Starting phenix.real_space_refine on Sun Aug 24 12:39:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb4_40290/08_2025/8sb4_40290_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb4_40290/08_2025/8sb4_40290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sb4_40290/08_2025/8sb4_40290_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb4_40290/08_2025/8sb4_40290_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sb4_40290/08_2025/8sb4_40290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb4_40290/08_2025/8sb4_40290.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 12525 2.51 5 N 3345 2.21 5 O 4036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s 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: 20041 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} 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: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" 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: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "I" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "K" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" 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: "M" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 3.37, per 1000 atoms: 0.17 Number of scatterers: 20041 At special positions: 0 Unit cell: (158.834, 159.9, 137.514, 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 4036 8.00 N 3345 7.00 C 12525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 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 E 4 " - " MAN E 5 " " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN U 4 " - " MAN U 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 8 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 8 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 S 2 " - " BMA S 3 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 768.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4578 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 35 sheets defined 19.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.882A pdb=" N CYS A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.157A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.962A pdb=" N ASP A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.919A 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 475 through 481 Processing helix chain 'B' and resid 529 through 535 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.562A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.626A pdb=" N TRP B 614 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 611 through 615' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.653A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.164A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (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 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.753A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 61 removed outlier: 4.488A pdb=" N TYR F 61 " --> pdb=" O ALA F 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 58 through 61' Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.110A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 334 through 351 removed outlier: 3.973A pdb=" N ASP F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.544A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 535 Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 573 through 596 removed outlier: 3.545A pdb=" N ALA G 582 " --> pdb=" O ALA G 578 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL G 583 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP G 596 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 removed outlier: 3.581A pdb=" N TRP G 614 " --> pdb=" O ASN G 611 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER G 615 " --> pdb=" O SER G 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 611 through 615' Processing helix chain 'G' and resid 618 through 624 removed outlier: 3.658A pdb=" N ILE G 622 " --> pdb=" O ASN G 618 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP G 624 " --> pdb=" O SER G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.756A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 636 " --> pdb=" O ASP G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 664 removed outlier: 4.413A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN G 656 " --> pdb=" O GLN G 652 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 657 " --> pdb=" O GLN G 653 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA G 662 " --> pdb=" O GLN G 658 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.728A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 61 removed outlier: 4.413A pdb=" N TYR K 61 " --> pdb=" O ALA K 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 58 through 61' Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.813A pdb=" N CYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 116 removed outlier: 4.190A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 116 " --> pdb=" O TRP K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 351 removed outlier: 3.973A pdb=" N ASP K 340 " --> pdb=" O GLU K 336 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN K 343 " --> pdb=" O ASN K 339 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU K 348 " --> pdb=" O LYS K 344 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS K 351 " --> pdb=" O ILE K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 475 through 481 Processing helix chain 'K' and resid 482 through 484 No H-bonds generated for 'chain 'K' and resid 482 through 484' Processing helix chain 'L' and resid 529 through 535 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 573 through 596 removed outlier: 3.536A pdb=" N ALA L 582 " --> pdb=" O ALA L 578 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 removed outlier: 3.803A pdb=" N TRP L 614 " --> pdb=" O ASN L 611 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER L 615 " --> pdb=" O SER L 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 611 through 615' Processing helix chain 'L' and resid 618 through 624 removed outlier: 3.560A pdb=" N ASP L 624 " --> pdb=" O SER L 620 " (cutoff:3.500A) Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.722A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE L 635 " --> pdb=" O TRP L 631 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER L 636 " --> pdb=" O ASP L 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 664 removed outlier: 4.099A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN L 651 " --> pdb=" O GLU L 647 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU L 657 " --> pdb=" O GLN L 653 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA L 662 " --> pdb=" O GLN L 658 