Starting phenix.real_space_refine on Sun Aug 24 12:45:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sax_40283/08_2025/8sax_40283_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sax_40283/08_2025/8sax_40283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sax_40283/08_2025/8sax_40283_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sax_40283/08_2025/8sax_40283_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sax_40283/08_2025/8sax_40283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sax_40283/08_2025/8sax_40283.map" } resolution = 4.0 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= 0.058 sd= 0.370 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 135 5.16 5 C 12405 2.51 5 N 3330 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19860 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3582 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "D" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 800 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "E" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3582 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "G" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "H" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 800 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "I" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3582 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "K" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 800 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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 Chain: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.95, per 1000 atoms: 0.20 Number of scatterers: 19860 At special positions: 0 Unit cell: (165.24, 166.86, 142.56, 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 135 16.00 O 3990 8.00 N 3330 7.00 C 12405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, 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 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " 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 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG M 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN E 301 " " NAG S 1 " - " ASN E 156 " " NAG T 1 " - " ASN E 442 " " NAG U 1 " - " ASN I 301 " " NAG W 1 " - " ASN I 156 " " NAG X 1 " - " ASN I 442 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 773.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4572 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 18.6% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.032A pdb=" N LYS A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.712A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.052A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 481 removed outlier: 4.205A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.245A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.604A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 579 removed outlier: 3.670A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 596 removed outlier: 4.623A pdb=" N ARG B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.697A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 664 removed outlier: 3.537A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.670A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 63 removed outlier: 4.032A pdb=" N LYS E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.712A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.052A pdb=" N LYS E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 481 removed outlier: 4.205A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 4.246A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.604A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 579 removed outlier: 3.670A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 596 removed outlier: 4.624A pdb=" N ARG F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 587 " --> pdb=" O VAL F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.697A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 664 removed outlier: 3.537A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.670A pdb=" N GLU H 85 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 63 removed outlier: 4.033A pdb=" N LYS I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.712A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 351 removed outlier: 4.052A pdb=" N LYS I 351 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 474 through 481 removed outlier: 4.204A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 535 removed outlier: 4.246A pdb=" N MET J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 543 removed outlier: 3.604A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 579 removed outlier: 3.669A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 576 " --> pdb=" O GLY J 572 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 596 removed outlier: 4.623A pdb=" N ARG J 585 " --> pdb=" O LEU J 581 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU J 587 " --> pdb=" O VAL J 583 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 624 removed outlier: 3.697A pdb=" N ILE J 622 " --> pdb=" O ASN J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 639 through 664 removed outlier: 3.536A pdb=" N GLU J 648 " --> pdb=" O GLY J 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP J 664 " --> pdb=" O LEU J 660 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.670A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.843A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.902A 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 91 through 94 removed outlier: 4.366A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A 239 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 260 removed outlier: 4.232A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 removed outlier: 6.947A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 304 removed outlier: 6.302A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.657A pdb=" N THR