503 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 1)) selection = (chain 'B' and (resid 34 through 45 or (resid 46 through 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 56 or (resid 57 through \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 63 and (n \ ame N or name CA or name C or name O or name CB )) or resid 72 through 77 or (re \ sid 78 and (name N or name CA or name C or name O or name CB )) or resid 79 thro \ ugh 119 or (resid 120 through 121 and (name N or name CA or name C or name O or \ name CB )) or resid 122 or (resid 123 and (name N or name CA or name C or name O \ or name CB )) or resid 124 or (resid 125 through 131 and (name N or name CA or \ name C or name O or name CB )) or resid 132 through 194 or (resid 195 and (name \ N or name CA or name C or name O or name CB )) or resid 196 through 231 or (resi \ d 232 and (name N or name CA or name C or name O or name CB )) or resid 233 thro \ ugh 267 or resid 270 through 306 or resid 315 through 324 or resid 326 through 3 \ 52 or resid 356 through 391 or (resid 392 and (name N or name CA or name C or na \ me O or name CB )) or resid 393 through 396 or resid 415 through 420 or (resid 4 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 422 through \ 457 or resid 467 through 483 or (resid 484 through 485 and (name N or name CA o \ r name C or name O or name CB )) or resid 486 through 503 or resid 602)) selection = (chain 'C' and ((resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 45 or (resid 46 through 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 58 or (resid 71 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 75 through 113 or re \ sid 119 through 125 or (resid 126 and (name N or name CA or name C or name O or \ name CB )) or (resid 130 through 131 and (name N or name CA or name C or name O \ or name CB )) or resid 132 through 138 or (resid 151 through 153 and (name N or \ name CA or name C or name O or name CB )) or resid 154 through 162 or resid 172 \ through 194 or (resid 195 and (name N or name CA or name C or name O or name CB \ )) or resid 196 through 207 or resid 210 or (resid 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 267 or resid 270 through 30 \ 6 or resid 315 through 324 or resid 326 through 499 or (resid 500 through 503 an \ d (name N or name CA or name C or name O or name CB )) or resid 601)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' } ncs_group { reference = (chain 'H' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 71 or (resid 72 and (n \ ame N or name CA or name C or name O or name CB )) or resid 73 or resid 76 throu \ gh 96 or (resid 97 through 98 and (name N or name CA or name C or name O or name \ CB )) or resid 99 through 111)) selection = (chain 'I' and (resid 2 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB )) or resid 65 through 71 or (resid 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 or resid 76 through 111)) selection = (chain 'P' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 96 or (resid 97 through 98 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 111)) } ncs_group { reference = (chain 'J' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 95A through 106)) selection = (chain 'L' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 95A or (resid 95B and (name N or \ name CA or name C or name O or name CB )) or resid 96 through 106)) selection = (chain 'Q' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 59 or (resid 60 and (name N or name \ CA or name C or name O or name CB )) or resid 61 through 106)) } ncs_group { reference = (chain 'X' and (resid 522 through 534 or (resid 535 through 536 and (name N or n \ ame CA or name C or name O or name CB )) or resid 537 through 540 or (resid 563 \ through 564 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 5 through 570 or (resid 571 and (name N or name CA or name C or name O or name C \ B )) or resid 572 through 647 or (resid 648 and (name N or name CA or name C or \ name O or name CB )) or resid 649 through 654)) selection = (chain 'Y' and (resid 522 through 537 or (resid 538 through 539 and (name N or n \ ame CA or name C or name O or name CB )) or resid 540 or (resid 563 through 564 \ and (name N or name CA or name C or name O or name CB )) or resid 565 through 58 \ 7 or (resid 588 and (name N or name CA or name C or name O or name CB )) or resi \ d 589 through 594 or (resid 595 and (name N or name CA or name C or name O or na \ me