Starting phenix.real_space_refine on Thu Mar 5 20:51:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzj_48758/03_2026/9mzj_48758.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzj_48758/03_2026/9mzj_48758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mzj_48758/03_2026/9mzj_48758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzj_48758/03_2026/9mzj_48758.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mzj_48758/03_2026/9mzj_48758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzj_48758/03_2026/9mzj_48758.map" } resolution = 3.74 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= 0.003 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 15717 2.51 5 N 4020 2.21 5 O 4695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 24568 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5972 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 728} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 5996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5996 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 732} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5974 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 728} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 5999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5999 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 732} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "H" 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: "I" 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: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "P" 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: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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 Time building chain proxies: 6.00, per 1000 atoms: 0.24 Number of scatterers: 24568 At special positions: 0 Unit cell: (126.14, 157.94, 183.38, 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 136 16.00 O 4695 8.00 N 4020 7.00 C 15717 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " NAG J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " NAG K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " NAG O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " NAG Q 3 " NAG-ASN " NAG A1001 " - " ASN A 423 " " NAG A1002 " - " ASN A 751 " " NAG A1003 " - " ASN A 546 " " NAG B1001 " - " ASN B 286 " " NAG B1002 " - " ASN B 412 " " NAG B1003 " - " ASN B 275 " " NAG B1004 " - " ASN B 73 " " NAG C1001 " - " ASN C 412 " " NAG C1002 " - " ASN C 423 " " NAG C1003 " - " ASN C 751 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG E 1 " - " ASN A 412 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN A 67 " " NAG H 1 " - " ASN A 275 " " NAG I 1 " - " ASN A 430 " " NAG J 1 " - " ASN B 67 " " NAG K 1 " - " ASN B 378 " " NAG L 1 " - " ASN C 378 " " NAG M 1 " - " ASN C 430 " " NAG N 1 " - " ASN C 67 " " NAG O 1 " - " ASN C 275 " " NAG P 1 " - " ASN D 378 " " NAG Q 1 " - " ASN D 67 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5654 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 34 sheets defined 47.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 100 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.671A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 4.149A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 184 removed outlier: 3.538A pdb=" N ARG A 184 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.109A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.501A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.636A pdb=" N TYR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 317 through 335 Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 462 through 474 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.993A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 562 through 580 Processing helix chain 'A' and resid 634 through 663 Processing helix chain 'A' and resid 671 through 677 removed outlier: 3.513A pdb=" N CYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.551A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.573A pdb=" N SER A 731 " --> pdb=" O ARG A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 773 through 789 removed outlier: 3.770A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 Processing helix chain 'A' and resid 819 through 824 removed outlier: 3.778A pdb=" N ILE A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.522A pdb=" N LEU B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.654A pdb=" N ALA B 115 " --> pdb=" O HIS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.765A pdb=" N ARG B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.533A pdb=" N LEU B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.709A pdb=" N ARG B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 317 through 335 removed outlier: 3.541A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.671A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 removed outlier: 3.952A pdb=" N LEU B 505 " --> pdb=" O MET B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 Processing helix chain 'B' and resid 551 through 557 removed outlier: 3.968A pdb=" N PHE B 555 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.608A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 665 removed outlier: 3.516A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.992A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 697 removed outlier: 3.598A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 712 Processing helix chain 'B' and resid 712 through 717 Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 739 through 749 Processing helix chain 'B' and resid 772 through 788 removed outlier: 3.591A pdb=" N ASP B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.543A pdb=" N MET B 793 " --> pdb=" O GLY B 789 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 810 removed outlier: 3.593A pdb=" N SER B 809 " --> pdb=" O GLU B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 838 removed outlier: 3.559A pdb=" N PHE B 824 " --> pdb=" O ILE B 820 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 836 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 838 " --> pdb=" O SER B 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 111 through 125 removed outlier: 4.019A pdb=" N ASN C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.615A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.162A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.470A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 317 through 337 removed outlier: 3.511A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 366 removed outlier: 3.612A pdb=" N MET C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 560 through 