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.794A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.452A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.263A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 166 through 176 removed outlier: 6.181A pdb=" N LYS A 168 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR A 163 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.622A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.550A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 386 current: chain 'A' and resid 467 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.551A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 32 through 39 removed outlier: 6.599A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 59 current: chain 'C' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'D' and resid 20 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.391A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.440A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR G 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.374A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AB6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'F' and resid 166 through 176 removed outlier: 6.165A pdb=" N LYS F 168 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR F 163 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.602A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 260 current: chain 'F' and resid 284 through 308 removed outlier: 6.457A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 316 through 323 current: chain 'F' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 386 current: chain 'F' and resid 467 through 470 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.623A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.660A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.592A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 20 through 22 Processing sheet with id=AC5, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.506A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.481A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR L 606 " --> pdb=" O VAL K 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.204A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AC9, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AD1, first strand: chain 'K' and resid 166 through 176 removed outlier: 6.128A pdb=" N LYS K 168 " --> pdb=" O THR K 163 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR K 163 " --> pdb=" O LYS K 168 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS K 170 " --> pdb=" O THR K 161 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.562A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 271 through 273 removed outlier: 6.556A pdb=" N ASN K 301 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE K 322 " --> pdb=" O ASN K 301 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 316 through 323 current: chain 'K' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 381 through 386 current: chain 'K' and resid 467 through 470 Processing sheet with id=AD4, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.594A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.682A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AD7, first strand: chain 'N' and resid 20 through 23 Processing sheet with id=AD8, first strand: chain 'N' and resid 47 through 50 removed outlier: 6.432A pdb=" N TRP N 37 " --> pdb=" O ILE N 49 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1419 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: 3.31 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6356 1.35 - 1.49: 5447 1.49 - 1.62: 8481 1.62 - 1.76: 0 1.76 - 1.89: 183 Bond restraints: 20467 Sorted by residual: bond pdb=" N VAL N 60 " pdb=" CA VAL N 60 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.10e-02 8.26e+03 9.37e+00 bond pdb=" C2 MAN R 5 " pdb=" O2 MAN R 5 " ideal model delta sigma weight residual 1.407 1.467 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" C HIS N 41 " pdb=" N PRO N 42 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.12e-02 7.97e+03 8.62e+00 bond pdb=" C1 MAN J 8 " pdb=" C2 MAN J 8 " ideal model delta sigma weight residual 1.526 1.585 -0.059 2.00e-02 2.50e+03 8.57e+00 bond pdb=" N VAL D 60 " pdb=" CA VAL D 60 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.50e+00 ... (remaining 20462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 26941 2.28 - 4.56: 744 4.56 - 6.84: 128 6.84 - 9.12: 21 9.12 - 11.40: 6 Bond angle restraints: 27840 Sorted by residual: angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 133.10 -11.40 1.80e+00 3.09e-01 4.01e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 132.65 -10.95 1.80e+00 3.09e-01 3.70e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 132.16 -10.46 1.80e+00 3.09e-01 3.38e+01 angle pdb=" C ASN A 403 " pdb=" N SER A 404 " pdb=" CA SER A 404 " ideal model delta sigma weight residual 121.70 131.95 -10.25 1.80e+00 3.09e-01 3.24e+01 angle pdb=" C ASN K 403 " pdb=" N SER K 404 " pdb=" CA SER K 404 " ideal model delta sigma weight residual 121.70 131.90 -10.20 1.80e+00 3.09e-01 3.21e+01 ... (remaining 27835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 11970 21.59 - 43.18: 781 43.18 - 64.77: 78 64.77 - 86.36: 83 86.36 - 107.94: 38 Dihedral angle restraints: 12950 sinusoidal: 5786 harmonic: 7164 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -173.13 87.13 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS L 598 " pdb=" SG CYS L 598 " pdb=" SG CYS L 604 " pdb=" CB CYS L 604 " ideal model delta sinusoidal sigma weight residual -86.00 -159.15 73.15 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N ARG A 432 " pdb=" CA ARG A 432 " ideal model delta harmonic sigma weight residual -180.00 -148.67 -31.33 0 5.00e+00 4.00e-02 3.93e+01 ... (remaining 12947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2690 0.062 - 0.123: 466 0.123 - 0.184: 115 0.184 - 0.246: 8 0.246 - 0.307: 10 Chirality restraints: 3289 Sorted by residual: chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 3286 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 75 " -0.062 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO K 76 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO K 76 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 76 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 112 " -0.018 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP F 112 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP F 112 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 112 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP F 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 112 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 112 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 112 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 112 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 