CB )) or resid 596 through 615 or (resid 616 and (name N or name CA or name C \ or name O or name CB )) or resid 617 through 646 or (resid 647 through 648 and \ (name N or name CA or name C or name O or name CB )) or resid 649 through 654)) selection = (chain 'Z' and (resid 522 through 535 or (resid 536 and (name N or name CA or na \ me C or name O or name CB )) or resid 537 or (resid 538 through 539 and (name N \ or name CA or name C or name O or name CB )) or resid 540 or (resid 563 through \ 564 and (name N or name CA or name C or name O or name CB )) or resid 565 throug \ h 566 or (resid 567 and (name N or name CA or name C or name O or name CB )) or \ resid 568 through 570 or (resid 571 and (name N or name CA or name C or name O o \ r name CB )) or resid 572 through 587 or (resid 588 and (name N or name CA or na \ me C or name O or name CB )) or resid 589 through 594 or (resid 595 and (name N \ or name CA or name C or name O or name CB )) or resid 596 through 615 or (resid \ 616 and (name N or name CA or name C or name O or name CB )) or resid 617 throug \ h 654)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 16.040 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.352 18182 Z= 0.347 Angle : 0.832 44.934 24749 Z= 0.448 Chirality : 0.053 0.767 2859 Planarity : 0.011 0.299 3095 Dihedral : 14.987 108.107 6724 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.66 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 covalent geometry : bond 0.00562 (18130) covalent geometry : angle 0.73621 (24624) SS BOND : bond 0.06336 ( 31) SS BOND : angle 5.81015 ( 62) hydrogen bonds : bond 0.28360 ( 526) hydrogen bonds : angle 9.40527 ( 1368) link_ALPHA1-3 : bond 0.00142 ( 1) link_ALPHA1-3 : angle 1.69588 ( 3) link_ALPHA1-6 : bond 0.00525 ( 1) link_ALPHA1-6 : angle 1.33605 ( 3) link_BETA1-4 : bond 0.00519 ( 9) link_BETA1-4 : angle 2.20558 ( 27) link_NAG-ASN : bond 0.10398 ( 10) link_NAG-ASN : angle 7.14730 ( 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 : 0.686 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: 0.1343 time to fit residues: 60.4733 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 : 0.642 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN B 105 HIS B 258 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 289 ASN L 38 GLN Y 543 ASN Z 607 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.081899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.068456 restraints weight = 74324.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068527 restraints weight = 64902.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069114 restraints weight = 53424.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069241 restraints weight = 46678.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.069420 restraints weight = 42223.181| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18182 Z= 0.189 Angle : 0.725 16.266 24749 Z= 0.362 Chirality : 0.047 0.234 2859 Planarity : 0.005 0.082 3095 Dihedral : 8.760 66.388 2847 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.37 % Allowed : 6.42 % Favored : 93.21 % 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: -1.27 (0.18), residues: 2195 helix: 0.74 (0.26), residues: 384 sheet: -0.32 (0.21), residues: 621 loop : -1.71 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 617 TYR 0.023 0.002 TYR C 191 PHE 0.026 0.002 PHE I 99 TRP 0.031 0.002 TRP Z 628 HIS 0.009 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00435 (18130) covalent geometry : angle 0.68922 (24624) SS BOND : bond 0.00305 ( 31) SS BOND : angle 1.46076 ( 62) hydrogen bonds : bond 0.04798 ( 526) hydrogen bonds : angle 6.25458 ( 1368) link_ALPHA1-3 : bond 0.00976 ( 1) link_ALPHA1-3 : angle 3.37655 ( 3) link_ALPHA1-6 : bond 0.01386 ( 1) link_ALPHA1-6 : angle 1.39126 ( 3) link_BETA1-4 : bond 0.00591 ( 9) link_BETA1-4 : angle 2.58654 ( 27) link_NAG-ASN : bond 0.00620 ( 10) link_NAG-ASN : angle 5.63368 ( 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 213 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5963 (p-90) cc_final: 0.4364 (m100) REVERT: B 248 THR cc_start: 0.7663 (p) cc_final: 0.7161 (t) REVERT: C 203 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7148 (pt0) REVERT: H 105 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7023 (mtm-85) REVERT: I 29 PHE cc_start: 0.4306 (m-10) cc_final: 0.4006 (m-10) REVERT: J 45 LYS cc_start: 0.7797 (tptp) cc_final: 0.7338 (pttt) REVERT: P 62 LYS cc_start: 0.8077 (pptt) cc_final: 0.7080 (ptpt) REVERT: Q 104 LEU cc_start: 0.8648 (tp) cc_final: 0.8317 (tp) REVERT: X 535 MET cc_start: 0.8251 (mpp) cc_final: 0.7729 (mpp) REVERT: Y 543 ASN cc_start: 0.6594 (OUTLIER) cc_final: 0.6372 (t0) REVERT: Y 573 ILE cc_start: 0.8927 (mm) cc_final: 0.8321 (mm) REVERT: Y 620 SER cc_start: 0.6998 (m) cc_final: 0.6565 (p) REVERT: Y 633 LYS cc_start: 0.8328 (mppt) cc_final: 0.8014 (mtpt) outliers start: 7 outliers final: 2 residues processed: 212 average time/residue: 0.1152 time to fit residues: 39.0889 Evaluate side-chains 134 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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: 5.9990 chunk 168 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.082997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.069096 restraints weight = 74464.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.068985 restraints weight = 55890.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.069523 restraints weight = 47304.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.069755 restraints weight = 41111.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069788 restraints weight = 39587.040| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2702 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= 0.131 Angle : 0.621 13.627 24749 Z= 0.311 Chirality : 0.045 0.245 2859 Planarity : 0.004 0.063 3095 Dihedral : 6.845 59.302 2847 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.08 % 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: 382 sheet: -0.35 (0.21), residues: 639 loop : -1.53 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 18 TYR 0.023 0.001 TYR J 30 PHE 0.022 0.001 PHE P 99 TRP 0.028 0.002 TRP Z 628 HIS 0.011 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00285 (18130) covalent geometry : angle 0.59082 (24624) SS BOND : bond 0.00291 ( 31) SS BOND : angle 1.42406 ( 62) hydrogen bonds : bond 0.04422 ( 526) hydrogen bonds : angle 5.76762 ( 1368) link_ALPHA1-3 : bond 0.00955 ( 1) link_ALPHA1-3 : angle 1.67840 ( 3) link_ALPHA1-6 : bond 0.01397 ( 1) link_ALPHA1-6 : angle 1.44187 ( 3) link_BETA1-4 : bond 0.00686 ( 9) link_BETA1-4 : angle 2.22279 ( 27) link_NAG-ASN : bond 0.00725 ( 10) link_NAG-ASN : angle 4.74756 ( 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 211 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6003 (p-90) cc_final: 0.4303 (m100) REVERT: B 248 THR cc_start: 0.7636 (p) cc_final: 0.7229 (t) REVERT: C 203 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6745 (pp30) REVERT: H 105 ARG cc_start: 0.8155 (mmm160) cc_final: 0.6983 (mtm-85) REVERT: J 27 ASN cc_start: 0.5983 (m-40) cc_final: 0.5379 (p0) REVERT: J 42 MET cc_start: 0.7856 (mpp) cc_final: 0.7502 (ttm) REVERT: P 62 LYS cc_start: 0.8220 (pptt) cc_final: 0.7029 (ptpt) REVERT: Q 104 LEU cc_start: 0.8628 (tp) cc_final: 0.8277 (tp) REVERT: X 535 MET cc_start: 0.8383 (mpp) cc_final: 0.7765 (mpp) REVERT: Y 573 ILE cc_start: 0.8919 (mm) cc_final: 0.7856 (mm) REVERT: Y 624 ASP cc_start: 0.6262 (t70) cc_final: 0.5928 (t0) REVERT: Y 633 LYS cc_start: 0.8237 (mppt) cc_final: 0.7998 (mtpt) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1147 time to fit residues: 38.2894 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 : 0.591 ------------------------------------------------------------------------------- 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: 0.4980 chunk 162 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 258 GLN B 289 ASN B 332 ASN C 203 GLN C 301 ASN ** C 448 ASN ** 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 = 0.3627 r_free = 0.3627 target = 0.080879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067091 restraints weight = 74941.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.067221 restraints weight = 64994.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067722 restraints weight = 55594.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067968 restraints weight = 48644.