581 removed outlier: 3.539A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 665 Processing helix chain 'C' and resid 671 through 677 removed outlier: 4.102A pdb=" N GLN C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 696 Processing helix chain 'C' and resid 699 through 713 removed outlier: 3.960A pdb=" N LYS C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 716 No H-bonds generated for 'chain 'C' and resid 714 through 716' Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'C' and resid 775 through 788 Processing helix chain 'C' and resid 790 through 799 Processing helix chain 'C' and resid 817 through 820 removed outlier: 3.529A pdb=" N ILE C 820 " --> pdb=" O VAL C 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 817 through 820' Processing helix chain 'C' and resid 821 through 837 removed outlier: 3.662A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 152 through 168 Processing helix chain 'D' and resid 179 through 185 removed outlier: 4.550A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 190 through 195 removed outlier: 4.271A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 removed outlier: 3.702A pdb=" N ASP D 210 " --> pdb=" O ASP D 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 207 through 210' Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 299 Processing helix chain 'D' and resid 306 through 310 removed outlier: 3.580A pdb=" N GLY D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 337 Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 454 through 459 removed outlier: 4.034A pdb=" N PHE D 459 " --> pdb=" O ASN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 501 through 508 Processing helix chain 'D' and resid 520 through 527 Processing helix chain 'D' and resid 560 through 579 removed outlier: 3.731A pdb=" N TRP D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR D 566 " --> pdb=" O ASP D 562 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D 567 " --> pdb=" O ILE D 563 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU D 569 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER D 575 " --> pdb=" O TYR D 571 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE D 579 " --> pdb=" O SER D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 664 Processing helix chain 'D' and resid 670 through 677 removed outlier: 3.786A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 697 Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.531A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 738 through 749 removed outlier: 3.672A pdb=" N VAL D 745 " --> pdb=" O THR D 741 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR D 746 " --> pdb=" O ILE D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.727A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.598A pdb=" N ARG D 800 " --> pdb=" O GLU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 840 removed outlier: 4.296A pdb=" N ILE D 820 " --> pdb=" O GLY D 816 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLY D 822 " --> pdb=" O GLN D 818 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE D 824 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 838 " --> pdb=" O SER D 834 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 83 removed outlier: 6.056A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.110A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 395 removed outlier: 6.680A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 412 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 435 through 437 removed outlier: 6.298A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 446 Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA8, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.674A pdb=" N THR A 753 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 735 through 738 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 43 removed outlier: 6.380A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.708A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.697A pdb=" N VAL B 172 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.697A pdb=" N VAL B 172 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 277 through 280 Processing sheet with id=AB6, first strand: chain 'B' and resid 403 through 406 Processing sheet with id=AB7, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AB8, first strand: chain 'B' and resid 682 through 684 removed outlier: 3.521A pdb=" N TYR B 542 " --> pdb=" O THR B 753 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 37 removed outlier: 5.668A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AC2, first strand: chain 'C' and resid 106 through 107 removed outlier: 6.560A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.207A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 389 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 400 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 478 through 482 removed outlier: 6.670A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC6, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.506A pdb=" N GLN C 497 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AC8, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.995A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 735 through 738 removed outlier: 3.650A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 74 through 83 removed outlier: 5.590A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 105 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 41 " --> pdb=" O PHE D 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AD3, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.542A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 404 through 406 removed outlier: 4.005A pdb=" N ASP D 406 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 434 through 435 Processing sheet with id=AD6, first strand: chain 'D' and resid 540 through 542 removed outlier: 3.652A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 682 through 683 1012 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 3.18 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: 7686 1.34 - 1.46: 5914 1.46 - 1.58: 11260 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 25092 Sorted by residual: bond pdb=" N MET D 664 " pdb=" CA MET D 664 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.18e-02 7.18e+03 6.54e+00 bond pdb=" N MET A 664 " pdb=" CA MET A 664 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.25e-02 6.40e+03 5.64e+00 bond pdb=" N MET C 664 " pdb=" CA MET C 664 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.53e+00 bond pdb=" N THR C 652 " pdb=" CA THR C 652 " ideal model delta sigma weight residual 1.459 1.476 -0.017 1.19e-02 7.06e+03 2.00e+00 