Starting phenix.real_space_refine on Thu Feb 5 01:54:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8v_46649/02_2026/9d8v_46649.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8v_46649/02_2026/9d8v_46649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d8v_46649/02_2026/9d8v_46649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8v_46649/02_2026/9d8v_46649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d8v_46649/02_2026/9d8v_46649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8v_46649/02_2026/9d8v_46649.map" } resolution = 2.9 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= 0.002 sd= 0.037 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 102 5.16 5 C 8903 2.51 5 N 2413 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14219 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3447 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3447 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3447 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "K" 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: "L" 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: "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: 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: "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: 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 3.45, per 1000 atoms: 0.24 Number of scatterers: 14219 At special positions: 0 Unit cell: (121.472, 127.296, 115.648, 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 102 16.00 O 2801 8.00 N 2413 7.00 C 8903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.05 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 156 " " NAG A 604 " - " ASN A 160 " " NAG A 605 " - " ASN A 197 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 234 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 197 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 392 " " NAG C 609 " - " ASN C 448 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 234 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 392 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 295 " " NAG I 1 " - " ASN A 332 " " NAG J 1 " - " ASN A 363 " " NAG K 1 " - " ASN A 386 " " NAG L 1 " - " ASN C 262 " " NAG M 1 " - " ASN C 295 " " NAG N 1 " - " ASN C 332 " " NAG O 1 " - " ASN C 363 " " NAG P 1 " - " ASN C 386 " " NAG Q 1 " - " ASN E 295 " " NAG R 1 " - " ASN E 332 " " NAG S 1 " - " ASN E 363 " " NAG T 1 " - " ASN E 386 " " NAG U 1 " - " ASN E 448 " " NAG V 1 " - " ASN E 262 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 521.5 milliseconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3168 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 28 sheets defined 25.5% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.929A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.615A pdb=" N ARG A 151 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.762A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.195A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.597A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.608A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.611A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.798A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.945A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.648A pdb=" N ARG C 151 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.674A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 535 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.231A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.628A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.546A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.847A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.961A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.553A pdb=" N MET E 150 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG E 151 " --> pdb=" O ASP E 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 147 through 151' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.267A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.660A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 removed outlier: 3.885A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.239A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.598A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.668A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.935A pdb=" N HIS A 66 