C 124 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 99 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB6, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.891A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.366A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS E 239 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 259 through 260 removed outlier: 4.232A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 272 through 273 removed outlier: 6.946A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 302 through 304 removed outlier: 6.302A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AC7, first strand: chain 'E' and resid 423 through 425 Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.658A pdb=" N THR G 124 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY G 99 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AD2, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AD3, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'I' and resid 494 through 499 removed outlier: 4.940A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.366A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS I 239 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'I' and resid 259 through 260 removed outlier: 4.232A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 272 through 273 removed outlier: 6.947A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY I 393 " --> pdb=" O TYR I 361 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 302 through 304 removed outlier: 6.302A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 307 through 308 Processing sheet with id=AE4, first strand: chain 'I' and resid 423 through 425 Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.500A pdb=" N GLU K 10 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR K 124 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY K 99 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE9, first strand: chain 'L' and resid 18 through 23 668 hydrogen bonds defined for protein. 1752 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: 2.70 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6318 1.34 - 1.46: 4887 1.46 - 1.58: 8883 1.58 - 1.70: 0 1.70 - 1.81: 183 Bond restraints: 20271 Sorted by residual: bond pdb=" C3 MAN N 7 " pdb=" O3 MAN N 7 " ideal model delta sigma weight residual 1.408 1.484 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C3 MAN V 7 " pdb=" O3 MAN V 7 " ideal model delta sigma weight residual 1.408 1.484 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C3 MAN R 7 " pdb=" O3 MAN R 7 " ideal model delta sigma weight residual 1.408 1.484 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 MAN V 8 " pdb=" C2 MAN V 8 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C1 MAN R 8 " pdb=" C2 MAN R 8 " ideal model delta sigma weight residual 1.526 1.573 -0.047 2.00e-02 2.50e+03 5.64e+00 ... (remaining 20266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 27140 2.12 - 4.25: 304 4.25 - 6.37: 99 6.37 - 8.50: 9 8.50 - 10.62: 6 Bond angle restraints: 27558 Sorted by residual: angle pdb=" C LEU I 122 " pdb=" N THR I 123 " pdb=" CA THR I 123 " ideal model delta sigma weight residual 121.80 131.62 -9.82 2.44e+00 1.68e-01 1.62e+01 angle pdb=" C LEU A 122 " pdb=" N THR A 123 " pdb=" CA THR A 123 " ideal model delta sigma weight residual 121.80 131.58 -9.78 2.44e+00 1.68e-01 1.61e+01 angle pdb=" C LEU E 122 " pdb=" N THR E 123 " pdb=" CA THR E 123 " ideal model delta sigma weight residual 121.80 131.54 -9.74 2.44e+00 1.68e-01 1.59e+01 angle pdb=" C2 MAN V 7 " pdb=" C3 MAN V 7 " pdb=" O3 MAN V 7 " ideal model delta sigma weight residual 107.58 118.20 -10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C2 MAN N 7 " pdb=" C3 MAN N 7 " pdb=" O3 MAN N 7 " ideal model delta sigma weight residual 107.58 118.20 -10.62 3.00e+00 1.11e-01 1.25e+01 ... (remaining 27553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 12349 24.55 - 49.11: 272 49.11 - 73.66: 39 73.66 - 98.22: 48 98.22 - 122.77: 24 Dihedral angle restraints: 12732 sinusoidal: 5571 harmonic: 7161 Sorted by residual: dihedral pdb=" CA VAL B 580 " pdb=" C VAL B 580 " pdb=" N LEU B 581 " pdb=" CA LEU B 581 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA VAL F 580 " pdb=" C VAL F 580 " pdb=" N LEU F 581 " pdb=" CA LEU F 581 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA VAL J 580 " pdb=" C VAL J 580 " pdb=" N LEU J 581 " pdb=" CA LEU J 581 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 12729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 3231 0.209 - 0.417: 9 0.417 - 0.626: 0 0.626 - 0.834: 0 0.834 - 1.043: 3 Chirality restraints: 3243 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 442 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 442 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN I 442 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.71e+01 ... (remaining 3240 not shown) Planarity restraints: 3459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 298 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO E 299 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 299 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 299 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 298 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.03e+00 pdb=" N PRO A 299 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 298 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO I 299 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 299 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 299 " 0.020 5.00e-02 4.00e+02 ... (remaining 3456 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 185 2.61 - 3.18: 17039 3.18 - 3.75: 27253 3.75 - 4.33: 36691 4.33 - 4.90: 62884 Nonbonded interactions: 144052 Sorted by model distance: nonbonded pdb=" O4 BMA R 3 " pdb=" O6 MAN R 5 " model vdw 2.035 3.040 nonbonded pdb=" O4 BMA N 3 " pdb=" O6 MAN N 5 " model vdw 2.035 3.040 nonbonded pdb=" O4 BMA V 3 " pdb=" O6 MAN V 5 " model vdw 2.035 3.040 nonbonded pdb=" O3 