585 " -0.236 9.50e-02 1.11e+02 1.06e-01 7.40e+00 pdb=" NE ARG B 585 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 585 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 585 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 585 " -0.004 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 234 2.64 - 3.20: 18054 3.20 - 3.77: 28572 3.77 - 4.33: 41555 4.33 - 4.90: 68057 Nonbonded interactions: 156472 Sorted by model distance: nonbonded pdb=" OG1 THR D 5 " pdb=" OG1 THR D 23 " model vdw 2.071 3.040 nonbonded pdb=" OG1 THR N 5 " pdb=" OG1 THR N 23 " model vdw 2.073 3.040 nonbonded pdb=" OG1 THR I 5 " pdb=" OG1 THR I 23 " model vdw 2.090 3.040 nonbonded pdb=" O THR M 30 " pdb=" OG SER M 54 " model vdw 2.098 3.040 nonbonded pdb=" OG1 THR F 163 " pdb=" OE1 GLU F 164 " model vdw 2.117 3.040 ... (remaining 156467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'J' and (resid 2 or resid 5 through 9)) selection = (chain 'R' and (resid 1 or resid 4 through 8)) selection = (chain 'V' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' 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: 0.450 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.650 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.006 0.084 20565 Z= 0.273 Angle : 0.973 11.405 28092 Z= 0.498 Chirality : 0.054 0.307 3289 Planarity : 0.006 0.106 3480 Dihedral : 16.323 107.944 8246 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.83 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -1.55 (0.16), residues: 2466 helix: -1.74 (0.24), residues: 354 sheet: -0.26 (0.19), residues: 660 loop : -1.20 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 252 TYR 0.020 0.002 TYR D 51 PHE 0.017 0.002 PHE K 391 TRP 0.052 0.002 TRP F 112 HIS 0.008 0.002 HIS I 41 Details of bonding type rmsd covalent geometry : bond 0.00563 (20467) covalent geometry : angle 0.93279 (27840) SS BOND : bond 0.00473 ( 42) SS BOND : angle 1.79668 ( 84) hydrogen bonds : bond 0.21934 ( 534) hydrogen bonds : angle 8.46713 ( 1419) link_ALPHA1-2 : bond 0.01461 ( 11) link_ALPHA1-2 : angle 3.99413 ( 33) link_ALPHA1-3 : bond 0.00922 ( 6) link_ALPHA1-3 : angle 4.06036 ( 18) link_ALPHA1-6 : bond 0.01107 ( 6) link_ALPHA1-6 : angle 3.87267 ( 18) link_BETA1-4 : bond 0.00604 ( 21) link_BETA1-4 : angle 3.69812 ( 63) link_NAG-ASN : bond 0.00079 ( 12) link_NAG-ASN : angle 2.08267 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.6775 (m-30) cc_final: 0.6558 (m-30) REVERT: A 121 LYS cc_start: 0.7017 (ptpt) cc_final: 0.6690 (ttmm) REVERT: B 535 MET cc_start: 0.8113 (mtt) cc_final: 0.7419 (mtt) REVERT: B 632 ASP cc_start: 0.7977 (t70) cc_final: 0.7567 (t0) REVERT: B 661 LEU cc_start: 0.8854 (tp) cc_final: 0.8464 (mt) REVERT: C 7 SER cc_start: 0.7703 (p) cc_final: 0.7294 (p) REVERT: C 21 SER cc_start: 0.7955 (p) cc_final: 0.7624 (t) REVERT: C 43 GLN cc_start: 0.7377 (tp40) cc_final: 0.6784 (mp10) REVERT: C 84 ASN cc_start: 0.8031 (t0) cc_final: 0.7797 (t0) REVERT: D 92 SER cc_start: 0.8913 (p) cc_final: 0.8694 (p) REVERT: F 54 CYS cc_start: 0.5359 (p) cc_final: 0.5135 (p) REVERT: F 103 GLN cc_start: 0.7654 (mt0) cc_final: 0.7147 (tm-30) REVERT: F 442 ASN cc_start: 0.8083 (p0) cc_final: 0.7856 (p0) REVERT: G 604 CYS cc_start: 0.6761 (t) cc_final: 0.6486 (t) REVERT: G 632 ASP cc_start: 0.7831 (t70) cc_final: 0.7432 (t0) REVERT: G 660 LEU cc_start: 0.7691 (mt) cc_final: 0.7289 (tt) REVERT: G 661 LEU cc_start: 0.8850 (tp) cc_final: 0.8438 (mt) REVERT: H 13 LYS cc_start: 0.7485 (mmpt) cc_final: 0.7262 (mmtt) REVERT: H 43 GLN cc_start: 0.7495 (tp40) cc_final: 0.6728 (mp10) REVERT: H 84 ASN cc_start: 0.8452 (t0) cc_final: 0.8184 (t0) REVERT: I 25 THR cc_start: 0.8086 (t) cc_final: 0.7589 (m) REVERT: I 36 SER cc_start: 0.8859 (m) cc_final: 0.8655 (t) REVERT: I 38 TYR cc_start: 0.8087 (m-80) cc_final: 0.7114 (m-80) REVERT: I 93 TYR cc_start: 0.8918 (t80) cc_final: 0.8390 (t80) REVERT: K 162 THR cc_start: 0.8345 (m) cc_final: 0.8053 (p) REVERT: K 474 ASP cc_start: 0.6732 (t0) cc_final: 0.6498 (t0) REVERT: L 608 VAL cc_start: 0.8485 (t) cc_final: 0.7964 (t) REVERT: L 634 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7845 (mt-10) REVERT: M 122 LEU cc_start: 0.7846 (mt) cc_final: 0.7435 (mp) outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.1387 time to fit residues: 134.0328 Evaluate side-chains 417 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS B 630 GLN B 658 GLN C 6 GLN F 287 HIS G 575 GLN H 43 GLN H 113 ASN K 287 HIS L 630 GLN L 658 GLN M 6 GLN M 39 GLN M 43 GLN N 41 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.159877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121117 restraints weight = 29662.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121315 restraints weight = 23336.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122397 restraints weight = 23983.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124520 restraints weight = 17401.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124723 restraints weight = 15122.317| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20565 Z= 0.209 Angle : 0.769 9.995 28092 Z= 0.391 Chirality : 0.050 0.348 3289 Planarity : 0.005 0.059 3480 Dihedral : 11.850 77.333 3794 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.38 % Favored : 95.26 % Rotamer: Outliers : 2.51 % Allowed : 10.21 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -1.34 (0.16), residues: 2466 helix: -1.48 (0.25), residues: 375 sheet: -0.22 (0.19), residues: 711 loop : -1.04 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 63 TYR 0.025 0.002 TYR D 93 PHE 0.017 0.002 PHE F 376 TRP 0.027 0.002 TRP K 35 HIS 0.005 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00486 (20467) covalent geometry : angle 0.75003 (27840) SS BOND : bond 0.00610 ( 42) SS BOND : angle 1.40255 ( 84) hydrogen bonds : bond 0.05050 ( 534) hydrogen bonds : angle 6.46505 ( 1419) link_ALPHA1-2 : bond 0.00726 ( 11) link_ALPHA1-2 : angle 2.27149 ( 33) link_ALPHA1-3 : bond 0.00987 ( 6) link_ALPHA1-3 : angle 2.25232 ( 18) link_ALPHA1-6 : bond 0.00599 ( 6) link_ALPHA1-6 : angle 2.05753 ( 18) link_BETA1-4 : bond 0.00422 ( 21) link_BETA1-4 : angle 2.41147 ( 63) link_NAG-ASN : bond 0.00222 ( 12) link_NAG-ASN : angle 1.67757 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 436 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7296 (ptpt) cc_final: 0.7015 (ttmm) REVERT: A 207 LYS cc_start: 0.7310 (tmtt) cc_final: 0.6620 (tmtt) REVERT: A 211 GLU cc_start: 0.8038 (tt0) cc_final: 0.7753 (pt0) REVERT: B 632 ASP cc_start: 0.7968 (t0) cc_final: 0.7479 (t0) REVERT: B 661 LEU cc_start: 0.8696 (tp) cc_final: 0.8430 (mt) REVERT: C 7 SER cc_start: 0.8024 (p) cc_final: 0.7729 (p) REVERT: C 13 LYS cc_start: 0.7090 (mmtt) cc_final: 0.6753 (mmmt) REVERT: C 21 SER cc_start: 0.8119 (p) cc_final: 0.7813 (t) REVERT: C 43 GLN cc_start: 0.7073 (tp40) cc_final: 