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.741A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.860A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.044A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.200A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.144A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.367A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.077A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.367A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.144A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.529A pdb=" N GLN A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.336A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.627A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.873A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.656A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.798A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.988A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.123A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.333A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 274 removed outlier: 11.052A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.333A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.569A pdb=" N GLN C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.870A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.570A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.854A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.748A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.809A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.063A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.114A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.337A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 274 removed outlier: 11.089A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.337A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.493A pdb=" N GLN E 315 " --> pdb=" O ILE E 311 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.90 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: 4507 1.34 - 1.47: 3567 1.47 - 1.60: 6274 1.60 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 14486 Sorted by residual: bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" N LEU E 261 " pdb=" CA LEU E 261 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.27e-02 6.20e+03 4.71e+00 bond pdb=" C1 NAG E 605 " pdb=" O5 NAG E 605 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.91e+00 ... (remaining 14481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 18800 1.45 - 2.90: 727 2.90 - 4.35: 102 4.35 - 5.80: 18 5.80 - 7.25: 7 Bond angle restraints: 19654 Sorted by residual: angle pdb=" CA ASN E 262 " pdb=" C ASN E 262 " pdb=" O ASN E 262 " ideal model delta sigma weight residual 122.14 117.97 4.17 1.24e+00 6.50e-01 1.13e+01 angle pdb=" CA PRO C 240 " pdb=" N PRO C 240 " pdb=" CD PRO C 240 " ideal model delta sigma weight residual 112.00 107.56 4.44 1.40e+00 5.10e-01 1.00e+01 angle pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 114.40 121.65 -7.25 2.30e+00 1.89e-01 9.95e+00 angle pdb=" CA CYS C 247 " pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " ideal model delta sigma weight residual 114.40 121.15 -6.75 2.30e+00 1.89e-01 8.62e+00 angle pdb=" CA CYS E 247 " pdb=" CB CYS E 247 " pdb=" SG CYS E 247 " ideal model delta sigma weight residual 114.40 121.12 -6.72 2.30e+00 1.89e-01 8.53e+00 ... (remaining 19649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.35: 8856 21.35 - 42.70: 554 42.70 - 64.05: 109 64.05 - 85.40: 34 85.40 - 106.75: 20 Dihedral angle restraints: 9573 sinusoidal: 4692 harmonic: 4881 Sorted by residual: dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 37.16 55.84 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CB CYS E 218 " pdb=" SG CYS E 218 " pdb=" SG CYS E 247 " pdb=" CB CYS E 247 " ideal model delta sinusoidal sigma weight residual 93.00 37.21 55.79 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CB CYS C 218 " pdb=" SG CYS C 218 " pdb=" SG CYS C 247 " pdb=" CB CYS C 247 " ideal model delta sinusoidal sigma weight residual 93.00 37.49 55.51 1 1.00e+01 1.00e-02 4.16e+01 ... (remaining 9570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2252 0.100 - 0.200: 146 0.200 - 0.300: 6 0.300 - 0.400: 2 0.400 - 0.500: 1 Chirality restraints: 2407 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.76e+02 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.16e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN E 332 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.25e+00 ... (remaining 2404 not shown) Planarity restraints: 2463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 2 " -0.137 