bond pdb=" N PRO A 805 " pdb=" CA PRO A 805 " ideal model delta sigma weight residual 1.469 1.477 -0.008 7.40e-03 1.83e+04 1.12e+00 ... (remaining 25087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 33561 2.17 - 4.35: 342 4.35 - 6.52: 52 6.52 - 8.70: 23 8.70 - 10.87: 7 Bond angle restraints: 33985 Sorted by residual: angle pdb=" C TYR C 651 " pdb=" N THR C 652 " pdb=" CA THR C 652 " ideal model delta sigma weight residual 120.44 115.37 5.07 1.30e+00 5.92e-01 1.52e+01 angle pdb=" CB MET D 298 " pdb=" CG MET D 298 " pdb=" SD MET D 298 " ideal model delta sigma weight residual 112.70 123.51 -10.81 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CB MET A 340 " pdb=" CG MET A 340 " pdb=" SD MET A 340 " ideal model delta sigma weight residual 112.70 123.23 -10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CB MET B 770 " pdb=" CG MET B 770 " pdb=" SD MET B 770 " ideal model delta sigma weight residual 112.70 122.36 -9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C2 NAG Q 1 " pdb=" N2 NAG Q 1 " pdb=" C7 NAG Q 1 " ideal model delta sigma weight residual 124.56 134.21 -9.65 3.00e+00 1.11e-01 1.04e+01 ... (remaining 33980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 13476 17.83 - 35.66: 1594 35.66 - 53.48: 414 53.48 - 71.31: 51 71.31 - 89.14: 22 Dihedral angle restraints: 15557 sinusoidal: 6763 harmonic: 8794 Sorted by residual: dihedral pdb=" CB CYS B 750 " pdb=" SG CYS B 750 " pdb=" SG CYS B 804 " pdb=" CB CYS B 804 " ideal model delta sinusoidal sigma weight residual 93.00 7.01 85.99 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS C 750 " pdb=" SG CYS C 750 " pdb=" SG CYS C 804 " pdb=" CB CYS C 804 " ideal model delta sinusoidal sigma weight residual -86.00 -147.72 61.72 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 347 " pdb=" CB CYS C 347 " ideal model delta sinusoidal sigma weight residual 93.00 141.95 -48.95 1 1.00e+01 1.00e-02 3.30e+01 ... (remaining 15554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3749 0.086 - 0.172: 204 0.172 - 0.257: 5 0.257 - 0.343: 2 0.343 - 0.429: 1 Chirality restraints: 3961 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" C1 NAG C1003 " pdb=" ND2 ASN C 751 " pdb=" C2 NAG C1003 " pdb=" O5 NAG C1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C3 NAG K 1 " pdb=" C2 NAG K 1 " pdb=" C4 NAG K 1 " pdb=" O3 NAG K 1 " both_signs ideal model delta sigma weight residual False 2.45 2.17 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 3958 not shown) Planarity restraints: 4262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 191 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO D 192 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 498 " 0.015 2.00e-02 2.50e+03 1.45e-02 5.28e+00 pdb=" CG TRP B 498 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 498 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 498 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 498 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 498 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 498 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 498 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 498 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 498 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 127 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO B 128 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 128 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 128 " 0.024 5.00e-02 4.00e+02 ... (remaining 4259 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 13374 2.99 - 3.47: 26566 3.47 - 3.95: 39815 3.95 - 4.42: 45729 4.42 - 4.90: 70329 Nonbonded interactions: 195813 Sorted by model distance: nonbonded pdb=" C4 NAG J 2 " pdb=" O5 NAG J 3 " model vdw 2.518 2.776 nonbonded pdb=" C4 NAG Q 1 " pdb=" O5 NAG Q 2 " model vdw 2.528 2.776 nonbonded pdb=" O5 NAG M 1 " pdb=" O6 NAG M 1 " model vdw 2.552 2.432 nonbonded pdb=" O ASN B 196 " pdb=" ND2 ASN B 196 " model vdw 2.552 3.120 nonbonded pdb=" O2 BMA H 3 " pdb=" O3 BMA H 3 " model vdw 2.566 2.432 ... (remaining 195808 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 33 through 582 or resid 631 through 836 or resid 1002 thro \ ugh 1003)) selection = (chain 'B' and (resid 33 through 582 or resid 631 through 836 or resid 1003 thro \ ugh 1004)) selection = (chain 'C' and (resid 33 through 836 or resid 1002 through 1003)) selection = (chain 'D' and (resid 33 through 836 or resid 1001 through 1002)) } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.860 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.002 0.034 25145 Z= 0.113 Angle : 0.616 12.215 34136 Z= 0.294 Chirality : 0.042 0.429 3961 Planarity : 0.003 0.065 4237 Dihedral : 15.883 89.139 9879 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.45 % Allowed : 20.97 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.16), residues: 3020 helix: 0.64 (0.15), residues: 1254 sheet: -1.94 (0.27), residues: 383 loop : -1.29 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 184 TYR 0.017 0.001 TYR B 566 PHE 0.023 0.001 PHE A 315 TRP 0.038 0.001 TRP B 498 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00242 (25092) covalent geometry : angle 0.59108 (33985) SS BOND : bond 0.00130 ( 8) SS BOND : angle 0.63728 ( 16) hydrogen bonds : bond 0.22229 ( 1008) hydrogen bonds : angle 7.21747 ( 2913) link_BETA1-4 : bond 0.00460 ( 20) link_BETA1-4 : angle 2.21621 ( 60) link_NAG-ASN : bond 0.00632 ( 25) link_NAG-ASN : angle 3.19323 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7816 (tpp) cc_final: 0.7422 (tpp) REVERT: A 111 HIS cc_start: 0.7758 (t-90) cc_final: 0.7123 (t-90) REVERT: A 171 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8211 (t) REVERT: A 360 MET cc_start: 0.8997 (tpt) cc_final: 0.8719 (tpp) REVERT: A 565 MET cc_start: 0.6654 (mmp) cc_final: 0.6115 (mmp) REVERT: B 360 MET cc_start: 0.8780 (mmm) cc_final: 0.8295 (tpp) REVERT: B 498 TRP cc_start: 0.5450 (m100) cc_final: 0.4666 (m100) REVERT: B 501 MET cc_start: 0.8386 (mmp) cc_final: 0.7582 (mmm) REVERT: B 541 LEU cc_start: 0.8720 (tp) cc_final: 0.8297 (tp) REVERT: B 566 TYR cc_start: 0.8310 (m-80) cc_final: 0.7978 (m-80) REVERT: B 706 TRP cc_start: 0.8560 (t60) cc_final: 0.8293 (t60) REVERT: B 737 MET cc_start: 0.8773 (ppp) cc_final: 0.7817 (ppp) REVERT: C 101 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9027 (tt) REVERT: C 774 TYR cc_start: 0.8074 (m-80) cc_final: 0.7787 (m-10) REVERT: D 251 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8550 (p90) REVERT: D 770 MET cc_start: 0.7225 (pmm) cc_final: 0.6868 (pmm) outliers start: 38 outliers final: 33 residues processed: 303 average time/residue: 0.1370 time to fit residues: 71.7242 Evaluate side-chains 298 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 567 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0370 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.109472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082507 restraints weight = 61533.