NAG X 1 " pdb=" O5 NAG X 2 " model vdw 2.159 3.040 nonbonded pdb=" O3 NAG P 1 " pdb=" O5 NAG P 2 " model vdw 2.159 3.040 ... (remaining 144047 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.520 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.004 0.076 20349 Z= 0.201 Angle : 0.774 25.146 27762 Z= 0.336 Chirality : 0.056 1.043 3243 Planarity : 0.003 0.036 3450 Dihedral : 13.454 122.772 8070 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.67 % Favored : 96.97 % Rotamer: Outliers : 2.12 % Allowed : 4.67 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: -0.49 (0.17), residues: 2472 helix: 1.48 (0.30), residues: 366 sheet: 0.22 (0.19), residues: 657 loop : -1.09 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.008 0.001 TYR H 93 PHE 0.007 0.001 PHE G 114 TRP 0.006 0.001 TRP F 571 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00413 (20271) covalent geometry : angle 0.65193 (27558) SS BOND : bond 0.00218 ( 30) SS BOND : angle 0.66779 ( 60) hydrogen bonds : bond 0.16446 ( 638) hydrogen bonds : angle 6.40057 ( 1752) link_ALPHA1-2 : bond 0.00490 ( 6) link_ALPHA1-2 : angle 1.99175 ( 18) link_ALPHA1-3 : bond 0.01824 ( 9) link_ALPHA1-3 : angle 5.58765 ( 27) link_ALPHA1-6 : bond 0.00575 ( 6) link_ALPHA1-6 : angle 1.33898 ( 18) link_BETA1-4 : bond 0.00649 ( 18) link_BETA1-4 : angle 2.61643 ( 54) link_NAG-ASN : bond 0.02161 ( 9) link_NAG-ASN : angle 11.48210 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 362 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ILE cc_start: 0.6888 (mt) cc_final: 0.6622 (mm) REVERT: A 390 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8856 (tp) REVERT: B 534 SER cc_start: 0.8886 (t) cc_final: 0.8547 (p) REVERT: B 535 MET cc_start: 0.7988 (mtm) cc_final: 0.7532 (mpp) REVERT: B 586 TYR cc_start: 0.6544 (t80) cc_final: 0.6204 (t80) REVERT: B 595 ILE cc_start: 0.9158 (mt) cc_final: 0.8954 (pt) REVERT: B 630 GLN cc_start: 0.8677 (pt0) cc_final: 0.8328 (pt0) REVERT: B 631 TRP cc_start: 0.8364 (t-100) cc_final: 0.7675 (t-100) REVERT: C 70 MET cc_start: 0.6771 (mtm) cc_final: 0.6451 (mtm) REVERT: C 81 MET cc_start: 0.8346 (tmm) cc_final: 0.8089 (tmm) REVERT: C 112 PRO cc_start: 0.9239 (Cg_endo) cc_final: 0.8958 (Cg_exo) REVERT: C 114 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.7016 (p90) REVERT: C 115 ASP cc_start: 0.6042 (t70) cc_final: 0.5795 (t0) REVERT: D 37 TRP cc_start: 0.7382 (m100) cc_final: 0.6772 (m100) REVERT: E 95 MET cc_start: 0.7955 (ttp) cc_final: 0.7555 (tmm) REVERT: E 101 VAL cc_start: 0.9350 (m) cc_final: 0.9082 (p) REVERT: E 287 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7370 (m-70) REVERT: F 534 SER cc_start: 0.8827 (t) cc_final: 0.8439 (p) REVERT: F 543 ASN cc_start: 0.8439 (m110) cc_final: 0.8228 (m110) REVERT: F 616 ASN cc_start: 0.8266 (t0) cc_final: 0.7974 (t0) REVERT: F 659 ASP cc_start: 0.6317 (m-30) cc_final: 0.5975 (m-30) REVERT: G 114 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6757 (p90) REVERT: H 48 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5234 (pt) REVERT: H 84 ASP cc_start: 0.6655 (m-30) cc_final: 0.5508 (m-30) REVERT: I 95 MET cc_start: 0.7816 (ttp) cc_final: 0.7102 (tmm) REVERT: I 333 ILE cc_start: 0.7035 (mt) cc_final: 0.6751 (mm) REVERT: I 369 MET cc_start: 0.8113 (ttm) cc_final: 0.7900 (ttt) REVERT: I 381 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7952 (mm-30) REVERT: I 390 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7855 (tp) REVERT: J 535 MET cc_start: 0.8604 (mtm) cc_final: 0.7995 (mpp) REVERT: J 543 ASN cc_start: 0.8548 (m110) cc_final: 0.8173 (m110) REVERT: J 659 ASP cc_start: 0.6711 (m-30) cc_final: 0.6228 (m-30) REVERT: K 12 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7376 (mmmm) REVERT: K 81 MET cc_start: 0.9086 (tmm) cc_final: 0.8616 (tmm) REVERT: K 90 ASP cc_start: 0.7001 (t0) cc_final: 0.6526 (p0) REVERT: K 105 TYR cc_start: 0.8509 (m-80) cc_final: 0.8098 (m-80) REVERT: K 116 TYR cc_start: 0.7295 (m-80) cc_final: 0.6879 (m-80) REVERT: K 125 VAL cc_start: 0.5847 (OUTLIER) cc_final: 0.5147 (m) REVERT: L 33 ASN cc_start: 0.9026 (m-40) cc_final: 0.8807 (m-40) outliers start: 45 outliers final: 8 residues processed: 402 average time/residue: 0.1356 time to fit residues: 82.4490 Evaluate side-chains 192 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 279 ASN E 287 HIS E 374 HIS G 39 GLN I 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.084302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.068528 restraints weight = 80729.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.069427 restraints weight = 47504.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.069963 restraints weight = 37527.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.070325 restraints weight = 31969.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.070456 restraints weight = 30001.638| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 20349 Z= 0.309 Angle : 0.891 16.336 27762 Z= 0.434 Chirality : 0.052 0.388 3243 Planarity : 0.006 0.064 3450 Dihedral : 11.586 91.883 3724 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.94 % Favored : 94.70 % Rotamer: Outliers : 3.54 % Allowed : 9.54 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -1.08 (0.16), residues: 2472 helix: 0.59 (0.27), residues: 384 sheet: -0.04 (0.19), residues: 684 loop : -1.49 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 166 TYR 0.023 0.003 TYR C 95 PHE 0.028 0.003 PHE C 114 TRP 0.027 0.003 TRP C 101 HIS 0.010 0.002 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00688 (20271) covalent geometry : angle 0.85346 (27558) SS BOND : bond 0.00614 ( 30) SS BOND : angle 1.10365 ( 60) hydrogen bonds : bond 0.04657 ( 638) hydrogen bonds : angle 5.41741 ( 1752) link_ALPHA1-2 : bond 0.00414 ( 6) link_ALPHA1-2 : angle 2.35269 ( 18) link_ALPHA1-3 : bond 0.02359 ( 9) link_ALPHA1-3 : angle 5.74049 ( 27) link_ALPHA1-6 : bond 0.00783 ( 6) link_ALPHA1-6 : angle 2.31914 ( 18) link_BETA1-4 : bond 0.00475 ( 18) link_BETA1-4 : angle 3.17254 ( 54) link_NAG-ASN : bond 