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG V 2 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG V 2 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG V 2 " 0.186 2.00e-02 2.50e+03 pdb=" O7 NAG V 2 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 239 " 0.078 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO C 240 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 239 " -0.060 5.00e-02 4.00e+02 9.00e-02 1.29e+01 pdb=" N PRO E 240 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO E 240 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 240 " -0.049 5.00e-02 4.00e+02 ... (remaining 2460 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 387 2.70 - 3.25: 13439 3.25 - 3.80: 22674 3.80 - 4.35: 30230 4.35 - 4.90: 50297 Nonbonded interactions: 117027 Sorted by model distance: nonbonded pdb=" OD1 ASN C 197 " pdb=" OG1 THR C 198 " model vdw 2.152 3.040 nonbonded pdb=" O LEU E 369 " pdb=" OG1 THR E 373 " model vdw 2.195 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.197 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.198 3.040 nonbonded pdb=" O ASP F 632 " pdb=" OG SER F 636 " model vdw 2.200 3.040 ... (remaining 117022 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 609) selection = (chain 'C' and resid 33 through 609) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'V' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.040 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.005 0.065 14582 Z= 0.233 Angle : 0.730 12.068 19909 Z= 0.337 Chirality : 0.051 0.500 2407 Planarity : 0.005 0.116 2419 Dihedral : 14.636 106.751 6306 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -0.53 (0.20), residues: 1650 helix: 0.11 (0.26), residues: 393 sheet: -0.47 (0.27), residues: 384 loop : -0.40 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 542 TYR 0.016 0.001 TYR E 173 PHE 0.015 0.001 PHE E 383 TRP 0.022 0.001 TRP E 35 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00507 (14486) covalent geometry : angle 0.64058 (19654) SS BOND : bond 0.00547 ( 33) SS BOND : angle 2.00588 ( 66) hydrogen bonds : bond 0.22790 ( 519) hydrogen bonds : angle 8.42216 ( 1521) link_BETA1-4 : bond 0.01772 ( 19) link_BETA1-4 : angle 2.86853 ( 57) link_NAG-ASN : bond 0.01107 ( 44) link_NAG-ASN : angle 3.69753 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.7387 (mtt) cc_final: 0.6978 (mtt) REVERT: C 228 CYS cc_start: 0.7531 (t) cc_final: 0.7315 (t) REVERT: C 232 LYS cc_start: 0.8344 (ptpp) cc_final: 0.8049 (ptpp) REVERT: D 542 ARG cc_start: 0.7623 (ptm160) cc_final: 0.6886 (ptm-80) REVERT: D 647 GLU cc_start: 0.7181 (tt0) cc_final: 0.6944 (tt0) REVERT: F 542 ARG cc_start: 0.7908 (ptm160) cc_final: 0.7644 (ptm160) outliers start: 0 outliers final: 2 residues processed: 218 average time/residue: 0.6540 time to fit residues: 156.0594 Evaluate side-chains 149 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 577 GLN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102318 restraints weight = 18089.527| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.59 r_work: 0.3047 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 14582 Z= 0.313 Angle : 0.769 10.017 19909 Z= 0.374 Chirality : 0.051 0.235 2407 Planarity : 0.005 0.083 2419 Dihedral : 9.658 67.618 3133 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.42 % Allowed : 9.95 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1650 helix: 0.53 (0.26), residues: 402 sheet: -0.62 (0.25), residues: 393 loop : -0.51 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 585 TYR 0.020 0.002 TYR C 173 PHE 0.018 0.002 PHE E 383 TRP 0.016 0.002 TRP C 69 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00765 (14486) covalent geometry : angle 0.70106 (19654) SS BOND : bond 0.00614 ( 33) SS BOND : angle 1.77037 ( 66) hydrogen bonds : bond 0.05692 ( 519) hydrogen bonds : angle 5.73974 ( 1521) link_BETA1-4 : bond 0.00620 ( 19) link_BETA1-4 : angle 2.20045 ( 57) link_NAG-ASN : bond 0.00945 ( 44) link_NAG-ASN : angle 3.52568 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.7738 (ptm160) cc_final: 0.7476 (ptm160) REVERT: C 228 CYS cc_start: 0.7794 (t) cc_final: 0.7580 (t) REVERT: C 232 LYS cc_start: 0.8553 (ptpp) cc_final: 0.8261 (ptpp) REVERT: C 348 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.6395 (mp10) REVERT: C 455 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8200 (p) REVERT: C 502 LYS cc_start: 0.7382 (tttp) cc_final: 0.7169 (ptmt) REVERT: D 542 ARG cc_start: 0.7686 (ptm160) cc_final: 0.7266 (ptm160) REVERT: D 575 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: D 632 ASP cc_start: 0.8546 (t0) cc_final: 0.8264 (t0) REVERT: F 542 ARG cc_start: 0.7854 (ptm160) cc_final: 0.7431 (ptm160) outliers start: 36 outliers final: 20 residues processed: 187 average time/residue: 0.5830 time to fit residues: 120.5778 Evaluate side-chains 173 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** F 650 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 = 0.3618 r_free = 0.3618 target = 0.135630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106691 restraints weight = 18070.871| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.59 r_work: 0.3113 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14582 Z= 0.136 Angle : 0.616 11.334 19909 Z= 0.299 Chirality : 0.045 0.246 2407 Planarity : 0.004 0.068 2419 Dihedral : 7.840 59.168 3131 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.28 % Allowed : 11.76 % Favored : 85.95 % 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: -0.19 (0.20), residues: 1650 helix: 0.96 (0.27), residues: 405 sheet: -0.43 (0.25), residues: 387 loop : -0.42 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 500 TYR 0.009 0.001 TYR C 191 PHE 0.012 0.001 PHE A 383 TRP 0.012 0.001 TRP A 35 HIS 0.002 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00310 (14486) covalent geometry : angle 0.54876 (19654) SS BOND : bond 0.00344 ( 33) SS BOND : angle 1.33084 ( 66) hydrogen bonds : bond 0.04419 ( 519) hydrogen bonds : angle 5.27379 ( 1521) link_BETA1-4 : bond 0.00655 ( 19) link_BETA1-4 : angle 1.97375 ( 57) link_NAG-ASN : bond 0.01003 ( 44) link_NAG-ASN : angle 3.12070 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.565 Fit side-chains REVERT: A 371 VAL cc_start: 0.9156 (m) cc_final: 0.8843 (p) REVERT: A 428 GLN cc_start: 0.8853 (mt0) cc_final: 0.8559 (mt0) REVERT: A 492 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: B 530 MET cc_start: 0.6729 (mtt) cc_final: 0.6446 (mtt) REVERT: C 228 CYS cc_start: 0.7735 (t) cc_final: 0.7530 (t) REVERT: C 232 LYS cc_start: 0.8477 (ptpp) cc_final: 0.8215 (ptpp) REVERT: C 348 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.6255 (mp10) REVERT: C 426 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7486 (ttm) REVERT: C 502 LYS cc_start: 0.7369 (tttp) cc_final: 0.7053 (ptmt) REVERT: D 542 ARG cc_start: 0.7737 (ptm160) cc_final: 0.6681 (ptt-90) REVERT: D 575 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: D 647 GLU cc_start: 0.7244 (tt0) cc_final: 0.6929 (tt0) REVERT: F 542 ARG cc_start: 0.7861 (ptm160) cc_final: 0.7372 (ptm160) outliers start: 34 outliers final: 11 residues processed: 188 average time/residue: 0.5738 time to fit residues: 119.3576 Evaluate side-chains 165 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 605 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 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 = 0.3586 r_free = 0.3586 target = 0.132791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103749 restraints weight = 18118.550| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.59 r_work: 0.3068 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14582 Z= 0.219 Angle : 0.664 10.996 19909 Z= 0.323 Chirality : 0.047 0.218 2407 Planarity : 0.004 0.065 2419 Dihedral : 7.218 59.199 3129 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.82 % Allowed : 12.23 % Favored : 84.95 % 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: -0.28 (0.20), residues: 1650 helix: 0.96 (0.27), residues: 405 sheet: -0.58 (0.25), residues: 387 loop : -0.46 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 500 TYR 0.024 0.001 TYR C 173 PHE 0.015 0.002 PHE A 383 TRP 0.016 0.002 TRP C 479 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00531 (14486) covalent geometry : angle 0.60124 (19654) SS BOND : bond 0.00482 ( 33) SS BOND : angle 1.48149 ( 66) hydrogen bonds : bond 0.04488 ( 519) hydrogen bonds : angle 5.15495 ( 1521) link_BETA1-4 : bond 0.00543 ( 19) link_BETA1-4 : angle 2.01183 ( 57) link_NAG-ASN : bond 0.00944 ( 44) link_NAG-ASN : angle 3.13191 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.594 Fit side-chains REVERT: A 428 GLN cc_start: 0.8873 (mt0) cc_final: 0.8595 (mt0) REVERT: A 492 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: B 542 ARG cc_start: 0.7706 (ptm160) cc_final: 0.7478 (ptm160) REVERT: C 228 CYS cc_start: 0.7769 (t) cc_final: 0.7540 (t) REVERT: C 232 LYS cc_start: 0.8550 (ptpp) cc_final: 0.8298 (ptpp) REVERT: C 348 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.6340 (mp10) REVERT: C 455 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8187 (p) REVERT: D 542 ARG