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082999 restraints weight = 39795.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.083031 restraints weight = 40807.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.083951 restraints weight = 26819.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084551 restraints weight = 22865.621| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25145 Z= 0.144 Angle : 0.601 11.248 34136 Z= 0.290 Chirality : 0.042 0.431 3961 Planarity : 0.004 0.059 4237 Dihedral : 7.902 69.300 4271 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.09 % Allowed : 20.17 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 3020 helix: 1.11 (0.14), residues: 1301 sheet: -1.93 (0.27), residues: 377 loop : -1.20 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 354 TYR 0.029 0.001 TYR B 566 PHE 0.018 0.001 PHE C 355 TRP 0.018 0.001 TRP B 498 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00323 (25092) covalent geometry : angle 0.57588 (33985) SS BOND : bond 0.00838 ( 8) SS BOND : angle 0.38770 ( 16) hydrogen bonds : bond 0.04634 ( 1008) hydrogen bonds : angle 4.92824 ( 2913) link_BETA1-4 : bond 0.00453 ( 20) link_BETA1-4 : angle 2.23231 ( 60) link_NAG-ASN : bond 0.00595 ( 25) link_NAG-ASN : angle 3.16248 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 276 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: A 247 MET cc_start: 0.8819 (mmm) cc_final: 0.8592 (mmm) REVERT: A 248 MET cc_start: 0.8473 (mmm) cc_final: 0.8225 (tpp) REVERT: B 138 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8872 (p) REVERT: B 360 MET cc_start: 0.8768 (mmm) cc_final: 0.8240 (tpp) REVERT: B 501 MET cc_start: 0.8582 (mmp) cc_final: 0.7717 (mmm) REVERT: B 541 LEU cc_start: 0.8759 (tp) cc_final: 0.8377 (tp) REVERT: B 566 TYR cc_start: 0.8249 (m-80) cc_final: 0.7829 (m-80) REVERT: B 706 TRP cc_start: 0.8575 (t60) cc_final: 0.8213 (t60) REVERT: B 737 MET cc_start: 0.8139 (ppp) cc_final: 0.7336 (ppp) REVERT: C 101 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8860 (tt) REVERT: C 579 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.7075 (t80) REVERT: D 152 ASP cc_start: 0.8817 (t0) cc_final: 0.8514 (t0) REVERT: D 488 TYR cc_start: 0.4504 (OUTLIER) cc_final: 0.3728 (t80) REVERT: D 770 MET cc_start: 0.7397 (pmm) cc_final: 0.7182 (pmm) REVERT: D 794 MET cc_start: 0.4025 (tmm) cc_final: 0.2441 (tpt) outliers start: 81 outliers final: 48 residues processed: 339 average time/residue: 0.1377 time to fit residues: 80.7809 Evaluate side-chains 305 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 488 TYR Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 294 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.106933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.073795 restraints weight = 61768.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.075894 restraints weight = 36545.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.077321 restraints weight = 26347.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.078264 restraints weight = 21356.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.078847 restraints weight = 18702.207| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25145 Z= 0.234 Angle : 0.649 10.818 34136 Z= 0.314 Chirality : 0.044 0.409 3961 Planarity : 0.004 0.058 4237 Dihedral : 7.912 67.542 4249 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.16 % Allowed : 20.70 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 3020 helix: 1.27 (0.15), residues: 1294 sheet: -1.96 (0.26), residues: 391 loop : -1.33 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 354 TYR 0.020 0.001 TYR B 566 PHE 0.020 0.001 PHE C 355 TRP 0.023 0.002 TRP B 498 HIS 0.006 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00531 (25092) covalent geometry : angle 0.62570 (33985) SS BOND : bond 0.00227 ( 8) SS BOND : angle 1.25145 ( 16) hydrogen bonds : bond 0.04188 ( 1008) hydrogen bonds : angle 4.78462 ( 2913) link_BETA1-4 : bond 0.00411 ( 20) link_BETA1-4 : angle 2.28992 ( 60) link_NAG-ASN : bond 0.00616 ( 25) link_NAG-ASN : angle 3.14114 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 255 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: A 323 MET cc_start: 0.9327 (tpp) cc_final: 0.9111 (tpp) REVERT: B 111 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7403 (t70) REVERT: B 138 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8903 (p) REVERT: B 322 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8862 (mm) REVERT: B 360 MET cc_start: 0.8774 (mmm) cc_final: 0.8558 (mmm) REVERT: B 501 MET cc_start: 0.8628 (mmp) cc_final: 0.7886 (mmm) REVERT: B 541 LEU cc_start: 0.8840 (tp) cc_final: 0.8435 (tp) REVERT: B 566 TYR cc_start: 0.8308 (m-80) cc_final: 0.7815 (m-80) REVERT: B 571 TYR cc_start: 0.8408 (t80) cc_final: 0.8155 (t80) REVERT: B 706 TRP cc_start: 0.8544 (t60) cc_final: 0.8217 (t60) REVERT: C 101 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8858 (tt) REVERT: C 400 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: C 579 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7177 (t80) REVERT: D 152 ASP cc_start: 0.8781 (t0) cc_final: 0.8490 (t0) REVERT: D 251 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8823 (p90) REVERT: D 269 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8894 (m-80) REVERT: D 445 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.6978 (tp) REVERT: D 488 TYR cc_start: 0.4598 (OUTLIER) cc_final: 0.3873 (t80) REVERT: D 794 MET cc_start: 0.4557 (tmm) cc_final: 0.3427 (tpt) outliers start: 109 outliers final: 73 residues processed: 335 average time/residue: 0.1354 time to fit residues: 79.0752 Evaluate side-chains 325 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 241 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 746 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 488 TYR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 202 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 818 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.109326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082097 restraints weight = 60835.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082881 restraints weight = 38131.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082889 restraints weight = 37930.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.083735 restraints weight = 25593.