0.00672 ( 9) link_NAG-ASN : angle 3.16095 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 177 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7346 (mmp) cc_final: 0.7029 (mmp) REVERT: B 534 SER cc_start: 0.8968 (t) cc_final: 0.8657 (p) REVERT: B 535 MET cc_start: 0.8304 (mtm) cc_final: 0.8065 (mpp) REVERT: B 586 TYR cc_start: 0.7954 (t80) cc_final: 0.7708 (t80) REVERT: C 81 MET cc_start: 0.8389 (tmm) cc_final: 0.8184 (tmm) REVERT: E 52 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8787 (mm) REVERT: E 95 MET cc_start: 0.8016 (ttp) cc_final: 0.7771 (tmm) REVERT: E 104 MET cc_start: 0.9152 (tpp) cc_final: 0.8819 (tpp) REVERT: E 287 HIS cc_start: 0.8451 (OUTLIER) cc_final: 0.7231 (m90) REVERT: E 381 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8113 (mm-30) REVERT: E 434 MET cc_start: 0.7704 (ttp) cc_final: 0.7394 (ttp) REVERT: F 534 SER cc_start: 0.9058 (t) cc_final: 0.8709 (p) REVERT: F 543 ASN cc_start: 0.8397 (m110) cc_final: 0.8117 (m110) REVERT: F 621 GLU cc_start: 0.8347 (tt0) cc_final: 0.8106 (pt0) REVERT: F 659 ASP cc_start: 0.7074 (m-30) cc_final: 0.6690 (m-30) REVERT: H 49 MET cc_start: 0.7106 (mmm) cc_final: 0.6890 (mmm) REVERT: I 104 MET cc_start: 0.8986 (tmm) cc_final: 0.8676 (tmm) REVERT: I 123 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8509 (t) REVERT: I 258 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: J 535 MET cc_start: 0.8757 (mtm) cc_final: 0.8295 (mpp) REVERT: J 659 ASP cc_start: 0.7246 (m-30) cc_final: 0.6721 (m-30) REVERT: K 12 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7657 (mmmt) REVERT: K 115 ASP cc_start: 0.8356 (p0) cc_final: 0.7548 (p0) REVERT: K 116 TYR cc_start: 0.7734 (m-80) cc_final: 0.7407 (m-80) REVERT: K 125 VAL cc_start: 0.6845 (OUTLIER) cc_final: 0.6594 (m) outliers start: 75 outliers final: 37 residues processed: 240 average time/residue: 0.1154 time to fit residues: 44.3603 Evaluate side-chains 182 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 88 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 162 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 160 optimal weight: 40.0000 chunk 7 optimal weight: 5.9990 chunk 134 optimal weight: 0.2980 chunk 135 optimal weight: 3.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN F 575 GLN H 81 GLN J 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.080401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.065872 restraints weight = 80205.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.066659 restraints weight = 51688.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.067205 restraints weight = 45869.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067699 restraints weight = 37123.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067830 restraints weight = 33981.097| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20349 Z= 0.148 Angle : 0.691 17.141 27762 Z= 0.330 Chirality : 0.046 0.408 3243 Planarity : 0.004 0.056 3450 Dihedral : 10.509 92.044 3715 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.44 % Favored : 96.20 % Rotamer: Outliers : 2.88 % Allowed : 11.28 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: -0.86 (0.17), residues: 2472 helix: 0.95 (0.29), residues: 387 sheet: 0.13 (0.19), residues: 717 loop : -1.45 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 59 TYR 0.019 0.001 TYR H 51 PHE 0.021 0.002 PHE J 522 TRP 0.015 0.001 TRP D 37 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00326 (20271) covalent geometry : angle 0.64994 (27558) SS BOND : bond 0.00287 ( 30) SS BOND : angle 0.71548 ( 60) hydrogen bonds : bond 0.03862 ( 638) hydrogen bonds : angle 4.96312 ( 1752) link_ALPHA1-2 : bond 0.00495 ( 6) link_ALPHA1-2 : angle 2.23832 ( 18) link_ALPHA1-3 : bond 0.02562 ( 9) link_ALPHA1-3 : angle 5.83249 ( 27) link_ALPHA1-6 : bond 0.00530 ( 6) link_ALPHA1-6 : angle 2.03374 ( 18) link_BETA1-4 : bond 0.00379 ( 18) link_BETA1-4 : angle 2.50891 ( 54) link_NAG-ASN : bond 0.00257 ( 9) link_NAG-ASN : angle 2.36411 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8128 (p) REVERT: B 530 MET cc_start: 0.7441 (mmp) cc_final: 0.6971 (mmp) REVERT: B 534 SER cc_start: 0.8941 (t) cc_final: 0.8663 (p) REVERT: B 631 TRP cc_start: 0.8566 (t-100) cc_final: 0.7553 (t-100) REVERT: C 81 MET cc_start: 0.8294 (tmm) cc_final: 0.8030 (tmm) REVERT: E 287 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.7460 (m90) REVERT: E 426 MET cc_start: 0.6751 (mtm) cc_final: 0.6458 (mtm) REVERT: E 434 MET cc_start: 0.7447 (ttp) cc_final: 0.7172 (ttp) REVERT: F 534 SER cc_start: 0.8910 (t) cc_final: 0.8698 (p) REVERT: F 543 ASN cc_start: 0.8328 (m110) cc_final: 0.8101 (m110) REVERT: F 659 ASP cc_start: 0.7058 (m-30) cc_final: 0.6686 (m-30) REVERT: I 104 MET cc_start: 0.8741 (tmm) cc_final: 0.8272 (tmm) REVERT: I 123 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8470 (t) REVERT: J 659 ASP cc_start: 0.7408 (m-30) cc_final: 0.6871 (m-30) REVERT: K 115 ASP cc_start: 0.8118 (p0) cc_final: 0.7279 (p0) REVERT: K 116 TYR cc_start: 0.7570 (m-80) cc_final: 0.7249 (m-80) outliers start: 61 outliers final: 40 residues processed: 201 average time/residue: 0.1215 time to fit residues: 39.2675 Evaluate side-chains 183 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 178 optimal weight: 0.0370 chunk 149 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 200 optimal weight: 50.0000 chunk 81 optimal weight: 8.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS E 374 HIS I 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.063927 restraints weight = 80936.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064575 restraints weight = 54146.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.065234 restraints weight = 45895.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.065621 restraints weight = 37713.