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068127 restraints weight = 45926.990| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18182 Z= 0.196 Angle : 0.670 16.651 24749 Z= 0.339 Chirality : 0.046 0.266 2859 Planarity : 0.005 0.067 3095 Dihedral : 6.323 57.623 2847 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.12 % Rotamer: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.39 % 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: 0.96 (0.27), residues: 380 sheet: -0.37 (0.21), residues: 614 loop : -1.65 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 94 TYR 0.017 0.002 TYR J 87 PHE 0.026 0.002 PHE P 99 TRP 0.032 0.002 TRP Z 628 HIS 0.008 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00454 (18130) covalent geometry : angle 0.64301 (24624) SS BOND : bond 0.00698 ( 31) SS BOND : angle 1.36633 ( 62) hydrogen bonds : bond 0.03990 ( 526) hydrogen bonds : angle 5.72352 ( 1368) link_ALPHA1-3 : bond 0.01185 ( 1) link_ALPHA1-3 : angle 2.05934 ( 3) link_ALPHA1-6 : bond 0.00945 ( 1) link_ALPHA1-6 : angle 1.41035 ( 3) link_BETA1-4 : bond 0.00509 ( 9) link_BETA1-4 : angle 2.15939 ( 27) link_NAG-ASN : bond 0.00599 ( 10) link_NAG-ASN : angle 4.71715 ( 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 182 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.5340 (ttm170) cc_final: 0.5075 (ttt180) REVERT: B 69 TRP cc_start: 0.6020 (p-90) cc_final: 0.4311 (m100) REVERT: B 248 THR cc_start: 0.7531 (p) cc_final: 0.7064 (t) REVERT: C 203 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6760 (pp30) REVERT: C 318 TYR cc_start: 0.7439 (m-10) cc_final: 0.7187 (m-10) REVERT: H 105 ARG cc_start: 0.8164 (mmm160) cc_final: 0.6984 (mtm-85) REVERT: Q 104 LEU cc_start: 0.8776 (tp) cc_final: 0.8526 (tp) REVERT: X 535 MET cc_start: 0.8225 (mpp) cc_final: 0.7664 (mpp) REVERT: Y 633 LYS cc_start: 0.8183 (mppt) cc_final: 0.7961 (mtpt) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.1186 time to fit residues: 34.1846 Evaluate side-chains 123 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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: 9.9990 chunk 125 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 179 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 330 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.079619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066004 restraints weight = 74814.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066041 restraints weight = 63925.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066546 restraints weight = 54485.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.066718 restraints weight = 48019.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066827 restraints weight = 43622.055| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18182 Z= 0.218 Angle : 0.688 14.497 24749 Z= 0.350 Chirality : 0.047 0.263 2859 Planarity : 0.005 0.073 3095 Dihedral : 6.388 59.818 2847 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.97 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % 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: -1.43 (0.18), residues: 2195 helix: 0.66 (0.27), residues: 386 sheet: -0.34 (0.22), residues: 590 loop : -1.87 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 273 TYR 0.023 0.002 TYR L 95B PHE 0.020 0.002 PHE C 288 TRP 0.032 0.002 TRP Z 628 HIS 0.008 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00503 (18130) covalent geometry : angle 0.66160 (24624) SS BOND : bond 0.00455 ( 31) SS BOND : angle 1.48211 ( 62) hydrogen bonds : bond 0.04093 ( 526) hydrogen bonds : angle 5.82850 ( 1368) link_ALPHA1-3 : bond 0.01033 ( 1) link_ALPHA1-3 : angle 1.98968 ( 3) link_ALPHA1-6 : bond 0.01245 ( 1) link_ALPHA1-6 : angle 1.22565 ( 3) link_BETA1-4 : bond 0.00533 ( 9) link_BETA1-4 : angle 2.00876 ( 27) link_NAG-ASN : bond 0.00547 ( 10) link_NAG-ASN : angle 4.71736 ( 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 176 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6091 (p-90) cc_final: 0.4250 (m100) REVERT: B 248 THR cc_start: 0.7421 (p) cc_final: 0.6897 (t) REVERT: X 535 MET cc_start: 0.8286 (mpp) cc_final: 0.7689 (mpp) REVERT: Z 632 ASP cc_start: 0.8206 (p0) cc_final: 0.7962 (p0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1182 time to fit residues: 33.4140 Evaluate side-chains 122 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 0.9990 chunk 181 optimal weight: 0.0170 chunk 140 optimal weight: 0.3980 chunk 162 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 180 optimal weight: 0.0870 chunk 113 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN B 332 ASN C 287 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.081940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068676 restraints weight = 73431.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068481 restraints weight = 65676.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068783 restraints weight = 55925.