0.6686 (mp10) REVERT: D 23 THR cc_start: 0.7432 (p) cc_final: 0.7116 (t) REVERT: D 47 LYS cc_start: 0.7826 (tptp) cc_final: 0.7575 (tttm) REVERT: D 63 ARG cc_start: 0.7150 (mtp-110) cc_final: 0.6324 (ptm-80) REVERT: F 54 CYS cc_start: 0.5402 (p) cc_final: 0.5120 (p) REVERT: F 57 ASP cc_start: 0.7423 (t0) cc_final: 0.6996 (p0) REVERT: F 103 GLN cc_start: 0.7767 (mt0) cc_final: 0.7232 (tm-30) REVERT: F 164 GLU cc_start: 0.7390 (pm20) cc_final: 0.7050 (pm20) REVERT: F 343 GLN cc_start: 0.7612 (mt0) cc_final: 0.7285 (pt0) REVERT: G 632 ASP cc_start: 0.7852 (t70) cc_final: 0.7490 (t0) REVERT: G 659 ASP cc_start: 0.8224 (m-30) cc_final: 0.7836 (t70) REVERT: G 661 LEU cc_start: 0.8924 (tp) cc_final: 0.8443 (mt) REVERT: H 6 GLN cc_start: 0.8145 (mt0) cc_final: 0.7929 (mt0) REVERT: H 43 GLN cc_start: 0.7705 (tp-100) cc_final: 0.7193 (mp10) REVERT: H 81 MET cc_start: 0.7785 (tmm) cc_final: 0.7477 (tmm) REVERT: I 20 ILE cc_start: 0.6996 (mt) cc_final: 0.6779 (mt) REVERT: I 36 SER cc_start: 0.9006 (m) cc_final: 0.8708 (t) REVERT: I 38 TYR cc_start: 0.8148 (m-80) cc_final: 0.7532 (m-80) REVERT: I 93 TYR cc_start: 0.9019 (t80) cc_final: 0.8740 (t80) REVERT: K 107 ASP cc_start: 0.7787 (t0) cc_final: 0.7559 (t0) REVERT: K 154 MET cc_start: 0.7557 (mtp) cc_final: 0.7240 (mtt) REVERT: K 162 THR cc_start: 0.8259 (m) cc_final: 0.8050 (p) REVERT: K 207 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7665 (tttp) REVERT: L 584 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7838 (mt-10) REVERT: L 632 ASP cc_start: 0.8052 (t70) cc_final: 0.7552 (t0) REVERT: M 70 MET cc_start: 0.8863 (mtm) cc_final: 0.8634 (mtm) REVERT: N 18 ILE cc_start: 0.6102 (tt) cc_final: 0.5888 (tp) REVERT: N 63 ARG cc_start: 0.6717 (mtp-110) cc_final: 0.6440 (ptm-80) outliers start: 54 outliers final: 30 residues processed: 459 average time/residue: 0.1513 time to fit residues: 106.5724 Evaluate side-chains 398 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 368 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 283 ILE Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain N residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 243 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 630 GLN C 6 GLN D 40 GLN D 62 ASN F 114 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 GLN I 6 GLN N 40 GLN N 41 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.159108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114498 restraints weight = 29984.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118424 restraints weight = 19323.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120941 restraints weight = 15051.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122480 restraints weight = 12989.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123429 restraints weight = 11901.450| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20565 Z= 0.157 Angle : 0.680 10.109 28092 Z= 0.345 Chirality : 0.046 0.345 3289 Planarity : 0.005 0.055 3480 Dihedral : 9.914 69.396 3794 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.46 % Favored : 95.17 % Rotamer: Outliers : 2.41 % Allowed : 14.48 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -1.08 (0.16), residues: 2466 helix: -1.19 (0.25), residues: 393 sheet: 0.01 (0.19), residues: 708 loop : -0.93 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 63 TYR 0.028 0.002 TYR I 51 PHE 0.013 0.002 PHE A 391 TRP 0.020 0.002 TRP F 45 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00364 (20467) covalent geometry : angle 0.66336 (27840) SS BOND : bond 0.00379 ( 42) SS BOND : angle 1.21957 ( 84) hydrogen bonds : bond 0.04308 ( 534) hydrogen bonds : angle 5.86238 ( 1419) link_ALPHA1-2 : bond 0.00711 ( 11) link_ALPHA1-2 : angle 2.13152 ( 33) link_ALPHA1-3 : bond 0.00945 ( 6) link_ALPHA1-3 : angle 1.71814 ( 18) link_ALPHA1-6 : bond 0.00659 ( 6) link_ALPHA1-6 : angle 1.75686 ( 18) link_BETA1-4 : bond 0.00450 ( 21) link_BETA1-4 : angle 2.05924 ( 63) link_NAG-ASN : bond 0.00105 ( 12) link_NAG-ASN : angle 1.46556 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 394 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7359 (t0) cc_final: 0.7040 (p0) REVERT: A 207 LYS cc_start: 0.7162 (tmtt) cc_final: 0.6592 (tmtt) REVERT: A 211 GLU cc_start: 0.7913 (tt0) cc_final: 0.7688 (pt0) REVERT: B 607 ASN cc_start: 0.8516 (t0) cc_final: 0.7712 (p0) REVERT: B 632 ASP cc_start: 0.8058 (t0) cc_final: 0.7560 (t0) REVERT: B 647 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6844 (mp0) REVERT: B 661 LEU cc_start: 0.8822 (tp) cc_final: 0.8356 (mt) REVERT: C 21 SER cc_start: 0.8194 (p) cc_final: 0.7896 (t) REVERT: C 43 GLN cc_start: 0.7112 (tp40) cc_final: 0.6686 (mp10) REVERT: D 23 THR cc_start: 0.7385 (p) cc_final: 0.7080 (t) REVERT: D 47 LYS cc_start: 0.7808 (tptp) cc_final: 0.7590 (tttm) REVERT: D 63 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6541 (ptm-80) REVERT: F 103 GLN cc_start: 0.7802 (mt0) cc_final: 0.7463 (tm-30) REVERT: F 114 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: F 164 GLU cc_start: 0.7261 (pm20) cc_final: 0.6937 (pm20) REVERT: G 629 LEU cc_start: 0.7331 (tt) cc_final: 0.7121 (tt) REVERT: G 632 ASP cc_start: 0.7893 (t70) cc_final: 0.7491 (t0) REVERT: G 661 LEU cc_start: 0.8732 (tp) cc_final: 0.8498 (mt) REVERT: H 38 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8153 (ttp80) REVERT: H 43 GLN cc_start: 0.7426 (tp-100) cc_final: 0.7180 (mp10) REVERT: H 81 MET cc_start: 0.7532 (tmm) cc_final: 0.7172 (tmm) REVERT: H 90 ASP cc_start: 0.8001 (m-30) cc_final: 0.7693 (m-30) REVERT: I 23 THR cc_start: 0.7340 (p) cc_final: 0.6936 (t) REVERT: I 36 SER cc_start: 0.9026 (m) cc_final: 0.8638 (t) REVERT: I 38 TYR cc_start: 0.8186 (m-80) cc_final: 0.7704 (m-80) REVERT: I 63 ARG cc_start: 0.6680 (mtp-110) cc_final: 0.6412 (ptm-80) REVERT: I 68 LYS cc_start: 0.7453 (tttt) cc_final: 0.7033 (tttp) REVERT: I 77 ILE cc_start: 0.7511 (tt) cc_final: 0.6243 (tt) REVERT: K 107 ASP cc_start: 0.7888 (t0) cc_final: 0.7634 (t0) REVERT: K 154 MET cc_start: 0.7750 (mtp) cc_final: 0.7529 (mtm) REVERT: K 162 THR cc_start: 0.8316 (m) cc_final: 0.8089 (p) REVERT: K 207 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7597 (tttp) REVERT: L 584 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7688 (mt-10) REVERT: L 607 ASN cc_start: 0.8800 (t0) cc_final: 0.8179 (m-40) REVERT: L 632 ASP cc_start: 0.8056 (t70) cc_final: 0.7579 (t0) REVERT: L 655 LYS cc_start: 0.8544 (tppp) cc_final: 0.8309 (ttmt) REVERT: M 21 SER cc_start: 0.7953 (p) cc_final: 0.7547 (t) REVERT: M 43 GLN cc_start: 0.6951 (tp-100) cc_final: 0.6499 (mp10) REVERT: M 70 MET cc_start: 0.8916 (mtm) cc_final: 0.8515 (mtm) outliers start: 52 outliers final: 35 residues processed: 426 average time/residue: 0.1562 time to fit residues: 102.3408 Evaluate side-chains 394 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 357 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 91 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 245 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 92 optimal weight: 0.0040 chunk 150 optimal weight: 5.9990 overall best weight: 2.