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065786 restraints weight = 35062.332| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20349 Z= 0.186 Angle : 0.702 16.825 27762 Z= 0.337 Chirality : 0.047 0.370 3243 Planarity : 0.004 0.053 3450 Dihedral : 9.421 83.522 3714 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.22 % Favored : 94.42 % Rotamer: Outliers : 3.68 % Allowed : 11.57 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: -0.96 (0.17), residues: 2472 helix: 0.95 (0.28), residues: 387 sheet: 0.01 (0.18), residues: 750 loop : -1.54 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 59 TYR 0.023 0.001 TYR D 51 PHE 0.017 0.002 PHE I 53 TRP 0.031 0.002 TRP D 37 HIS 0.006 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00414 (20271) covalent geometry : angle 0.66547 (27558) SS BOND : bond 0.00370 ( 30) SS BOND : angle 0.64705 ( 60) hydrogen bonds : bond 0.03806 ( 638) hydrogen bonds : angle 4.86154 ( 1752) link_ALPHA1-2 : bond 0.00303 ( 6) link_ALPHA1-2 : angle 2.27124 ( 18) link_ALPHA1-3 : bond 0.02482 ( 9) link_ALPHA1-3 : angle 5.75849 ( 27) link_ALPHA1-6 : bond 0.00552 ( 6) link_ALPHA1-6 : angle 1.80439 ( 18) link_BETA1-4 : bond 0.00444 ( 18) link_BETA1-4 : angle 2.32089 ( 54) link_NAG-ASN : bond 0.00279 ( 9) link_NAG-ASN : angle 2.20968 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 148 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7541 (mmp) cc_final: 0.7119 (mmp) REVERT: B 534 SER cc_start: 0.8835 (t) cc_final: 0.8551 (p) REVERT: C 81 MET cc_start: 0.8379 (tmm) cc_final: 0.8078 (tmm) REVERT: C 115 ASP cc_start: 0.8293 (p0) cc_final: 0.8036 (p0) REVERT: E 287 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.7562 (m90) REVERT: E 426 MET cc_start: 0.6816 (mtm) cc_final: 0.6557 (mtm) REVERT: F 534 SER cc_start: 0.9072 (t) cc_final: 0.8826 (p) REVERT: F 543 ASN cc_start: 0.8379 (m110) cc_final: 0.8138 (m110) REVERT: F 659 ASP cc_start: 0.7201 (m-30) cc_final: 0.6823 (m-30) REVERT: G 12 LYS cc_start: 0.8379 (mmmm) cc_final: 0.8170 (mmtp) REVERT: H 49 MET cc_start: 0.7113 (mmm) cc_final: 0.6846 (mmm) REVERT: I 104 MET cc_start: 0.8758 (tmm) cc_final: 0.8233 (tmm) REVERT: I 123 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8477 (t) REVERT: J 659 ASP cc_start: 0.7497 (m-30) cc_final: 0.6953 (m-30) REVERT: K 34 MET cc_start: 0.8705 (mmt) cc_final: 0.8494 (mmt) REVERT: K 115 ASP cc_start: 0.8264 (p0) cc_final: 0.7397 (p0) REVERT: K 116 TYR cc_start: 0.7646 (m-80) cc_final: 0.7242 (m-80) outliers start: 78 outliers final: 53 residues processed: 211 average time/residue: 0.1203 time to fit residues: 40.9591 Evaluate side-chains 188 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 133 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 154 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 9 optimal weight: 0.0030 chunk 54 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 206 optimal weight: 30.0000 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN I 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.079329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064646 restraints weight = 79751.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.065524 restraints weight = 51372.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066039 restraints weight = 45592.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.066266 restraints weight = 37337.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.066614 restraints weight = 34640.238| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20349 Z= 0.138 Angle : 0.662 16.986 27762 Z= 0.315 Chirality : 0.046 0.390 3243 Planarity : 0.004 0.051 3450 Dihedral : 8.875 82.058 3712 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.37 % Favored : 95.27 % Rotamer: Outliers : 3.12 % Allowed : 12.65 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: -0.86 (0.17), residues: 2472 helix: 1.07 (0.29), residues: 387 sheet: 0.16 (0.18), residues: 738 loop : -1.54 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 87 TYR 0.021 0.001 TYR D 51 PHE 0.015 0.001 PHE I 53 TRP 0.022 0.001 TRP D 37 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00301 (20271) covalent geometry : angle 0.62277 (27558) SS BOND : bond 0.00292 ( 30) SS BOND : angle 0.56192 ( 60) hydrogen bonds : bond 0.03521 ( 638) hydrogen bonds : angle 4.72163 ( 1752) link_ALPHA1-2 : bond 0.00388 ( 6) link_ALPHA1-2 : angle 2.14396 ( 18) link_ALPHA1-3 : bond 0.02494 ( 9) link_ALPHA1-3 : angle 5.85523 ( 27) link_ALPHA1-6 : bond 0.00749 ( 6) link_ALPHA1-6 : angle 1.91079 ( 18) link_BETA1-4 : bond 0.00380 ( 18) link_BETA1-4 : angle 2.16580 ( 54) link_NAG-ASN : bond 0.00293 ( 9) link_NAG-ASN : angle 2.09370 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 144 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7514 (ttp) cc_final: 0.7258 (ttp) REVERT: B 530 MET cc_start: 0.7522 (mmp) cc_final: 0.7128 (mmp) REVERT: B 534 SER cc_start: 0.8841 (t) cc_final: 0.8629 (p) REVERT: C 81 MET cc_start: 0.8347 (tmm) cc_final: 0.8051 (tmm) REVERT: D 83 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8856 (tt0) REVERT: E 104 MET cc_start: 0.9103 (ttp) cc_final: 0.8722 (ttp) REVERT: E 287 HIS cc_start: 0.8575 (OUTLIER) cc_final: 0.7530 (m90) REVERT: E 475 MET cc_start: 0.8037 (mmm) cc_final: 0.7829 (mmm) REVERT: F 534 SER cc_start: 0.8951 (t) cc_final: 0.8689 (p) REVERT: F 543 ASN cc_start: 0.8391 (m110) cc_final: 0.8126 (m110) REVERT: F 659 ASP cc_start: 0.7225 (m-30) cc_final: 0.6800 (m-30) REVERT: I 104 MET cc_start: 0.8740 (tmm) cc_final: 0.8383 (tmm) REVERT: J 655 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8604 (tppp) REVERT: J 657 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8450 (mm-30) REVERT: J 659 ASP cc_start: 0.7502 (m-30) cc_final: 0.6943 (m-30) REVERT: K 115 ASP cc_start: 0.8162 (p0) cc_final: 0.7302 (p0) REVERT: K 116 TYR cc_start: 0.7655 (m-80) cc_final: 0.7246 (m-80) outliers start: 66 outliers final: 47 residues processed: 196 average time/residue: 0.1222 time to fit residues: 37.8943 Evaluate side-chains 182 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 84 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 24 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 161 optimal weight: 7.9990 chunk 209 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.064704 restraints weight = 79578.