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068998 restraints weight = 52633.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.069097 restraints weight = 49035.048| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3921 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= 0.110 Angle : 0.598 11.501 24749 Z= 0.301 Chirality : 0.045 0.256 2859 Planarity : 0.004 0.051 3095 Dihedral : 5.804 57.447 2847 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 0.05 % Allowed : 1.59 % Favored : 98.36 % 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: -1.15 (0.18), residues: 2195 helix: 1.05 (0.27), residues: 380 sheet: -0.24 (0.21), residues: 617 loop : -1.71 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 94 TYR 0.013 0.001 TYR L 91 PHE 0.022 0.001 PHE C 288 TRP 0.032 0.002 TRP Z 628 HIS 0.007 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00247 (18130) covalent geometry : angle 0.57809 (24624) SS BOND : bond 0.00291 ( 31) SS BOND : angle 1.16647 ( 62) hydrogen bonds : bond 0.03516 ( 526) hydrogen bonds : angle 5.31190 ( 1368) link_ALPHA1-3 : bond 0.01242 ( 1) link_ALPHA1-3 : angle 1.48852 ( 3) link_ALPHA1-6 : bond 0.00676 ( 1) link_ALPHA1-6 : angle 1.37484 ( 3) link_BETA1-4 : bond 0.00552 ( 9) link_BETA1-4 : angle 1.67384 ( 27) link_NAG-ASN : bond 0.00449 ( 10) link_NAG-ASN : angle 3.88294 ( 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 191 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6003 (p-90) cc_final: 0.4236 (m100) REVERT: B 248 THR cc_start: 0.7389 (p) cc_final: 0.6778 (t) REVERT: I 100 MET cc_start: 0.6600 (ppp) cc_final: 0.5772 (ppp) REVERT: J 45 LYS cc_start: 0.7589 (pttt) cc_final: 0.7349 (mttp) REVERT: L 48 ILE cc_start: 0.9591 (tt) cc_final: 0.9355 (pt) REVERT: X 535 MET cc_start: 0.8167 (mpp) cc_final: 0.7602 (mpp) outliers start: 1 outliers final: 1 residues processed: 191 average time/residue: 0.1043 time to fit residues: 33.2033 Evaluate side-chains 131 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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: 2.9990 chunk 166 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 79 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 332 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.080463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067182 restraints weight = 74398.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066879 restraints weight = 65518.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.067088 restraints weight = 58370.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067442 restraints weight = 53208.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067550 restraints weight = 47048.207| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18182 Z= 0.176 Angle : 0.630 9.852 24749 Z= 0.319 Chirality : 0.045 0.255 2859 Planarity : 0.004 0.053 3095 Dihedral : 5.794 56.917 2847 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.42 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -1.22 (0.18), residues: 2195 helix: 0.90 (0.27), residues: 381 sheet: -0.37 (0.21), residues: 636 loop : -1.68 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.019 0.002 TYR J 87 PHE 0.027 0.002 PHE P 99 TRP 0.039 0.002 TRP C 45 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00412 (18130) covalent geometry : angle 0.61010 (24624) SS BOND : bond 0.00446 ( 31) SS BOND : angle 1.32387 ( 62) hydrogen bonds : bond 0.03558 ( 526) hydrogen bonds : angle 5.46235 ( 1368) link_ALPHA1-3 : bond 0.00855 ( 1) link_ALPHA1-3 : angle 1.64291 ( 3) link_ALPHA1-6 : bond 0.00898 ( 1) link_ALPHA1-6 : angle 1.31405 ( 3) link_BETA1-4 : bond 0.00530 ( 9) link_BETA1-4 : angle 1.75597 ( 27) link_NAG-ASN : bond 0.00473 ( 10) link_NAG-ASN : angle 3.82710 ( 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: 0 poor density : 173 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5971 (p-90) cc_final: 0.4229 (m100) REVERT: B 248 THR cc_start: 0.7441 (p) cc_final: 0.6780 (t) REVERT: L 48 ILE cc_start: 0.9648 (tt) cc_final: 0.9365 (pt) REVERT: Q 60 ASP cc_start: 0.7896 (t0) cc_final: 0.7696 (t0) REVERT: X 535 MET cc_start: 0.8232 (mpp) cc_final: 0.7628 (mpp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1151 time to fit residues: 32.2809 Evaluate side-chains 121 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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: 5.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.081278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.067824 restraints weight = 73526.