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084194 restraints weight = 22079.969| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25145 Z= 0.116 Angle : 0.597 11.117 34136 Z= 0.281 Chirality : 0.042 0.422 3961 Planarity : 0.003 0.058 4237 Dihedral : 7.612 65.754 4247 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.78 % Allowed : 22.04 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 3020 helix: 1.30 (0.15), residues: 1310 sheet: -1.86 (0.26), residues: 389 loop : -1.28 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 133 TYR 0.020 0.001 TYR B 566 PHE 0.018 0.001 PHE C 355 TRP 0.026 0.001 TRP B 498 HIS 0.006 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00259 (25092) covalent geometry : angle 0.57220 (33985) SS BOND : bond 0.00293 ( 8) SS BOND : angle 0.74111 ( 16) hydrogen bonds : bond 0.03497 ( 1008) hydrogen bonds : angle 4.45334 ( 2913) link_BETA1-4 : bond 0.00451 ( 20) link_BETA1-4 : angle 2.21271 ( 60) link_NAG-ASN : bond 0.00626 ( 25) link_NAG-ASN : angle 3.16898 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 279 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8196 (t) REVERT: A 187 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: A 323 MET cc_start: 0.9279 (tpp) cc_final: 0.8900 (tpp) REVERT: B 111 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.7409 (t70) REVERT: B 138 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8887 (p) REVERT: B 350 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6690 (p90) REVERT: B 501 MET cc_start: 0.8520 (mmp) cc_final: 0.7756 (mmm) REVERT: B 541 LEU cc_start: 0.8763 (tp) cc_final: 0.8413 (tp) REVERT: B 566 TYR cc_start: 0.8333 (m-80) cc_final: 0.7868 (m-80) REVERT: B 571 TYR cc_start: 0.8413 (t80) cc_final: 0.8186 (t80) REVERT: B 706 TRP cc_start: 0.8368 (t60) cc_final: 0.8138 (t60) REVERT: C 101 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8866 (tt) REVERT: C 177 ASP cc_start: 0.8297 (t70) cc_final: 0.8042 (t70) REVERT: C 400 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: C 423 ASN cc_start: 0.6664 (OUTLIER) cc_final: 0.6430 (m-40) REVERT: C 579 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.7092 (t80) REVERT: D 152 ASP cc_start: 0.8660 (t0) cc_final: 0.8354 (t0) REVERT: D 217 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8074 (tp30) REVERT: D 251 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8678 (p90) REVERT: D 269 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8884 (m-80) REVERT: D 488 TYR cc_start: 0.4700 (OUTLIER) cc_final: 0.3907 (t80) REVERT: D 794 MET cc_start: 0.4535 (tmm) cc_final: 0.3623 (tpt) outliers start: 99 outliers final: 57 residues processed: 359 average time/residue: 0.1363 time to fit residues: 84.6441 Evaluate side-chains 324 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 255 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 423 ASN Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 488 TYR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 673 ASP Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 221 optimal weight: 0.0970 chunk 246 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 275 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.109465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083019 restraints weight = 61079.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.083279 restraints weight = 41216.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.083558 restraints weight = 40548.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084484 restraints weight = 27362.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084965 restraints weight = 23468.854| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25145 Z= 0.124 Angle : 0.601 11.233 34136 Z= 0.282 Chirality : 0.042 0.419 3961 Planarity : 0.003 0.057 4237 Dihedral : 7.422 62.109 4245 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.78 % Allowed : 22.50 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.16), residues: 3020 helix: 1.36 (0.15), residues: 1311 sheet: -1.85 (0.26), residues: 394 loop : -1.28 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 354 TYR 0.017 0.001 TYR B 566 PHE 0.018 0.001 PHE C 355 TRP 0.026 0.001 TRP D 799 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00282 (25092) covalent geometry : angle 0.57532 (33985) SS BOND : bond 0.00279 ( 8) SS BOND : angle 1.34572 ( 16) hydrogen bonds : bond 0.03352 ( 1008) hydrogen bonds : angle 4.37351 ( 2913) link_BETA1-4 : bond 0.00440 ( 20) link_BETA1-4 : angle 2.25474 ( 60) link_NAG-ASN : bond 0.00614 ( 25) link_NAG-ASN : angle 3.14683 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 268 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8244 (t) REVERT: A 187 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: A 323 MET cc_start: 0.9284 (tpp) cc_final: 0.8923 (tpp) REVERT: A 565 MET cc_start: 0.6724 (mmp) cc_final: 0.6059 (mmm) REVERT: B 111 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7368 (t70) REVERT: B 138 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8958 (p) REVERT: B 350 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6561 (p90) REVERT: B 360 MET cc_start: 0.8671 (mmm) cc_final: 0.8190 (tpp) REVERT: B 501 MET cc_start: 0.8391 (mmp) cc_final: 0.7669 (mmm) REVERT: B 541 LEU cc_start: 0.8764 (tp) cc_final: 0.8407 (tp) REVERT: B 566 TYR cc_start: 0.8231 (m-80) cc_final: 0.7816 (m-80) REVERT: B 571 TYR cc_start: 0.8427 (t80) cc_final: 0.8213 (t80) REVERT: B 706 TRP cc_start: 0.8259 (t60) cc_final: 0.8013 (t60) REVERT: C 101 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8841 (tt) REVERT: C 140 ASP cc_start: 0.8394 (t70) cc_final: 0.8186 (t70) REVERT: C 177 ASP cc_start: 0.8234 (t70) cc_final: 0.8005 (t70) REVERT: C 400 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7678 (pm20) REVERT: C 423 ASN cc_start: 0.6545 (OUTLIER) cc_final: 0.6311 (m-40) REVERT: C 579 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.7056 (t80) REVERT: C 774 TYR cc_start: 0.8025 (m-10) cc_final: 0.7763 (m-10) REVERT: D 152 ASP cc_start: 0.8548 (t0) cc_final: 0.8296 (t0) REVERT: D 217 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8007 (tp30) REVERT: D 251 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8702 (p90) REVERT: D 269 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.8927 (m-80) REVERT: D 323 MET cc_start: 0.8848 (tpp) cc_final: 0.8257 (tpp) REVERT: D 488 TYR cc_start: 0.4800 (OUTLIER) cc_final: 0.3995 (t80) REVERT: D 794 MET cc_start: 0.4467 (tmm) cc_final: 0.3447 (tpt) outliers start: 99 outliers final: 61 residues processed: 347 average time/residue: 0.1402 time to fit residues: 83.4867 Evaluate side-chains 331 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 258 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 423 ASN Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 488 TYR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 673 ASP Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 203 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 113 optimal weight: 0.0030 chunk 252 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 278 optimal weight: 0.0980 chunk 297 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 overall best weight: 2.