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065592 restraints weight = 51259.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066139 restraints weight = 45698.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066353 restraints weight = 37018.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066611 restraints weight = 34450.200| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20349 Z= 0.131 Angle : 0.664 17.029 27762 Z= 0.315 Chirality : 0.045 0.388 3243 Planarity : 0.004 0.047 3450 Dihedral : 8.518 80.878 3712 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.57 % Favored : 95.06 % Rotamer: Outliers : 3.16 % Allowed : 12.56 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: -0.80 (0.17), residues: 2472 helix: 1.10 (0.29), residues: 387 sheet: 0.21 (0.19), residues: 738 loop : -1.50 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 87 TYR 0.013 0.001 TYR D 51 PHE 0.012 0.001 PHE K 114 TRP 0.014 0.001 TRP D 37 HIS 0.012 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00284 (20271) covalent geometry : angle 0.62599 (27558) SS BOND : bond 0.00254 ( 30) SS BOND : angle 0.51087 ( 60) hydrogen bonds : bond 0.03390 ( 638) hydrogen bonds : angle 4.69889 ( 1752) link_ALPHA1-2 : bond 0.00396 ( 6) link_ALPHA1-2 : angle 2.10559 ( 18) link_ALPHA1-3 : bond 0.02524 ( 9) link_ALPHA1-3 : angle 5.86191 ( 27) link_ALPHA1-6 : bond 0.00841 ( 6) link_ALPHA1-6 : angle 1.85340 ( 18) link_BETA1-4 : bond 0.00388 ( 18) link_BETA1-4 : angle 2.08684 ( 54) link_NAG-ASN : bond 0.00319 ( 9) link_NAG-ASN : angle 2.02118 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 139 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7504 (ttp) cc_final: 0.7253 (ttp) REVERT: A 104 MET cc_start: 0.8666 (ttp) cc_final: 0.8462 (ttp) REVERT: B 530 MET cc_start: 0.7518 (mmp) cc_final: 0.7159 (mmp) REVERT: B 534 SER cc_start: 0.8855 (t) cc_final: 0.8651 (p) REVERT: C 81 MET cc_start: 0.8357 (tmm) cc_final: 0.8074 (tmm) REVERT: D 83 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8861 (tt0) REVERT: E 104 MET cc_start: 0.9104 (ttp) cc_final: 0.8706 (ttp) REVERT: E 287 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.7596 (m90) REVERT: E 475 MET cc_start: 0.8072 (mmm) cc_final: 0.7791 (mmm) REVERT: F 534 SER cc_start: 0.8938 (t) cc_final: 0.8674 (p) REVERT: F 543 ASN cc_start: 0.8388 (m110) cc_final: 0.8146 (m110) REVERT: F 659 ASP cc_start: 0.7226 (m-30) cc_final: 0.6836 (m-30) REVERT: J 535 MET cc_start: 0.8407 (mpp) cc_final: 0.8165 (mpp) REVERT: J 655 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8591 (tppp) REVERT: J 657 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8460 (mm-30) REVERT: J 659 ASP cc_start: 0.7400 (m-30) cc_final: 0.6842 (m-30) REVERT: K 116 TYR cc_start: 0.7700 (m-80) cc_final: 0.7329 (m-80) REVERT: L 84 ASP cc_start: 0.7180 (m-30) cc_final: 0.6353 (m-30) outliers start: 67 outliers final: 47 residues processed: 197 average time/residue: 0.1211 time to fit residues: 38.7133 Evaluate side-chains 182 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 15 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 199 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 72 optimal weight: 40.0000 chunk 221 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 6 GLN E 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.076396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061805 restraints weight = 80841.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.062527 restraints weight = 54532.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.062971 restraints weight = 48831.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063371 restraints weight = 39900.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063488 restraints weight = 37078.894| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20349 Z= 0.257 Angle : 0.782 17.250 27762 Z= 0.377 Chirality : 0.048 0.320 3243 Planarity : 0.004 0.053 3450 Dihedral : 8.727 74.292 3712 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.83 % Favored : 93.81 % Rotamer: Outliers : 3.73 % Allowed : 12.98 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -1.15 (0.17), residues: 2472 helix: 0.75 (0.28), residues: 387 sheet: -0.04 (0.18), residues: 741 loop : -1.69 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 63 TYR 0.016 0.002 TYR A 384 PHE 0.019 0.002 PHE G 114 TRP 0.018 0.002 TRP A 112 HIS 0.009 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00579 (20271) covalent geometry : angle 0.74769 (27558) SS BOND : bond 0.00430 ( 30) SS BOND : angle 0.72001 ( 60) hydrogen bonds : bond 0.04179 ( 638) hydrogen bonds : angle 5.01341 ( 1752) link_ALPHA1-2 : bond 0.00264 ( 6) link_ALPHA1-2 : angle 2.17489 ( 18) link_ALPHA1-3 : bond 0.02450 ( 9) link_ALPHA1-3 : angle 6.02097 ( 27) link_ALPHA1-6 : bond 0.00639 ( 6) link_ALPHA1-6 : angle 1.83060 ( 18) link_BETA1-4 : bond 0.00471 ( 18) link_BETA1-4 : angle 2.20116 ( 54) link_NAG-ASN : bond 0.00298 ( 9) link_NAG-ASN : angle 2.34184 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 130 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7730 (ttp) cc_final: 0.7513 (ttp) REVERT: A 104 MET cc_start: 0.9014 (ttp) cc_final: 0.8539 (ttp) REVERT: C 81 MET cc_start: 0.8377 (tmm) cc_final: 0.8080 (tmm) REVERT: C 115 ASP cc_start: 0.8479 (p0) cc_final: 0.8199 (p0) REVERT: D 83 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8928 (tt0) REVERT: E 287 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.7695 (m90) REVERT: E 475 MET cc_start: 0.8372 (mmm) cc_final: 0.7661 (mmm) REVERT: F 543 ASN cc_start: 0.8420 (m110) cc_final: 0.8191 (m110) REVERT: F 659 ASP cc_start: 0.7094 (m-30) cc_final: 0.6768 (m-30) REVERT: J 535 MET cc_start: 0.8096 (mpp) cc_final: 0.7616 (mpp) REVERT: J 655 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8638 (tppp) REVERT: J 657 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8601 (mm-30) REVERT: J 659 ASP cc_start: 0.7677 (m-30) cc_final: 0.7129 (m-30) REVERT: K 115 ASP cc_start: 0.8277 (p0) cc_final: 0.7220 (p0) REVERT: K 116 TYR cc_start: 0.7829 (m-80) cc_final: 0.7347 (m-80) outliers start: 79 outliers final: 65 residues processed: 198 average time/residue: 0.1147 time to fit residues: 36.8342 Evaluate side-chains 193 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 126 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 202 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 200 optimal weight: 50.0000 chunk 122 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.082212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.065849 restraints weight = 79748.