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN D 40 GLN F 114 GLN F 352 HIS ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 HIS L 590 GLN N 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.161739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126124 restraints weight = 29038.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125145 restraints weight = 25856.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126409 restraints weight = 31167.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127360 restraints weight = 21690.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127870 restraints weight = 19532.194| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20565 Z= 0.163 Angle : 0.666 10.011 28092 Z= 0.337 Chirality : 0.046 0.342 3289 Planarity : 0.004 0.052 3480 Dihedral : 8.875 64.740 3794 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.62 % Favored : 95.05 % Rotamer: Outliers : 3.06 % Allowed : 16.48 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -0.99 (0.16), residues: 2466 helix: -1.01 (0.26), residues: 393 sheet: 0.20 (0.20), residues: 657 loop : -0.95 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 63 TYR 0.028 0.002 TYR I 51 PHE 0.015 0.002 PHE D 64 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00382 (20467) covalent geometry : angle 0.64945 (27840) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.42978 ( 84) hydrogen bonds : bond 0.03943 ( 534) hydrogen bonds : angle 5.61822 ( 1419) link_ALPHA1-2 : bond 0.00642 ( 11) link_ALPHA1-2 : angle 2.05010 ( 33) link_ALPHA1-3 : bond 0.00861 ( 6) link_ALPHA1-3 : angle 1.79016 ( 18) link_ALPHA1-6 : bond 0.00649 ( 6) link_ALPHA1-6 : angle 1.74345 ( 18) link_BETA1-4 : bond 0.00459 ( 21) link_BETA1-4 : angle 1.95271 ( 63) link_NAG-ASN : bond 0.00129 ( 12) link_NAG-ASN : angle 1.40893 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 371 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7435 (t0) cc_final: 0.7108 (p0) REVERT: A 207 LYS cc_start: 0.7236 (tmtt) cc_final: 0.6604 (tmtt) REVERT: A 211 GLU cc_start: 0.7975 (tt0) cc_final: 0.7701 (pt0) REVERT: B 607 ASN cc_start: 0.8446 (t0) cc_final: 0.7813 (p0) REVERT: B 632 ASP cc_start: 0.7939 (t70) cc_final: 0.7442 (t0) REVERT: B 647 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6682 (mt-10) REVERT: B 661 LEU cc_start: 0.8801 (tp) cc_final: 0.8322 (mt) REVERT: C 43 GLN cc_start: 0.6923 (tp40) cc_final: 0.6678 (mp10) REVERT: D 23 THR cc_start: 0.7189 (p) cc_final: 0.6921 (t) REVERT: D 63 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6577 (ptm-80) REVERT: F 57 ASP cc_start: 0.6629 (m-30) cc_final: 0.6218 (p0) REVERT: G 632 ASP cc_start: 0.7751 (t70) cc_final: 0.7378 (t0) REVERT: H 21 SER cc_start: 0.7708 (p) cc_final: 0.7485 (t) REVERT: H 81 MET cc_start: 0.7506 (tmm) cc_final: 0.7191 (tmm) REVERT: H 90 ASP cc_start: 0.8196 (m-30) cc_final: 0.7861 (m-30) REVERT: I 23 THR cc_start: 0.7317 (p) cc_final: 0.6943 (t) REVERT: I 36 SER cc_start: 0.8941 (m) cc_final: 0.8716 (t) REVERT: I 68 LYS cc_start: 0.7379 (tttt) cc_final: 0.6965 (tttp) REVERT: I 77 ILE cc_start: 0.7199 (tt) cc_final: 0.6642 (tt) REVERT: I 84 ASP cc_start: 0.6659 (m-30) cc_final: 0.6094 (m-30) REVERT: I 106 LYS cc_start: 0.7993 (tppt) cc_final: 0.7788 (tppt) REVERT: K 57 ASP cc_start: 0.7531 (t0) cc_final: 0.7127 (p0) REVERT: K 162 THR cc_start: 0.8314 (m) cc_final: 0.8098 (p) REVERT: K 207 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7654 (tttp) REVERT: L 584 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7604 (mt-10) REVERT: L 607 ASN cc_start: 0.8688 (t0) cc_final: 0.8209 (m-40) REVERT: L 632 ASP cc_start: 0.7924 (t70) cc_final: 0.7494 (t0) REVERT: M 13 LYS cc_start: 0.8133 (pptt) cc_final: 0.7274 (mmmt) REVERT: M 21 SER cc_start: 0.8003 (p) cc_final: 0.7676 (t) REVERT: M 43 GLN cc_start: 0.7038 (tp-100) cc_final: 0.6649 (mp10) REVERT: M 70 MET cc_start: 0.8989 (mtm) cc_final: 0.8663 (mtm) outliers start: 66 outliers final: 46 residues processed: 413 average time/residue: 0.1566 time to fit residues: 99.6338 Evaluate side-chains 394 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 347 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 54 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 23 optimal weight: 0.5980 chunk 159 optimal weight: 40.0000 chunk 120 optimal weight: 7.9990 chunk 236 optimal weight: 50.0000 chunk 214 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 160 optimal weight: 30.0000 chunk 92 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 616 ASN D 40 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN K 362 ASN L 658 GLN N 6 GLN N 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123601 restraints weight = 28954.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122557 restraints weight = 26029.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123484 restraints weight = 30699.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125375 restraints weight = 22752.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125630 restraints weight = 19632.034| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20565 Z= 0.179 Angle : 0.667 12.036 28092 Z= 0.338 Chirality : 0.046 0.339 3289 Planarity : 0.004 0.049 3480 Dihedral : 8.206 59.798 3794 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.99 % Favored : 94.65 % Rotamer: Outliers : 2.83 % Allowed : 18.06 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -1.01 (0.16), residues: 2466 helix: -0.94 (0.26), residues: 393 sheet: 0.24 (0.20), residues: 657 loop : -1.02 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 617 TYR 0.030 0.002 TYR I 51 PHE 0.012 0.002 PHE A 376 TRP 0.015 0.002 TRP F 45 HIS 0.005 0.001 HIS K 330 Details of bonding type rmsd covalent geometry : bond 0.00422 (20467) covalent geometry : angle 0.65030 (27840) SS BOND : bond 0.00534 ( 42) SS BOND : angle 1.43836 ( 84) hydrogen bonds : bond 0.04008 ( 534) hydrogen bonds : angle 5.55747 ( 1419) link_ALPHA1-2 : bond 0.00611 ( 11) link_ALPHA1-2 : angle 2.03020 ( 33) link_ALPHA1-3 : bond 0.00905 ( 6) link_ALPHA1-3 : angle 1.89955 ( 18) link_ALPHA1-6 : bond 0.00627 ( 6) link_ALPHA1-6 : angle 1.74462 ( 18) link_BETA1-4 : bond 0.00436 ( 21) link_BETA1-4 : angle 1.80999 ( 63) link_NAG-ASN : bond 0.00167 ( 12) link_NAG-ASN : angle 1.44290 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 366 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7372 (t0) cc_final: 0.7101 (p0) REVERT: A 207 LYS cc_start: 0.7039 (tmtt) cc_final: 0.6496 (tmtt) REVERT: B 632 ASP cc_start: 0.7812 (t70) cc_final: 0.7325 (t0) REVERT: B 661 LEU cc_start: 