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067956 restraints weight = 64763.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068663 restraints weight = 52694.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068737 restraints weight = 44538.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.068825 restraints weight = 41567.584| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18182 Z= 0.122 Angle : 0.594 9.667 24749 Z= 0.300 Chirality : 0.045 0.275 2859 Planarity : 0.004 0.051 3095 Dihedral : 5.544 55.946 2847 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 1.11 (0.27), residues: 375 sheet: -0.33 (0.21), residues: 623 loop : -1.62 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.015 0.001 TYR J 87 PHE 0.022 0.001 PHE C 288 TRP 0.036 0.002 TRP Z 628 HIS 0.007 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00284 (18130) covalent geometry : angle 0.57418 (24624) SS BOND : bond 0.00225 ( 31) SS BOND : angle 1.41940 ( 62) hydrogen bonds : bond 0.03356 ( 526) hydrogen bonds : angle 5.27797 ( 1368) link_ALPHA1-3 : bond 0.01025 ( 1) link_ALPHA1-3 : angle 1.51183 ( 3) link_ALPHA1-6 : bond 0.00723 ( 1) link_ALPHA1-6 : angle 1.31245 ( 3) link_BETA1-4 : bond 0.00521 ( 9) link_BETA1-4 : angle 1.65240 ( 27) link_NAG-ASN : bond 0.00449 ( 10) link_NAG-ASN : angle 3.64334 ( 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 174 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5975 (p-90) cc_final: 0.4244 (m100) REVERT: B 216 HIS cc_start: 0.7331 (m170) cc_final: 0.7055 (m170) REVERT: B 248 THR cc_start: 0.7401 (p) cc_final: 0.6595 (t) REVERT: L 48 ILE cc_start: 0.9621 (tt) cc_final: 0.9370 (pt) REVERT: P 81 ASP cc_start: 0.7893 (p0) cc_final: 0.7511 (p0) REVERT: Q 60 ASP cc_start: 0.7971 (t0) cc_final: 0.7715 (t0) REVERT: Q 76 THR cc_start: 0.8444 (m) cc_final: 0.8128 (p) REVERT: Q 104 LEU cc_start: 0.8861 (tp) cc_final: 0.8622 (tp) REVERT: X 535 MET cc_start: 0.8141 (mpp) cc_final: 0.7571 (mpp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1044 time to fit residues: 30.3903 Evaluate side-chains 125 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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: 4.9990 chunk 214 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 0.0670 chunk 89 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.081775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.069145 restraints weight = 73426.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068685 restraints weight = 62620.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069012 restraints weight = 55725.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.069326 restraints weight = 49395.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.069468 restraints weight = 43415.867| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18182 Z= 0.112 Angle : 0.620 16.934 24749 Z= 0.307 Chirality : 0.046 0.321 2859 Planarity : 0.004 0.050 3095 Dihedral : 5.539 56.419 2847 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z 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: -1.01 (0.18), residues: 2195 helix: 1.19 (0.27), residues: 377 sheet: -0.13 (0.21), residues: 616 loop : -1.64 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.021 0.001 TYR C 191 PHE 0.023 0.001 PHE C 288 TRP 0.037 0.001 TRP Z 628 HIS 0.008 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00254 (18130) covalent geometry : angle 0.57955 (24624) SS BOND : bond 0.00282 ( 31) SS BOND : angle 2.47198 ( 62) hydrogen bonds : bond 0.03193 ( 526) hydrogen bonds : angle 5.14013 ( 1368) link_ALPHA1-3 : bond 0.00746 ( 1) link_ALPHA1-3 : angle 1.27381 ( 3) link_ALPHA1-6 : bond 0.00640 ( 1) link_ALPHA1-6 : angle 1.36015 ( 3) link_BETA1-4 : bond 0.00590 ( 9) link_BETA1-4 : angle 1.71383 ( 27) link_NAG-ASN : bond 0.00630 ( 10) link_NAG-ASN : angle 5.04106 ( 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 179 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5995 (p-90) cc_final: 0.4255 (m100) REVERT: B 248 THR cc_start: 0.7444 (p) cc_final: 0.6745 (t) REVERT: J 45 LYS cc_start: 0.7616 (pttt) cc_final: 0.7374 (mttp) REVERT: L 48 ILE cc_start: 0.9608 (tt) cc_final: 0.9372 (pt) REVERT: P 81 ASP cc_start: 0.7883 (p0) cc_final: 0.7682 (p0) REVERT: Q 60 ASP cc_start: 0.7990 (t0) cc_final: 0.7743 (t0) REVERT: Q 76 THR cc_start: 0.8405 (m) cc_final: 0.8139 (p) REVERT: Q 104 LEU cc_start: 0.8834 (tp) cc_final: 0.8599 (tp) REVERT: X 535 MET cc_start: 0.8138 (mpp) cc_final: 0.7582 (mpp) REVERT: Y 626 MET cc_start: 0.6552 (tpt) cc_final: 0.5085 (tpp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1171 time to fit residues: 33.9187 Evaluate side-chains 131 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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: 4.9990 chunk 65 optimal weight: 8.9990 chunk 10 optimal weight: 0.0070 chunk 115 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.0170 chunk 51 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.080919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.068237 restraints weight = 73235.