cc_start: 0.7818 (ptm160) cc_final: 0.6775 (ptt-90) REVERT: D 575 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: F 530 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.5983 (mtt) REVERT: F 542 ARG cc_start: 0.7840 (ptm160) cc_final: 0.7504 (ptm160) outliers start: 42 outliers final: 20 residues processed: 181 average time/residue: 0.5646 time to fit residues: 113.2023 Evaluate side-chains 173 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 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 = 0.3592 r_free = 0.3592 target = 0.133438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104375 restraints weight = 18216.143| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.61 r_work: 0.3074 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14582 Z= 0.187 Angle : 0.635 11.265 19909 Z= 0.309 Chirality : 0.046 0.223 2407 Planarity : 0.004 0.060 2419 Dihedral : 6.809 59.112 3129 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.69 % Allowed : 13.24 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.22 (0.20), residues: 1650 helix: 1.00 (0.27), residues: 405 sheet: -0.58 (0.25), residues: 387 loop : -0.42 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 500 TYR 0.015 0.001 TYR E 173 PHE 0.014 0.001 PHE A 383 TRP 0.017 0.002 TRP C 479 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00450 (14486) covalent geometry : angle 0.57205 (19654) SS BOND : bond 0.00414 ( 33) SS BOND : angle 1.41032 ( 66) hydrogen bonds : bond 0.04244 ( 519) hydrogen bonds : angle 5.03589 ( 1521) link_BETA1-4 : bond 0.00517 ( 19) link_BETA1-4 : angle 1.87265 ( 57) link_NAG-ASN : bond 0.00853 ( 44) link_NAG-ASN : angle 3.08158 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: A 371 VAL cc_start: 0.9155 (m) cc_final: 0.8845 (p) REVERT: A 428 GLN cc_start: 0.8861 (mt0) cc_final: 0.8564 (mt0) REVERT: A 492 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: B 530 MET cc_start: 0.6888 (mtt) cc_final: 0.6402 (mtt) REVERT: C 35 TRP cc_start: 0.7774 (m100) cc_final: 0.7484 (m100) REVERT: C 228 CYS cc_start: 0.7808 (t) cc_final: 0.7578 (t) REVERT: C 232 LYS cc_start: 0.8533 (ptpp) cc_final: 0.8257 (ptpp) REVERT: C 348 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.6287 (mp10) REVERT: C 371 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8842 (p) REVERT: C 492 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: D 542 ARG cc_start: 0.7833 (ptm160) cc_final: 0.6785 (ptt-90) REVERT: D 575 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: F 530 MET cc_start: 0.6198 (OUTLIER) cc_final: 0.5948 (mtt) REVERT: F 542 ARG cc_start: 0.7814 (ptm160) cc_final: 0.7447 (ptm160) REVERT: F 575 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7431 (tt0) outliers start: 40 outliers final: 20 residues processed: 183 average time/residue: 0.5455 time to fit residues: 110.8953 Evaluate side-chains 181 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 0.0370 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 302 ASN C 195 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.105310 restraints weight = 18050.131| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.61 r_work: 0.3089 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14582 Z= 0.162 Angle : 0.611 11.369 19909 Z= 0.299 Chirality : 0.046 0.240 2407 Planarity : 0.004 0.056 2419 Dihedral : 6.469 59.630 3129 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.23 % Allowed : 13.78 % Favored : 83.00 % 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: -0.17 (0.20), residues: 1650 helix: 1.08 (0.27), residues: 405 sheet: -0.59 (0.24), residues: 417 loop : -0.35 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 500 TYR 0.026 0.001 TYR C 173 PHE 0.013 0.001 PHE A 383 TRP 0.019 0.001 TRP C 479 HIS 0.002 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00387 (14486) covalent geometry : angle 0.55237 (19654) SS BOND : bond 0.00493 ( 33) SS BOND : angle 1.42765 ( 66) hydrogen bonds : bond 0.04024 ( 519) hydrogen bonds : angle 4.93366 ( 1521) link_BETA1-4 : bond 0.00509 ( 19) link_BETA1-4 : angle 1.78488 ( 57) link_NAG-ASN : bond 0.00853 ( 44) link_NAG-ASN : angle 2.90560 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 84 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7623 (mp) REVERT: A 217 TYR cc_start: 0.8658 (m-80) cc_final: 0.8425 (m-80) REVERT: A 371 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8855 (p) REVERT: A 492 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: B 530 MET cc_start: 0.6977 (mtt) cc_final: 0.6577 (mtt) REVERT: C 228 CYS cc_start: 0.7806 (t) cc_final: 0.7577 (t) REVERT: C 232 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8250 (ptpp) REVERT: C 348 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6258 (mp10) REVERT: C 371 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8866 (p) REVERT: C 455 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8150 (p) REVERT: C 492 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: D 542 ARG cc_start: 0.7837 (ptm160) cc_final: 0.6774 (ptt-90) REVERT: D 575 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: F 530 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.5897 (mtt) REVERT: F 542 ARG cc_start: 0.7818 (ptm160) cc_final: 0.7443 (ptm160) REVERT: F 575 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7397 (tt0) outliers start: 48 outliers final: 23 residues processed: 192 average time/residue: 0.5603 time to fit residues: 119.0544 Evaluate side-chains 186 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 147 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 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 = 0.3605 r_free = 0.3605 target = 0.134659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105636 restraints weight = 18004.949| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.60 r_work: 0.3096 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14582 Z= 0.163 Angle : 0.613 11.340 19909 Z= 0.300 Chirality : 0.046 0.218 2407 Planarity : 0.004 0.055 2419 Dihedral : 6.332 59.209 3129 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.82 % Allowed : 14.45 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.14 (0.21), residues: 1650 helix: 1.09 (0.27), residues: 405 sheet: -0.61 (0.24), residues: 417 loop : -0.30 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 151 TYR 0.020 0.001 TYR E 173 PHE 0.013 0.001 PHE A 383 TRP 0.021 0.001 TRP C 479 HIS 0.002 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00391 (14486) covalent geometry : angle 0.55551 (19654) SS BOND : bond 0.00432 ( 33) SS BOND : angle 1.47656 ( 66) hydrogen bonds : bond 0.03966 ( 519) hydrogen bonds : angle 4.86970 ( 1521) link_BETA1-4 : bond 0.00512 ( 19) link_BETA1-4 : angle 1.71513 ( 57) link_NAG-ASN : bond 0.00784 ( 44) link_NAG-ASN : angle 2.87866 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 84 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7643 (mp) REVERT: A 217 TYR cc_start: 0.8624 (m-80) cc_final: 0.8410 (m-80) REVERT: A 371 VAL cc_start: 0.9168 (m) cc_final: 0.8859 (p) REVERT: A 492 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: A 498 PRO cc_start: 0.8735 (Cg_endo) cc_final: 0.8396 (Cg_exo) REVERT: B 530 MET cc_start: 0.7009 (mtt) cc_final: 0.6656 (mtt) REVERT: C 35 TRP cc_start: 0.7723 (m100) cc_final: 0.7463 (m100) REVERT: C 228 CYS cc_start: 0.7792 (t) cc_final: 0.7560 (t) REVERT: C 232 LYS cc_start: 0.8470 (ptpp) cc_final: 0.8206 (ptpp) REVERT: C 348 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6261 (mp10) REVERT: C 371 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8890 (p) REVERT: C 455 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8151 (p) REVERT: C 492 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: D 530 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.6024 (mmt) REVERT: D 542 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7551 (ptm160) REVERT: D 575 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: F 530 MET cc_start: 0.6207 (OUTLIER) cc_final: 0.5950 (mtt) REVERT: F 542 ARG cc_start: 0.7777 (ptm160) cc_final: 0.7407 (ptm160) REVERT: F 575 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7433 (tt0) outliers start: 42 outliers final: 23 residues processed: 187 average time/residue: 0.5455 time to fit residues: 113.1200 Evaluate side-chains 183 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 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 = 0.3597 r_free = 0.3597 target = 0.133899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104934 restraints weight = 17995.321| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.59 r_work: 0.3088 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14582 Z= 0.182 Angle : 0.624 11.210 19909 Z= 0.305 Chirality : 0.046 0.210 2407 Planarity : 0.004 0.054 2419 Dihedral : 6.311 59.592 3129 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.09 % Allowed : 14.25 % Favored : 82.66 % 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: -0.17 (0.21), residues: 1650 helix: 1.05 (0.28), residues: 405 sheet: -0.65 (0.24), residues: 417 loop : -0.29 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 151 TYR 0.028 