0.8723 (tp) cc_final: 0.8198 (mt) REVERT: C 43 GLN cc_start: 0.7119 (tp40) cc_final: 0.6881 (mp10) REVERT: C 48 MET cc_start: 0.7922 (mtp) cc_final: 0.7655 (mtm) REVERT: C 86 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8040 (tt) REVERT: D 63 ARG cc_start: 0.6603 (mtp-110) cc_final: 0.6258 (ptm-80) REVERT: F 57 ASP cc_start: 0.6881 (m-30) cc_final: 0.6531 (p0) REVERT: G 632 ASP cc_start: 0.7563 (t70) cc_final: 0.7219 (t0) REVERT: H 73 ASP cc_start: 0.7993 (m-30) cc_final: 0.7754 (m-30) REVERT: H 81 MET cc_start: 0.7517 (tmm) cc_final: 0.7177 (tmm) REVERT: I 23 THR cc_start: 0.7408 (p) cc_final: 0.7055 (t) REVERT: K 57 ASP cc_start: 0.7495 (t0) cc_final: 0.7026 (p0) REVERT: K 107 ASP cc_start: 0.7834 (t0) cc_final: 0.7632 (t0) REVERT: K 162 THR cc_start: 0.8369 (m) cc_final: 0.8136 (p) REVERT: K 207 LYS cc_start: 0.7794 (mtpp) cc_final: 0.7511 (tttp) REVERT: L 584 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7700 (mt-10) REVERT: L 607 ASN cc_start: 0.8671 (t0) cc_final: 0.8290 (m-40) REVERT: L 659 ASP cc_start: 0.7951 (m-30) cc_final: 0.7744 (t70) REVERT: M 13 LYS cc_start: 0.8152 (pptt) cc_final: 0.7357 (mmmt) REVERT: M 70 MET cc_start: 0.8996 (mtm) cc_final: 0.8709 (mtm) outliers start: 61 outliers final: 51 residues processed: 403 average time/residue: 0.1557 time to fit residues: 96.9155 Evaluate side-chains 375 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 54 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 210 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN B 540 GLN D 40 GLN D 62 ASN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN L 616 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.162432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127564 restraints weight = 28785.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126268 restraints weight = 26419.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127204 restraints weight = 29072.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129805 restraints weight = 21985.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129966 restraints weight = 17593.941| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20565 Z= 0.176 Angle : 0.687 20.883 28092 Z= 0.341 Chirality : 0.048 0.798 3289 Planarity : 0.004 0.048 3480 Dihedral : 7.887 59.476 3794 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.70 % Favored : 94.93 % Rotamer: Outliers : 3.62 % Allowed : 18.71 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -0.99 (0.16), residues: 2466 helix: -0.88 (0.26), residues: 393 sheet: 0.28 (0.20), residues: 657 loop : -1.05 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 38 TYR 0.028 0.002 TYR I 51 PHE 0.011 0.002 PHE K 376 TRP 0.022 0.001 TRP B 614 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00416 (20467) covalent geometry : angle 0.65532 (27840) SS BOND : bond 0.00348 ( 42) SS BOND : angle 1.41548 ( 84) hydrogen bonds : bond 0.03892 ( 534) hydrogen bonds : angle 5.46414 ( 1419) link_ALPHA1-2 : bond 0.00584 ( 11) link_ALPHA1-2 : angle 2.05641 ( 33) link_ALPHA1-3 : bond 0.00789 ( 6) link_ALPHA1-3 : angle 1.74791 ( 18) link_ALPHA1-6 : bond 0.00641 ( 6) link_ALPHA1-6 : angle 1.75297 ( 18) link_BETA1-4 : bond 0.00427 ( 21) link_BETA1-4 : angle 1.78545 ( 63) link_NAG-ASN : bond 0.00644 ( 12) link_NAG-ASN : angle 4.36145 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 356 time to evaluate : 0.817 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: A 207 LYS cc_start: 0.7083 (tmtt) cc_final: 0.6617 (tmtt) REVERT: B 632 ASP cc_start: 0.7709 (t70) cc_final: 0.7284 (t0) REVERT: B 661 LEU cc_start: 0.8768 (tp) cc_final: 0.8313 (mt) REVERT: C 83 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6917 (tt) REVERT: C 90 ASP cc_start: 0.8005 (m-30) cc_final: 0.7646 (m-30) REVERT: F 57 ASP cc_start: 0.6947 (m-30) cc_final: 0.6705 (p0) REVERT: G 632 ASP cc_start: 0.7405 (t70) cc_final: 0.7088 (t0) REVERT: H 13 LYS cc_start: 0.8226 (pptt) cc_final: 0.7328 (mmmt) REVERT: H 73 ASP cc_start: 0.7881 (m-30) cc_final: 0.7652 (m-30) REVERT: H 81 MET cc_start: 0.7443 (tmm) cc_final: 0.7082 (tmm) REVERT: K 57 ASP cc_start: 0.7463 (t0) cc_final: 0.7108 (p0) REVERT: K 162 THR cc_start: 0.8300 (m) cc_final: 0.8078 (p) REVERT: K 207 LYS cc_start: 0.7802 (mtpp) cc_final: 0.7559 (tttp) REVERT: L 607 ASN cc_start: 0.8616 (t0) cc_final: 0.8340 (m-40) REVERT: M 70 MET cc_start: 0.9049 (mtm) cc_final: 0.8675 (mtm) outliers start: 78 outliers final: 58 residues processed: 405 average time/residue: 0.1525 time to fit residues: 95.5964 Evaluate side-chains 390 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 181 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN F 343 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125540 restraints weight = 28990.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124615 restraints weight = 25394.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125804 restraints weight = 30311.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126804 restraints weight = 21330.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127245 restraints weight = 19340.298| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20565 Z= 0.224 Angle : 0.731 19.028 28092 Z= 0.362 Chirality : 0.047 0.336 3289 Planarity : 0.005 0.065 3480 Dihedral : 7.757 59.281 3794 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.23 % Favored : 94.40 % Rotamer: Outliers : 3.62 % Allowed : 19.55 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -1.11 (0.16), residues: 2466 helix: -0.88 (0.26), residues: 393 sheet: 0.24 (0.21), residues: 621 loop : -1.15 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 617 TYR 0.030 0.002 TYR I 51 PHE 0.015 0.002 PHE F 376 TRP 0.021 0.002 TRP B 614 HIS 0.005 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00534 (20467) covalent geometry : angle 0.70209 (27840) SS BOND : bond 0.00376 ( 42) SS BOND : angle 1.51926 ( 84) hydrogen bonds : bond 0.04129 ( 534) hydrogen bonds : angle 5.52154 ( 1419) link_ALPHA1-2 : bond 0.00584 ( 11) link_ALPHA1-2 : angle 2.08004 ( 33) link_ALPHA1-3 : bond 0.00862 ( 6) link_ALPHA1-3 : angle 1.79114 ( 18) link_ALPHA1-6 : bond 0.00586 ( 6) link_ALPHA1-6 : angle 1.81222 ( 18) link_BETA1-4 : bond 0.00437 ( 21) link_BETA1-4 : angle 1.83454 ( 63) link_NAG-ASN : bond 0.01229 ( 12) link_NAG-ASN : angle 4.16146 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 344 time to evaluate : 0.839 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: A 104 MET cc_start: 0.8420 (ttt) cc_final: 0.8051 (ttt) REVERT: A 207 LYS cc_start: 0.7163 (tmtt) cc_final: 0.6655 (tmtt) REVERT: B 607 ASN cc_start: 0.8469 (t0) cc_final: 0.8172 (m-40) REVERT: B 632 ASP cc_start: 0.7842 (t70) cc_final: 0.7379 (t0) REVERT: B 659 ASP cc_start: 0.8129 (m-30) cc_final: 0.7887 (t70) REVERT: B 661 LEU cc_start: 0.8891 (tp) cc_final: 0.8371 (mt) REVERT: C 83 