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.108332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078614 restraints weight = 61357.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.078256 restraints weight = 36355.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.078998 restraints weight = 29381.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.079352 restraints weight = 26522.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.079728 restraints weight = 23876.183| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25145 Z= 0.157 Angle : 0.617 11.423 34136 Z= 0.290 Chirality : 0.043 0.415 3961 Planarity : 0.003 0.056 4237 Dihedral : 7.302 61.054 4238 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.05 % Allowed : 22.61 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 3020 helix: 1.43 (0.15), residues: 1305 sheet: -1.87 (0.26), residues: 394 loop : -1.32 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 66 TYR 0.017 0.001 TYR C 86 PHE 0.019 0.001 PHE B 642 TRP 0.032 0.001 TRP D 799 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00360 (25092) covalent geometry : angle 0.59156 (33985) SS BOND : bond 0.00290 ( 8) SS BOND : angle 1.25665 ( 16) hydrogen bonds : bond 0.03310 ( 1008) hydrogen bonds : angle 4.36194 ( 2913) link_BETA1-4 : bond 0.00408 ( 20) link_BETA1-4 : angle 2.25868 ( 60) link_NAG-ASN : bond 0.00584 ( 25) link_NAG-ASN : angle 3.17180 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 266 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7722 (tpp) cc_final: 0.7249 (tpp) REVERT: A 171 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8232 (t) REVERT: A 187 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: A 360 MET cc_start: 0.9182 (mmm) cc_final: 0.8232 (tpp) REVERT: B 111 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7381 (t70) REVERT: B 138 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8941 (p) REVERT: B 350 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.6655 (p90) REVERT: B 360 MET cc_start: 0.8721 (mmm) cc_final: 0.8375 (tpp) REVERT: B 501 MET cc_start: 0.8667 (mmp) cc_final: 0.7808 (mmm) REVERT: B 541 LEU cc_start: 0.8854 (tp) cc_final: 0.8479 (tp) REVERT: B 566 TYR cc_start: 0.8263 (m-80) cc_final: 0.7768 (m-80) REVERT: B 742 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9402 (mm) REVERT: C 101 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8865 (tt) REVERT: C 140 ASP cc_start: 0.8492 (t70) cc_final: 0.8205 (t70) REVERT: C 400 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: C 423 ASN cc_start: 0.6706 (OUTLIER) cc_final: 0.6432 (m-40) REVERT: C 774 TYR cc_start: 0.8084 (m-10) cc_final: 0.7789 (m-10) REVERT: D 152 ASP cc_start: 0.8596 (t0) cc_final: 0.8352 (t0) REVERT: D 217 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8110 (tp30) REVERT: D 251 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8738 (p90) REVERT: D 488 TYR cc_start: 0.4724 (OUTLIER) cc_final: 0.3900 (t80) REVERT: D 794 MET cc_start: 0.4613 (tmm) cc_final: 0.3572 (tpt) outliers start: 106 outliers final: 73 residues processed: 347 average time/residue: 0.1304 time to fit residues: 77.3287 Evaluate side-chains 339 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 255 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 641 TRP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 423 ASN Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 488 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 673 ASP Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 189 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 chunk 290 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN C 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.104474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.074454 restraints weight = 62436.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.074374 restraints weight = 38179.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.075034 restraints weight = 29692.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.075362 restraints weight = 27265.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.075591 restraints weight = 24511.780| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 25145 Z= 0.368 Angle : 0.782 11.182 34136 Z= 0.378 Chirality : 0.047 0.390 3961 Planarity : 0.004 0.053 4237 Dihedral : 8.020 65.397 4238 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.70 % Allowed : 23.03 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 3020 helix: 1.26 (0.15), residues: 1300 sheet: -2.16 (0.25), residues: 399 loop : -1.51 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 712 TYR 0.020 0.002 TYR B 176 PHE 0.023 0.002 PHE C 355 TRP 0.043 0.002 TRP B 706 HIS 0.008 0.002 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00826 (25092) covalent geometry : angle 0.76094 (33985) SS BOND : bond 0.00466 ( 8) SS BOND : angle 1.25148 ( 16) hydrogen bonds : bond 0.03930 ( 1008) hydrogen bonds : angle 4.79460 ( 2913) link_BETA1-4 : bond 0.00456 ( 20) link_BETA1-4 : angle 2.48588 ( 60) link_NAG-ASN : bond 0.00782 ( 25) link_NAG-ASN : angle 3.25327 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 239 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9188 (mmm) cc_final: 0.8260 (tpp) REVERT: B 111 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7456 (t70) REVERT: B 350 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.6690 (p90) REVERT: B 360 MET cc_start: 0.8776 (mmm) cc_final: 0.8347 (tpp) REVERT: B 498 TRP cc_start: 0.5831 (m100) cc_final: 0.5220 (m100) REVERT: B 501 MET cc_start: 0.8503 (mmp) cc_final: 0.8093 (tpp) REVERT: B 541 LEU cc_start: 0.8947 (tp) cc_final: 0.8540 (tp) REVERT: B 566 TYR cc_start: 0.8295 (m-80) cc_final: 0.7745 (m-80) REVERT: B 742 ILE cc_start: 0.9629 (OUTLIER) cc_final: 0.9390 (mm) REVERT: C 101 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8815 (tt) REVERT: C 140 ASP cc_start: 0.8512 (t70) cc_final: 0.8222 (t70) REVERT: C 400 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: C 423 ASN cc_start: 0.6590 (OUTLIER) cc_final: 0.6287 (m-40) REVERT: D 152 ASP cc_start: 0.8818 (t0) cc_final: 0.8528 (t0) REVERT: D 153 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: D 488 TYR cc_start: 0.5105 (t80) cc_final: 0.4668 (t80) REVERT: D 794 MET cc_start: 0.4652 (tmm) cc_final: 0.3517 (tpt) outliers start: 123 outliers final: 86 residues processed: 342 average time/residue: 0.1319 time to fit residues: 78.5126 Evaluate side-chains 320 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 227 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 641 TRP Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 423 ASN Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 746 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 673 ASP Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 293 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 123 optimal weight: 0.0030 chunk 262 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 258 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.108677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.078772 restraints weight = 61067.