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067750 restraints weight = 61268.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067858 restraints weight = 56543.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068173 restraints weight = 53455.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.068243 restraints weight = 46243.143| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18182 Z= 0.146 Angle : 0.623 13.651 24749 Z= 0.313 Chirality : 0.046 0.291 2859 Planarity : 0.004 0.050 3095 Dihedral : 5.568 56.624 2847 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.56 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z 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: -1.05 (0.18), residues: 2195 helix: 1.16 (0.27), residues: 375 sheet: -0.20 (0.21), residues: 622 loop : -1.64 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 419 TYR 0.017 0.001 TYR C 191 PHE 0.025 0.001 PHE P 99 TRP 0.038 0.002 TRP Z 628 HIS 0.007 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00342 (18130) covalent geometry : angle 0.59773 (24624) SS BOND : bond 0.00340 ( 31) SS BOND : angle 1.37746 ( 62) hydrogen bonds : bond 0.03315 ( 526) hydrogen bonds : angle 5.23135 ( 1368) link_ALPHA1-3 : bond 0.00850 ( 1) link_ALPHA1-3 : angle 1.50251 ( 3) link_ALPHA1-6 : bond 0.00777 ( 1) link_ALPHA1-6 : angle 1.31902 ( 3) link_BETA1-4 : bond 0.00515 ( 9) link_BETA1-4 : angle 1.65117 ( 27) link_NAG-ASN : bond 0.00508 ( 10) link_NAG-ASN : angle 4.50667 ( 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 164 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5987 (p-90) cc_final: 0.4177 (m100) REVERT: B 216 HIS cc_start: 0.7512 (m170) cc_final: 0.7246 (m170) REVERT: B 248 THR cc_start: 0.7440 (p) cc_final: 0.6641 (t) REVERT: Q 60 ASP cc_start: 0.8025 (t0) cc_final: 0.7771 (t0) REVERT: Q 76 THR cc_start: 0.8465 (m) cc_final: 0.8173 (p) REVERT: Q 104 LEU cc_start: 0.8888 (tp) cc_final: 0.8645 (tp) REVERT: X 535 MET cc_start: 0.8167 (mpp) cc_final: 0.7586 (mpp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1017 time to fit residues: 28.5209 Evaluate side-chains 126 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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: 8.9990 chunk 85 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.080805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.067070 restraints weight = 73490.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.067218 restraints weight = 65476.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067909 restraints weight = 53357.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068024 restraints weight = 46154.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068143 restraints weight = 43744.610| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18182 Z= 0.152 Angle : 0.624 12.990 24749 Z= 0.313 Chirality : 0.046 0.285 2859 Planarity : 0.004 0.050 3095 Dihedral : 5.618 56.476 2847 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.12 (0.18), residues: 2195 helix: 1.01 (0.27), residues: 382 sheet: -0.23 (0.21), residues: 613 loop : -1.66 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 273 TYR 0.017 0.001 TYR C 191 PHE 0.024 0.002 PHE P 99 TRP 0.043 0.002 TRP Z 628 HIS 0.008 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00355 (18130) covalent geometry : angle 0.59914 (24624) SS BOND : bond 0.00450 ( 31) SS BOND : angle 1.39585 ( 62) hydrogen bonds : bond 0.03321 ( 526) hydrogen bonds : angle 5.27846 ( 1368) link_ALPHA1-3 : bond 0.00795 ( 1) link_ALPHA1-3 : angle 1.46633 ( 3) link_ALPHA1-6 : bond 0.00786 ( 1) link_ALPHA1-6 : angle 1.28779 ( 3) link_BETA1-4 : bond 0.00510 ( 9) link_BETA1-4 : angle 1.66776 ( 27) link_NAG-ASN : bond 0.00505 ( 10) link_NAG-ASN : angle 4.38921 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2288.72 seconds wall clock time: 40 minutes 41.89 seconds (2441.89 seconds total)