0.001 TYR C 173 PHE 0.013 0.001 PHE A 383 TRP 0.021 0.002 TRP C 479 HIS 0.002 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00439 (14486) covalent geometry : angle 0.56862 (19654) SS BOND : bond 0.00464 ( 33) SS BOND : angle 1.46131 ( 66) hydrogen bonds : bond 0.04078 ( 519) hydrogen bonds : angle 4.87165 ( 1521) link_BETA1-4 : bond 0.00497 ( 19) link_BETA1-4 : angle 1.71543 ( 57) link_NAG-ASN : bond 0.00769 ( 44) link_NAG-ASN : angle 2.87262 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 84 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7642 (mp) REVERT: A 232 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8331 (pttt) REVERT: A 371 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 492 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: A 498 PRO cc_start: 0.8736 (Cg_endo) cc_final: 0.8400 (Cg_exo) REVERT: B 530 MET cc_start: 0.7103 (mtt) cc_final: 0.6753 (mtt) REVERT: B 542 ARG cc_start: 0.7766 (ptm160) cc_final: 0.6728 (ptt-90) REVERT: C 228 CYS cc_start: 0.7795 (t) cc_final: 0.7556 (t) REVERT: C 232 LYS cc_start: 0.8443 (ptpp) cc_final: 0.8212 (ptpp) REVERT: C 348 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.6282 (mp10) REVERT: C 371 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8893 (p) REVERT: C 455 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8176 (p) REVERT: C 492 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: D 530 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.6003 (mmt) REVERT: D 542 ARG cc_start: 0.7864 (ptm160) cc_final: 0.7553 (ptm160) REVERT: F 530 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.5858 (mtt) REVERT: F 542 ARG cc_start: 0.7762 (ptm160) cc_final: 0.7379 (ptm160) REVERT: F 575 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7408 (tt0) outliers start: 46 outliers final: 25 residues processed: 186 average time/residue: 0.5503 time to fit residues: 113.7145 Evaluate side-chains 191 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 60 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 155 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 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 = 0.3627 r_free = 0.3627 target = 0.136691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107784 restraints weight = 17898.393| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.59 r_work: 0.3129 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14582 Z= 0.122 Angle : 0.582 11.430 19909 Z= 0.284 Chirality : 0.045 0.226 2407 Planarity : 0.003 0.052 2419 Dihedral : 5.911 59.113 3129 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.22 % Allowed : 15.12 % Favored : 82.66 % 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: -0.03 (0.21), residues: 1650 helix: 1.20 (0.28), residues: 405 sheet: -0.54 (0.25), residues: 417 loop : -0.24 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 500 TYR 0.021 0.001 TYR E 173 PHE 0.011 0.001 PHE A 383 TRP 0.021 0.001 TRP C 479 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00283 (14486) covalent geometry : angle 0.52687 (19654) SS BOND : bond 0.00397 ( 33) SS BOND : angle 1.32017 ( 66) hydrogen bonds : bond 0.03675 ( 519) hydrogen bonds : angle 4.71374 ( 1521) link_BETA1-4 : bond 0.00538 ( 19) link_BETA1-4 : angle 1.56298 ( 57) link_NAG-ASN : bond 0.00716 ( 44) link_NAG-ASN : angle 2.81318 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7509 (tt0) cc_final: 0.7213 (pt0) REVERT: A 217 TYR cc_start: 0.8594 (m-80) cc_final: 0.8313 (m-80) REVERT: A 232 LYS cc_start: 0.8592 (ptpp) cc_final: 0.8295 (pttt) REVERT: A 371 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8852 (p) REVERT: A 492 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: A 498 PRO cc_start: 0.8688 (Cg_endo) cc_final: 0.8381 (Cg_exo) REVERT: B 530 MET cc_start: 0.6901 (mtt) cc_final: 0.6531 (mtt) REVERT: B 542 ARG cc_start: 0.7697 (ptm160) cc_final: 0.6608 (ptt-90) REVERT: C 207 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8003 (mmpt) REVERT: C 228 CYS cc_start: 0.7779 (t) cc_final: 0.7560 (t) REVERT: C 232 LYS cc_start: 0.8411 (ptpp) cc_final: 0.8121 (ptpp) REVERT: C 348 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.6243 (mp10) REVERT: C 371 VAL cc_start: 0.9211 (m) cc_final: 0.8899 (p) REVERT: D 530 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5825 (mmt) REVERT: D 535 MET cc_start: 0.6737 (tpp) cc_final: 0.6291 (mmm) REVERT: D 542 ARG cc_start: 0.7855 (ptm160) cc_final: 0.7551 (ptm160) REVERT: D 647 GLU cc_start: 0.7262 (tt0) cc_final: 0.6987 (tt0) REVERT: F 530 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5881 (mtt) REVERT: F 542 ARG cc_start: 0.7699 (ptm160) cc_final: 0.7327 (ptm160) REVERT: F 575 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7360 (tt0) outliers start: 33 outliers final: 19 residues processed: 189 average time/residue: 0.5576 time to fit residues: 117.0675 Evaluate side-chains 185 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 4 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 40 optimal weight: 0.4980 chunk 163 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 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 = 0.3607 r_free = 0.3607 target = 0.135015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105882 restraints weight = 17955.547| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.61 r_work: 0.3101 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14582 Z= 0.163 Angle : 0.614 11.170 19909 Z= 0.298 Chirality : 0.045 0.211 2407 Planarity : 0.003 0.052 2419 Dihedral : 6.019 59.932 3129 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.81 % Allowed : 15.39 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.21), residues: 1650 helix: 1.15 (0.28), residues: 405 sheet: -0.58 (0.25), residues: 417 loop : -0.26 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 585 TYR 0.021 0.001 TYR E 173 PHE 0.013 0.001 PHE A 383 TRP 0.024 0.002 TRP C 479 HIS 0.002 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00391 (14486) covalent geometry : angle 0.56230 (19654) SS BOND : bond 0.00421 ( 33) SS BOND : angle 1.36815 ( 66) hydrogen bonds : bond 0.03876 ( 519) hydrogen bonds : angle 4.76175 ( 1521) link_BETA1-4 : bond 0.00520 ( 19) link_BETA1-4 : angle 1.61258 ( 57) link_NAG-ASN : bond 0.00765 ( 44) link_NAG-ASN : angle 2.78351 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7621 (mp) REVERT: A 87 GLU cc_start: 0.7517 (tt0) cc_final: 0.7273 (pt0) REVERT: A 371 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8848 (p) REVERT: A 492 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: A 498 PRO cc_start: 0.8695 (Cg_endo) cc_final: 0.8397 (Cg_exo) REVERT: B 530 MET cc_start: 0.7104 (mtt) cc_final: 0.6737 (mtt) REVERT: B 542 ARG cc_start: 0.7784 (ptm160) cc_final: 0.7480 (ptm160) REVERT: C 207 LYS cc_start: 0.8675 (mtmt) cc_final: 0.8027 (mmpt) REVERT: C 228 CYS cc_start: 0.7784 (t) cc_final: 0.7553 (t) REVERT: C 232 LYS cc_start: 0.8446 (ptpp) cc_final: 0.8162 (ptpp) REVERT: C 348 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.6309 (mp10) REVERT: C 371 VAL cc_start: 0.9224 (m) cc_final: 0.8909 (p) REVERT: D 530 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5992 (mmt) REVERT: D 535 MET cc_start: 0.6755 (tpp) cc_final: 0.6309 (mmm) REVERT: D 542 ARG cc_start: 0.7867 (ptm160) cc_final: 0.7569 (ptm160) REVERT: E 35 TRP cc_start: 0.8090 (m100) cc_final: 0.7763 (m100) REVERT: F 530 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5930 (mtt) REVERT: F 542 ARG cc_start: 0.7730 (ptm160) cc_final: 0.7356 (ptm160) REVERT: F 575 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7391 (tt0) outliers start: 27 outliers final: 19 residues processed: 177 average time/residue: 0.5585 time to fit residues: 109.9093 Evaluate side-chains 182 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 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 = 0.3583 r_free = 0.3583 target = 0.132517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103263 restraints weight = 18013.591| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.59 r_work: 0.3061 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 14582 Z= 0.234 Angle : 0.681 10.830 19909 Z= 0.331 Chirality : 0.047 0.198 2407 Planarity : 0.004 0.053 2419 Dihedral : 6.426 59.166 3129 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.02 % Allowed : 15.59 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.21), residues: 1650 helix: 0.98 (0.27), residues: 405 sheet: -0.82 (0.24), residues: 423 loop : -0.27 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 151 TYR 0.020 0.001 TYR E 173 PHE 0.014 0.002 PHE A 383 TRP 0.030 0.002 TRP C 479 HIS 0.003 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00569 (14486) covalent geometry : angle 0.62866 (19654) SS BOND : bond 0.00514 ( 33) SS BOND : angle 1.54109 ( 66) hydrogen bonds : bond 0.04334 ( 519) hydrogen bonds : angle 4.94603 ( 1521) link_BETA1-4 : bond 0.00495 ( 19) link_BETA1-4 : angle 1.82480 ( 57) link_NAG-ASN : bond 0.00854 ( 44) link_NAG-ASN : angle 2.91238 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4729.45 seconds wall clock time: 81 minutes 40.40 seconds (4900.40 seconds total)