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078656 restraints weight = 36210.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.079441 restraints weight = 28433.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.079790 restraints weight = 25778.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080152 restraints weight = 23121.934| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25145 Z= 0.117 Angle : 0.638 12.908 34136 Z= 0.297 Chirality : 0.043 0.423 3961 Planarity : 0.003 0.056 4237 Dihedral : 7.505 62.180 4237 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.28 % Allowed : 24.41 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 3020 helix: 1.40 (0.15), residues: 1311 sheet: -1.98 (0.27), residues: 366 loop : -1.40 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 66 TYR 0.027 0.001 TYR C 764 PHE 0.021 0.001 PHE B 642 TRP 0.050 0.002 TRP B 706 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00263 (25092) covalent geometry : angle 0.61336 (33985) SS BOND : bond 0.00858 ( 8) SS BOND : angle 1.33682 ( 16) hydrogen bonds : bond 0.03201 ( 1008) hydrogen bonds : angle 4.37135 ( 2913) link_BETA1-4 : bond 0.00456 ( 20) link_BETA1-4 : angle 2.23583 ( 60) link_NAG-ASN : bond 0.00639 ( 25) link_NAG-ASN : angle 3.23866 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 274 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7772 (tpp) cc_final: 0.7388 (tpp) REVERT: A 247 MET cc_start: 0.8728 (mmm) cc_final: 0.8428 (mmm) REVERT: A 565 MET cc_start: 0.7048 (mmp) cc_final: 0.6443 (mmm) REVERT: B 50 MET cc_start: 0.8160 (mmt) cc_final: 0.7866 (mmt) REVERT: B 111 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7344 (t70) REVERT: B 350 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6656 (p90) REVERT: B 360 MET cc_start: 0.8689 (mmm) cc_final: 0.8318 (tpp) REVERT: B 501 MET cc_start: 0.8612 (mmp) cc_final: 0.8103 (tpp) REVERT: B 541 LEU cc_start: 0.8781 (tp) cc_final: 0.8402 (tp) REVERT: B 566 TYR cc_start: 0.8298 (m-80) cc_final: 0.7768 (m-80) REVERT: B 737 MET cc_start: 0.7769 (ppp) cc_final: 0.7449 (ppp) REVERT: B 742 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9324 (mm) REVERT: C 101 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8953 (tt) REVERT: C 140 ASP cc_start: 0.8510 (t70) cc_final: 0.8197 (t70) REVERT: C 400 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: C 423 ASN cc_start: 0.6554 (OUTLIER) cc_final: 0.6238 (m-40) REVERT: C 774 TYR cc_start: 0.7991 (m-10) cc_final: 0.7740 (m-10) REVERT: D 152 ASP cc_start: 0.8521 (t0) cc_final: 0.8310 (t0) REVERT: D 217 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8026 (tp30) REVERT: D 251 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8749 (p90) REVERT: D 323 MET cc_start: 0.8862 (tpp) cc_final: 0.8613 (tpp) REVERT: D 488 TYR cc_start: 0.4930 (OUTLIER) cc_final: 0.4297 (t80) REVERT: D 794 MET cc_start: 0.4518 (tmm) cc_final: 0.3445 (tpt) outliers start: 86 outliers final: 65 residues processed: 341 average time/residue: 0.1326 time to fit residues: 78.5665 Evaluate side-chains 325 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 252 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 423 ASN Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 746 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 488 TYR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 272 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.107884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.077385 restraints weight = 61355.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.077835 restraints weight = 35367.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078374 restraints weight = 27318.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.078748 restraints weight = 25105.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078876 restraints weight = 22801.640| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25145 Z= 0.158 Angle : 0.657 12.325 34136 Z= 0.305 Chirality : 0.043 0.415 3961 Planarity : 0.004 0.054 4237 Dihedral : 7.433 62.145 4237 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.06 % Allowed : 24.64 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 3020 helix: 1.41 (0.15), residues: 1306 sheet: -1.95 (0.26), residues: 386 loop : -1.38 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 481 TYR 0.022 0.001 TYR C 86 PHE 0.019 0.001 PHE C 355 TRP 0.058 0.002 TRP B 706 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00369 (25092) covalent geometry : angle 0.63333 (33985) SS BOND : bond 0.00444 ( 8) SS BOND : angle 0.91417 ( 16) hydrogen bonds : bond 0.03256 ( 1008) hydrogen bonds : angle 4.37566 ( 2913) link_BETA1-4 : bond 0.00425 ( 20) link_BETA1-4 : angle 2.31091 ( 60) link_NAG-ASN : bond 0.00618 ( 25) link_NAG-ASN : angle 3.17246 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 254 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7798 (tpp) cc_final: 0.7389 (tpp) REVERT: A 247 MET cc_start: 0.8738 (mmm) cc_final: 0.8215 (mmm) REVERT: A 360 MET cc_start: 0.9108 (mmm) cc_final: 0.8292 (tpp) REVERT: A 413 MET cc_start: 0.9056 (ptp) cc_final: 0.8778 (mtm) REVERT: A 565 MET cc_start: 0.7016 (mmp) cc_final: 0.6415 (mmm) REVERT: B 50 MET cc_start: 0.8214 (mmt) cc_final: 0.7930 (mmt) REVERT: B 111 HIS cc_start: 0.8173 (OUTLIER) cc_final: 0.7310 (t70) REVERT: B 350 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.6688 (p90) REVERT: B 360 MET cc_start: 0.8735 (mmm) cc_final: 0.8347 (tpp) REVERT: B 498 TRP cc_start: 0.5444 (m100) cc_final: 0.4766 (m100) REVERT: B 501 MET cc_start: 0.8557 (mmp) cc_final: 0.8081 (tpp) REVERT: B 541 LEU cc_start: 0.8835 (tp) cc_final: 0.8456 (tp) REVERT: B 566 TYR cc_start: 0.8312 (m-80) cc_final: 0.7781 (m-80) REVERT: B 696 LYS cc_start: 0.8429 (tttm) cc_final: 0.8223 (tmmt) REVERT: B 737 MET cc_start: 0.7769 (ppp) cc_final: 0.7403 (ppp) REVERT: B 742 ILE cc_start: 0.9625 (OUTLIER) cc_final: 0.9315 (mm) REVERT: C 101 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8899 (tt) REVERT: C 140 ASP cc_start: 0.8471 (t70) cc_final: 0.8153 (t70) REVERT: C 248 MET cc_start: 0.8564 (mmm) cc_final: 0.8097 (mmm) REVERT: C 400 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: C 423 ASN cc_start: 0.6543 (OUTLIER) cc_final: 0.6218 (m-40) REVERT: D 152 ASP cc_start: 0.8619 (t0) cc_final: 0.8333 (t0) REVERT: D 217 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8066 (tp30) REVERT: D 251 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.8938 (p90) REVERT: D 365 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: D 488 TYR cc_start: 0.5045 (t80) cc_final: 0.4430 (t80) REVERT: D 794 MET cc_start: 0.4390 (tmm) cc_final: 0.3307 (tpt) outliers start: 80 outliers final: 65 residues processed: 319 average time/residue: 0.1338 time to fit residues: 74.2807 Evaluate side-chains 322 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 249 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 423 ASN Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 746 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 228 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.109244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082208 restraints weight = 61307.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082720 restraints weight = 37569.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082904 restraints weight = 36884.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.083947 restraints weight = 25396.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.084339 restraints weight = 21650.452| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25145 Z= 0.122 Angle : 0.645 12.833 34136 Z= 0.299 Chirality : 0.043 0.421 3961 Planarity : 0.003 0.055 4237 Dihedral : 7.213 61.405 4235 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.83 % Allowed : 24.83 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 3020 helix: 1.39 (0.15), residues: 1302 sheet: -1.83 (0.27), residues: 375 loop : -1.36 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 481 TYR 0.019 0.001 TYR C 86 PHE 0.022 0.001 PHE B 642 TRP 0.064 0.002 TRP B 706 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00282 (25092) covalent geometry : angle 0.61947 (33985) SS BOND : bond 0.00388 ( 8) SS BOND : angle 2.20440 ( 16) hydrogen bonds : bond 0.03121 ( 1008) hydrogen bonds : angle 4.31703 ( 2913) link_BETA1-4 : bond 0.00442 ( 20) link_BETA1-4 : angle 2.28290 ( 60) link_NAG-ASN : bond 0.00631 ( 25) link_NAG-ASN : angle 3.18683 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 267 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7807 (tpp) cc_final: 0.7407 (tpp) REVERT: A 247 MET cc_start: 0.8822 (mmm) cc_final: 0.8355 (mmm) REVERT: A 360 MET cc_start: 0.9088 (mmm) cc_final: 0.8323 (tpp) REVERT: A 413 MET cc_start: 0.9026 (ptp) cc_final: 0.8732 (mtm) REVERT: A 565 MET cc_start: 0.6798 (mmp) cc_final: 0.6208 (mmm) REVERT: A 676 CYS cc_start: 0.9017 (m) cc_final: 0.8137 (p) REVERT: B 50 MET cc_start: 0.8218 (mmt) cc_final: 0.7932 (mmt) REVERT: B 111 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7275 (t70) REVERT: B 350 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6606 (p90) REVERT: B 360 MET cc_start: 0.8710 (mmm) cc_final: 0.8329 (tpp) REVERT: B 498 TRP cc_start: 0.5327 (m100) cc_final: 0.4583 (m100) REVERT: B 501 MET cc_start: 0.8466 (mmp) cc_final: 0.7947 (tpp) REVERT: B 541 LEU cc_start: 0.8774 (tp) cc_final: 0.8428 (tp) REVERT: B 566 TYR cc_start: 0.8269 (m-80) cc_final: 0.7849 (m-80) REVERT: B 696 LYS cc_start: 0.8283 (tttm) cc_final: 0.8066 (tmmt) REVERT: B 737 MET cc_start: 0.7860 (ppp) cc_final: 0.7548 (ppp) REVERT: B 742 ILE cc_start: 0.9603 (OUTLIER) cc_final: 0.9312 (mm) REVERT: C 101 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8901 (tt) REVERT: C 140 ASP cc_start: 0.8424 (t70) cc_final: 0.8116 (t70) REVERT: C 400 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: C 423 ASN cc_start: 0.6594 (OUTLIER) cc_final: 0.6293 (m-40) REVERT: C 774 TYR cc_start: 0.7995 (m-10) cc_final: 0.7759 (m-10) REVERT: D 152 ASP cc_start: 0.8563 (t0) cc_final: 0.8277 (t0) REVERT: D 217 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7954 (tp30) REVERT: D 251 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8803 (p90) REVERT: D 323 MET cc_start: 0.8906 (mmm) cc_final: 0.8607 (tpp) REVERT: D 365 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: D 488 TYR cc_start: 0.5232 (OUTLIER) cc_final: 0.4644 (t80) REVERT: D 794 MET cc_start: 0.4251 (tmm) cc_final: 0.3157 (tpt) outliers start: 74 outliers final: 61 residues processed: 326 average time/residue: 0.1341 time to fit residues: 75.4714 Evaluate side-chains 327 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 257 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 423 ASN Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 746 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 488 TYR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 259 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 255 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 52 optimal weight: 0.2980 chunk 296 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.109810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082729 restraints weight = 61104.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.083282 restraints weight = 38395.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.083422 restraints weight = 37764.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084508 restraints weight = 25568.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.084889 restraints weight = 21685.621| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25145 Z= 0.116 Angle : 0.640 12.704 34136 Z= 0.296 Chirality : 0.043 0.421 3961 Planarity : 0.003 0.054 4237 Dihedral : 7.022 60.677 4235 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.83 % Allowed : 24.94 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 3020 helix: 1.40 (0.15), residues: 1304 sheet: -1.81 (0.27), residues: 375 loop : -1.32 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 481 TYR 0.023 0.001 TYR C 86 PHE 0.025 0.001 PHE D 459 TRP 0.066 0.002 TRP B 706 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00267 (25092) covalent geometry : angle 0.61629 (33985) SS BOND : bond 0.00130 ( 8) SS BOND : angle 1.21225 ( 16) hydrogen bonds : bond 0.03011 ( 1008) hydrogen bonds : angle 4.26320 ( 2913) link_BETA1-4 : bond 0.00437 ( 20) link_BETA1-4 : angle 2.29510 ( 60) link_NAG-ASN : bond 0.00632 ( 25) link_NAG-ASN : angle 3.16205 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3791.55 seconds wall clock time: 66 minutes 55.82 seconds (4015.82 seconds total)