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.068318 restraints weight = 43644.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.068537 restraints weight = 29922.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.068619 restraints weight = 26963.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.068824 restraints weight = 26200.768| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20349 Z= 0.188 Angle : 0.721 17.408 27762 Z= 0.344 Chirality : 0.046 0.362 3243 Planarity : 0.004 0.049 3450 Dihedral : 8.519 73.946 3712 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.18 % Favored : 94.46 % Rotamer: Outliers : 3.82 % Allowed : 13.13 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.07 (0.17), residues: 2472 helix: 0.93 (0.28), residues: 387 sheet: -0.01 (0.18), residues: 735 loop : -1.67 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.012 0.001 TYR D 51 PHE 0.016 0.002 PHE G 114 TRP 0.013 0.002 TRP G 101 HIS 0.028 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00422 (20271) covalent geometry : angle 0.68460 (27558) SS BOND : bond 0.00346 ( 30) SS BOND : angle 0.62127 ( 60) hydrogen bonds : bond 0.03890 ( 638) hydrogen bonds : angle 4.84215 ( 1752) link_ALPHA1-2 : bond 0.00244 ( 6) link_ALPHA1-2 : angle 2.06377 ( 18) link_ALPHA1-3 : bond 0.02537 ( 9) link_ALPHA1-3 : angle 6.00607 ( 27) link_ALPHA1-6 : bond 0.00764 ( 6) link_ALPHA1-6 : angle 1.93926 ( 18) link_BETA1-4 : bond 0.00399 ( 18) link_BETA1-4 : angle 2.05317 ( 54) link_NAG-ASN : bond 0.00276 ( 9) link_NAG-ASN : angle 2.26163 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 134 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7732 (ttp) cc_final: 0.7528 (ttp) REVERT: C 81 MET cc_start: 0.8454 (tmm) cc_final: 0.8112 (tmm) REVERT: C 115 ASP cc_start: 0.8518 (p0) cc_final: 0.8178 (p0) REVERT: E 287 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.7643 (m90) REVERT: E 308 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7763 (ttt180) REVERT: E 475 MET cc_start: 0.8423 (mmm) cc_final: 0.7737 (mmm) REVERT: F 543 ASN cc_start: 0.8549 (m110) cc_final: 0.8262 (m110) REVERT: F 659 ASP cc_start: 0.7135 (m-30) cc_final: 0.6626 (m-30) REVERT: F 663 LEU cc_start: 0.8875 (tt) cc_final: 0.8606 (mm) REVERT: I 492 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: J 535 MET cc_start: 0.8189 (mpp) cc_final: 0.7612 (mpp) REVERT: J 655 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8592 (tppp) REVERT: J 657 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8614 (mm-30) REVERT: J 659 ASP cc_start: 0.7771 (m-30) cc_final: 0.7174 (m-30) REVERT: K 115 ASP cc_start: 0.8268 (p0) cc_final: 0.7332 (p0) REVERT: K 116 TYR cc_start: 0.7843 (m-80) cc_final: 0.7395 (m-80) outliers start: 81 outliers final: 63 residues processed: 205 average time/residue: 0.1147 time to fit residues: 38.8196 Evaluate side-chains 192 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 125 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 492 GLU Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 49 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 231 optimal weight: 0.0570 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.083090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.066998 restraints weight = 79760.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067867 restraints weight = 44844.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.068495 restraints weight = 35492.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.068902 restraints weight = 29623.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.069012 restraints weight = 27723.547| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20349 Z= 0.143 Angle : 0.706 17.418 27762 Z= 0.334 Chirality : 0.046 0.378 3243 Planarity : 0.004 0.051 3450 Dihedral : 8.285 74.314 3712 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.38 % Favored : 94.26 % Rotamer: Outliers : 3.07 % Allowed : 14.16 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.01 (0.17), residues: 2472 helix: 0.88 (0.28), residues: 387 sheet: 0.06 (0.18), residues: 735 loop : -1.60 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 617 TYR 0.012 0.001 TYR D 51 PHE 0.014 0.001 PHE I 53 TRP 0.013 0.001 TRP J 571 HIS 0.019 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00315 (20271) covalent geometry : angle 0.66979 (27558) SS BOND : bond 0.00283 ( 30) SS BOND : angle 0.55635 ( 60) hydrogen bonds : bond 0.03605 ( 638) hydrogen bonds : angle 4.73894 ( 1752) link_ALPHA1-2 : bond 0.00326 ( 6) link_ALPHA1-2 : angle 2.02694 ( 18) link_ALPHA1-3 : bond 0.02557 ( 9) link_ALPHA1-3 : angle 5.99889 ( 27) link_ALPHA1-6 : bond 0.00874 ( 6) link_ALPHA1-6 : angle 1.87380 ( 18) link_BETA1-4 : bond 0.00347 ( 18) link_BETA1-4 : angle 1.98182 ( 54) link_NAG-ASN : bond 0.00308 ( 9) link_NAG-ASN : angle 2.10224 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 135 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8945 (ttp) cc_final: 0.8442 (tmm) REVERT: C 46 GLU cc_start: 0.8054 (tp30) cc_final: 0.7706 (tt0) REVERT: C 81 MET cc_start: 0.8548 (tmm) cc_final: 0.8242 (tmm) REVERT: E 104 MET cc_start: 0.9238 (ttp) cc_final: 0.8690 (ttp) REVERT: E 287 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7582 (m90) REVERT: E 308 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7886 (ttt180) REVERT: E 475 MET cc_start: 0.8350 (mmm) cc_final: 0.7542 (mmm) REVERT: F 543 ASN cc_start: 0.8569 (m110) cc_final: 0.8268 (m110) REVERT: F 659 ASP cc_start: 0.7144 (m-30) cc_final: 0.6823 (m-30) REVERT: J 535 MET cc_start: 0.8197 (mpp) cc_final: 0.7615 (mpp) REVERT: J 655 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8561 (tppp) REVERT: J 659 ASP cc_start: 0.7796 (m-30) cc_final: 0.7217 (m-30) REVERT: K 115 ASP cc_start: 0.8147 (p0) cc_final: 0.7112 (p0) REVERT: K 116 TYR cc_start: 0.7856 (m-80) cc_final: 0.7401 (m-80) outliers start: 65 outliers final: 53 residues processed: 195 average time/residue: 0.1179 time to fit residues: 37.4414 Evaluate side-chains 186 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 237 optimal weight: 40.0000 chunk 112 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 155 optimal weight: 0.2980 chunk 103 optimal weight: 0.0070 chunk 127 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 overall best weight: 3.8604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS E 374 HIS J 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.082944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.066833 restraints weight = 79888.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.067732 restraints weight = 44629.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.068400 restraints weight = 35451.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.068698 restraints weight = 29435.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.068812 restraints weight = 27881.221| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20349 Z= 0.156 Angle : 0.723 17.426 27762 Z= 0.342 Chirality : 0.046 0.366 3243 Planarity : 0.004 0.047 3450 Dihedral : 8.156 73.738 3711 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.26 % Favored : 94.38 % Rotamer: Outliers : 2.79 % Allowed : 14.73 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.99 (0.17), residues: 2472 helix: 0.87 (0.29), residues: 387 sheet: 0.07 (0.19), residues: 720 loop : -1.58 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 617 TYR 0.020 0.001 TYR B 643 PHE 0.014 0.001 PHE I 53 TRP 0.013 0.001 TRP J 571 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00347 (20271) covalent geometry : angle 0.68879 (27558) SS BOND : bond 0.00303 ( 30) SS BOND : angle 0.54212 ( 60) hydrogen bonds : bond 0.03653 ( 638) hydrogen bonds : angle 4.76623 ( 1752) link_ALPHA1-2 : bond 0.00267 ( 6) link_ALPHA1-2 : angle 2.01686 ( 18) link_ALPHA1-3 : bond 0.02543 ( 9) link_ALPHA1-3 : angle 5.99686 ( 27) link_ALPHA1-6 : bond 0.00846 ( 6) link_ALPHA1-6 : angle 1.78197 ( 18) link_BETA1-4 : bond 0.00372 ( 18) link_BETA1-4 : angle 1.91458 ( 54) link_NAG-ASN : bond 0.00279 ( 9) link_NAG-ASN : angle 2.06250 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 136 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.5462 (mmm) cc_final: 0.4818 (mmm) REVERT: C 81 MET cc_start: 0.8567 (tmm) cc_final: 0.8262 (tmm) REVERT: E 287 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.7677 (m90) REVERT: E 308 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7760 (ttt180) REVERT: E 475 MET cc_start: 0.8368 (mmm) cc_final: 0.7563 (mmm) REVERT: F 543 ASN cc_start: 0.8593 (m110) cc_final: 0.8295 (m110) REVERT: F 659 ASP cc_start: 0.7198 (m-30) cc_final: 0.6880 (m-30) REVERT: H 107 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7705 (tt) REVERT: J 535 MET cc_start: 0.8248 (mpp) cc_final: 0.7684 (mpp) REVERT: J 655 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8634 (tppp) REVERT: J 659 ASP cc_start: 0.7848 (m-30) cc_final: 0.7268 (m-30) REVERT: K 115 ASP cc_start: 0.8228 (p0) cc_final: 0.7258 (p0) REVERT: K 116 TYR cc_start: 0.7846 (m-80) cc_final: 0.7406 (m-80) outliers start: 59 outliers final: 54 residues processed: 192 average time/residue: 0.1157 time to fit residues: 36.0787 Evaluate side-chains 188 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 130 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 138 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 160 optimal weight: 50.0000 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 210 optimal weight: 30.0000 chunk 239 optimal weight: 3.9990 chunk 151 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS E 216 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.083811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065507 restraints weight = 79444.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.067702 restraints weight = 44257.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069154 restraints weight = 31309.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070084 restraints weight = 25309.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.070644 restraints weight = 22231.104| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20349 Z= 0.126 Angle : 0.696 17.541 27762 Z= 0.328 Chirality : 0.046 0.388 3243 Planarity : 0.004 0.047 3450 Dihedral : 7.979 74.246 3711 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.02 % Favored : 94.62 % Rotamer: Outliers : 2.50 % Allowed : 15.01 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: -0.89 (0.17), residues: 2472 helix: 0.94 (0.29), residues: 384 sheet: 0.18 (0.19), residues: 714 loop : -1.52 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.016 0.001 TYR G 94 PHE 0.017 0.001 PHE E 376 TRP 0.021 0.001 TRP G 47 HIS 0.019 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00274 (20271) covalent geometry : angle 0.66029 (27558) SS BOND : bond 0.00247 ( 30) SS BOND : angle 0.52055 ( 60) hydrogen bonds : bond 0.03396 ( 638) hydrogen bonds : angle 4.65986 ( 1752) link_ALPHA1-2 : bond 0.00394 ( 6) link_ALPHA1-2 : angle 1.96399 ( 18) link_ALPHA1-3 : bond 0.02586 ( 9) link_ALPHA1-3 : angle 6.02376 ( 27) link_ALPHA1-6 : bond 0.00917 ( 6) link_ALPHA1-6 : angle 1.77745 ( 18) link_BETA1-4 : bond 0.00344 ( 18) link_BETA1-4 : angle 1.86470 ( 54) link_NAG-ASN : bond 0.00362 ( 9) link_NAG-ASN : angle 1.97994 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2327.50 seconds wall clock time: 41 minutes 31.35 seconds (2491.35 seconds total)