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6775 (tt) REVERT: D 42 PRO cc_start: 0.8480 (Cg_exo) cc_final: 0.8247 (Cg_endo) REVERT: F 104 MET cc_start: 0.8463 (ttt) cc_final: 0.8150 (ttt) REVERT: F 112 TRP cc_start: 0.8140 (t-100) cc_final: 0.7919 (t-100) REVERT: G 632 ASP cc_start: 0.7587 (t70) cc_final: 0.7227 (t0) REVERT: H 13 LYS cc_start: 0.8269 (pptt) cc_final: 0.7417 (mmmt) REVERT: H 73 ASP cc_start: 0.8027 (m-30) cc_final: 0.7806 (m-30) REVERT: H 81 MET cc_start: 0.7486 (tmm) cc_final: 0.7129 (tmm) REVERT: K 162 THR cc_start: 0.8424 (m) cc_final: 0.8186 (p) REVERT: K 207 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7509 (tptp) REVERT: L 607 ASN cc_start: 0.8701 (t0) cc_final: 0.8382 (m-40) REVERT: L 629 LEU cc_start: 0.7414 (tt) cc_final: 0.7008 (mt) REVERT: M 90 ASP cc_start: 0.7989 (m-30) cc_final: 0.7651 (m-30) outliers start: 78 outliers final: 70 residues processed: 394 average time/residue: 0.1537 time to fit residues: 93.5727 Evaluate side-chains 399 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 328 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 36 SER Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 224 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN G 630 GLN I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.164112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128976 restraints weight = 29022.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127948 restraints weight = 26748.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129733 restraints weight = 29626.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130648 restraints weight = 19852.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131437 restraints weight = 18311.522| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20565 Z= 0.127 Angle : 0.664 18.387 28092 Z= 0.331 Chirality : 0.045 0.341 3289 Planarity : 0.004 0.046 3480 Dihedral : 7.053 55.943 3794 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.30 % Favored : 95.38 % Rotamer: Outliers : 2.65 % Allowed : 20.66 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -1.02 (0.16), residues: 2466 helix: -0.88 (0.25), residues: 411 sheet: 0.33 (0.21), residues: 624 loop : -1.08 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 617 TYR 0.031 0.001 TYR I 51 PHE 0.010 0.001 PHE F 391 TRP 0.018 0.001 TRP G 614 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00286 (20467) covalent geometry : angle 0.63810 (27840) SS BOND : bond 0.00260 ( 42) SS BOND : angle 1.16709 ( 84) hydrogen bonds : bond 0.03592 ( 534) hydrogen bonds : angle 5.24331 ( 1419) link_ALPHA1-2 : bond 0.00606 ( 11) link_ALPHA1-2 : angle 2.07625 ( 33) link_ALPHA1-3 : bond 0.01026 ( 6) link_ALPHA1-3 : angle 1.59881 ( 18) link_ALPHA1-6 : bond 0.00774 ( 6) link_ALPHA1-6 : angle 1.66614 ( 18) link_BETA1-4 : bond 0.00426 ( 21) link_BETA1-4 : angle 1.56567 ( 63) link_NAG-ASN : bond 0.01047 ( 12) link_NAG-ASN : angle 3.89244 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 349 time to evaluate : 0.794 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: A 104 MET cc_start: 0.8330 (ttt) cc_final: 0.7939 (ttt) REVERT: A 207 LYS cc_start: 0.7172 (tmtt) cc_final: 0.6719 (tmtt) REVERT: B 632 ASP cc_start: 0.7688 (t70) cc_final: 0.7231 (t0) REVERT: B 661 LEU cc_start: 0.8807 (tp) cc_final: 0.8259 (mt) REVERT: C 83 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6710 (tt) REVERT: D 23 THR cc_start: 0.7187 (p) cc_final: 0.6843 (t) REVERT: D 42 PRO cc_start: 0.8437 (Cg_exo) cc_final: 0.8219 (Cg_endo) REVERT: F 283 ILE cc_start: 0.8669 (mt) cc_final: 0.8439 (tt) REVERT: G 632 ASP cc_start: 0.7335 (t70) cc_final: 0.7032 (t0) REVERT: H 13 LYS cc_start: 0.8137 (pptt) cc_final: 0.7342 (mmmt) REVERT: H 73 ASP cc_start: 0.7897 (m-30) cc_final: 0.7683 (m-30) REVERT: H 81 MET cc_start: 0.7372 (tmm) cc_final: 0.6970 (tmm) REVERT: K 57 ASP cc_start: 0.7254 (m-30) cc_final: 0.6626 (p0) REVERT: K 162 THR cc_start: 0.8235 (m) cc_final: 0.8026 (p) REVERT: K 207 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7604 (tptp) REVERT: L 607 ASN cc_start: 0.8588 (t0) cc_final: 0.8327 (m-40) REVERT: L 629 LEU cc_start: 0.7295 (tt) cc_final: 0.7039 (mt) REVERT: M 13 LYS cc_start: 0.8117 (pptt) cc_final: 0.7305 (mmmt) REVERT: M 90 ASP cc_start: 0.8018 (m-30) cc_final: 0.7746 (m-30) outliers start: 57 outliers final: 41 residues processed: 390 average time/residue: 0.1615 time to fit residues: 96.1699 Evaluate side-chains 376 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 19 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 218 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 146 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 chunk 174 optimal weight: 30.0000 overall best weight: 1.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN M 6 GLN N 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127529 restraints weight = 28785.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126189 restraints weight = 28122.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128184 restraints weight = 27595.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129352 restraints weight = 19372.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129742 restraints weight = 18189.707| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20565 Z= 0.135 Angle : 0.671 18.803 28092 Z= 0.334 Chirality : 0.045 0.339 3289 Planarity : 0.004 0.048 3480 Dihedral : 6.802 56.782 3794 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.87 % Favored : 94.81 % Rotamer: Outliers : 2.32 % Allowed : 20.94 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -0.94 (0.16), residues: 2466 helix: -0.77 (0.25), residues: 411 sheet: 0.38 (0.21), residues: 621 loop : -1.04 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 38 TYR 0.031 0.001 TYR I 51 PHE 0.010 0.001 PHE F 391 TRP 0.026 0.002 TRP G 628 HIS 0.003 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00309 (20467) covalent geometry : angle 0.64525 (27840) SS BOND : bond 0.00271 ( 42) SS BOND : angle 1.24730 ( 84) hydrogen bonds : bond 0.03628 ( 534) hydrogen bonds : angle 5.19157 ( 1419) link_ALPHA1-2 : bond 0.00605 ( 11) link_ALPHA1-2 : angle 2.08448 ( 33) link_ALPHA1-3 : bond 0.00931 ( 6) link_ALPHA1-3 : angle 1.52317 ( 18) link_ALPHA1-6 : bond 0.00779 ( 6) link_ALPHA1-6 : angle 1.67581 ( 18) link_BETA1-4 : bond 0.00416 ( 21) link_BETA1-4 : angle 1.51741 ( 63) link_NAG-ASN : bond 0.00923 ( 12) link_NAG-ASN : angle 3.94211 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 346 time to evaluate : 0.823 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: A 57 ASP cc_start: 0.7108 (m-30) cc_final: 0.6779 (p0) REVERT: A 104 MET cc_start: 0.8446 (ttt) cc_final: 0.8098 (ttt) REVERT: B 607 ASN cc_start: 0.8492 (t0) cc_final: 0.8047 (m-40) REVERT: B 632 ASP cc_start: 0.8043 (t70) cc_final: 0.7528 (t0) REVERT: B 661 LEU cc_start: 0.8736 (tp) cc_final: 0.8228 (mt) REVERT: C 83 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6484 (tt) REVERT: D 23 THR cc_start: 0.7162 (p) cc_final: 0.6775 (t) REVERT: D 42 PRO cc_start: 0.8555 (Cg_exo) cc_final: 0.8266 (Cg_endo) REVERT: F 283 ILE cc_start: 0.8764 (mt) cc_final: 0.8444 (tt) REVERT: G 632 ASP cc_start: 0.7624 (t70) cc_final: 0.7317 (t0) REVERT: H 13 LYS cc_start: 0.8233 (pptt) cc_final: 0.7395 (mmmt) REVERT: H 73 ASP cc_start: 0.8201 (m-30) cc_final: 0.7941 (m-30) REVERT: H 81 MET cc_start: 0.7589 (tmm) cc_final: 0.7200 (tmm) REVERT: K 57 ASP cc_start: 0.7471 (m-30) cc_final: 0.6574 (p0) REVERT: K 207 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7561 (tptp) REVERT: L 592 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9022 (tt) REVERT: L 607 ASN cc_start: 0.8688 (t0) cc_final: 0.8337 (m-40) REVERT: L 629 LEU cc_start: 0.7257 (tt) cc_final: 0.7006 (mt) REVERT: M 13 LYS cc_start: 0.8316 (pptt) cc_final: 0.7513 (mmmt) REVERT: M 90 ASP cc_start: 0.7980 (m-30) cc_final: 0.7687 (m-30) outliers start: 50 outliers final: 43 residues processed: 383 average time/residue: 0.1572 time to fit residues: 92.5310 Evaluate side-chains 373 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 328 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain N residue 39 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 240 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN K 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.161764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125165 restraints weight = 29205.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123352 restraints weight = 28165.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125801 restraints weight = 27388.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126330 restraints weight = 19228.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126776 restraints weight = 18871.800| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20565 Z= 0.183 Angle : 0.704 18.753 28092 Z= 0.351 Chirality : 0.047 0.337 3289 Planarity : 0.004 0.045 3480 Dihedral : 6.865 57.668 3794 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.19 % Favored : 94.48 % Rotamer: Outliers : 2.55 % Allowed : 20.98 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -1.01 (0.16), residues: 2466 helix: -0.74 (0.25), residues: 411 sheet: 0.31 (0.21), residues: 621 loop : -1.10 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 38 TYR 0.033 0.002 TYR L 638 PHE 0.012 0.002 PHE F 376 TRP 0.037 0.002 TRP G 628 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00432 (20467) covalent geometry : angle 0.67848 (27840) SS BOND : bond 0.00361 ( 42) SS BOND : angle 1.36461 ( 84) hydrogen bonds : bond 0.03890 ( 534) hydrogen bonds : angle 5.27309 ( 1419) link_ALPHA1-2 : bond 0.00594 ( 11) link_ALPHA1-2 : angle 2.09036 ( 33) link_ALPHA1-3 : bond 0.00858 ( 6) link_ALPHA1-3 : angle 1.54112 ( 18) link_ALPHA1-6 : bond 0.00714 ( 6) link_ALPHA1-6 : angle 1.73199 ( 18) link_BETA1-4 : bond 0.00407 ( 21) link_BETA1-4 : angle 1.59742 ( 63) link_NAG-ASN : bond 0.00951 ( 12) link_NAG-ASN : angle 3.96698 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 0.819 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: A 57 ASP cc_start: 0.7104 (m-30) cc_final: 0.6823 (p0) REVERT: A 104 MET cc_start: 0.8394 (ttt) cc_final: 0.7997 (ttt) REVERT: B 607 ASN cc_start: 0.8474 (t0) cc_final: 0.8216 (m-40) REVERT: B 632 ASP cc_start: 0.7940 (t70) cc_final: 0.7494 (t0) REVERT: B 655 LYS cc_start: 0.8356 (ttmt) cc_final: 0.8086 (ttmt) REVERT: B 661 LEU cc_start: 0.8809 (tp) cc_final: 0.8315 (mt) REVERT: C 83 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6519 (tt) REVERT: D 42 PRO cc_start: 0.8526 (Cg_exo) cc_final: 0.8263 (Cg_endo) REVERT: F 283 ILE cc_start: 0.8733 (mt) cc_final: 0.8444 (tt) REVERT: G 591 GLN cc_start: 0.8388 (tt0) cc_final: 0.8178 (tt0) REVERT: H 3 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7951 (tp40) REVERT: H 13 LYS cc_start: 0.8165 (pptt) cc_final: 0.7430 (mmmt) REVERT: H 73 ASP cc_start: 0.8083 (m-30) cc_final: 0.7820 (m-30) REVERT: H 81 MET cc_start: 0.7491 (tmm) cc_final: 0.7068 (tmm) REVERT: K 57 ASP cc_start: 0.7373 (m-30) cc_final: 0.6599 (p0) REVERT: K 112 TRP cc_start: 0.7995 (t-100) cc_final: 0.7754 (t-100) REVERT: K 207 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7481 (tptp) REVERT: L 545 LEU cc_start: 0.3782 (mt) cc_final: 0.2965 (pt) REVERT: L 569 THR cc_start: 0.2573 (OUTLIER) cc_final: 0.2269 (t) REVERT: L 607 ASN cc_start: 0.8671 (t0) cc_final: 0.8358 (m-40) REVERT: L 629 LEU cc_start: 0.7348 (tt) cc_final: 0.7060 (mt) REVERT: M 13 LYS cc_start: 0.8260 (pptt) cc_final: 0.7508 (mmmt) REVERT: M 90 ASP cc_start: 0.8112 (m-30) cc_final: 0.7852 (m-30) outliers start: 55 outliers final: 48 residues processed: 377 average time/residue: 0.1580 time to fit residues: 90.7177 Evaluate side-chains 383 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 333 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 77 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.162018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126918 restraints weight = 29002.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125381 restraints weight = 26169.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126339 restraints weight = 28927.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129094 restraints weight = 21771.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.129447 restraints weight = 16885.052| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20565 Z= 0.164 Angle : 0.699 18.723 28092 Z= 0.346 Chirality : 0.046 0.338 3289 Planarity : 0.004 0.044 3480 Dihedral : 6.753 57.320 3794 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.79 % Favored : 94.89 % Rotamer: Outliers : 2.60 % Allowed : 21.08 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -1.07 (0.16), residues: 2466 helix: -0.71 (0.26), residues: 408 sheet: 0.18 (0.21), residues: 639 loop : -1.14 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 617 TYR 0.031 0.002 TYR I 51 PHE 0.010 0.001 PHE F 376 TRP 0.031 0.002 TRP B 614 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00385 (20467) covalent geometry : angle 0.67426 (27840) SS BOND : bond 0.00326 ( 42) SS BOND : angle 1.28294 ( 84) hydrogen bonds : bond 0.03814 ( 534) hydrogen bonds : angle 5.21866 ( 1419) link_ALPHA1-2 : bond 0.00595 ( 11) link_ALPHA1-2 : angle 2.09809 ( 33) link_ALPHA1-3 : bond 0.00909 ( 6) link_ALPHA1-3 : angle 1.47841 ( 18) link_ALPHA1-6 : bond 0.00761 ( 6) link_ALPHA1-6 : angle 1.69690 ( 18) link_BETA1-4 : bond 0.00391 ( 21) link_BETA1-4 : angle 1.54479 ( 63) link_NAG-ASN : bond 0.00921 ( 12) link_NAG-ASN : angle 3.92821 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3651.74 seconds wall clock time: 64 minutes 5.79 seconds (3845.79 seconds total)