Starting phenix.real_space_refine (version: dev) on Mon May 16 15:59:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/05_2022/6cde_7459_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/05_2022/6cde_7459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/05_2022/6cde_7459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/05_2022/6cde_7459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/05_2022/6cde_7459_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/05_2022/6cde_7459_neut.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.093 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "h TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 108": "NH1" <-> "NH2" Residue "M ARG 30": "NH1" <-> "NH2" Residue "M TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "Q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 108": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 52": "NH1" <-> "NH2" Residue "q ARG 61": "NH1" <-> "NH2" Residue "q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 52": "NH1" <-> "NH2" Residue "5 ARG 61": "NH1" <-> "NH2" Residue "5 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 32973 Number of models: 1 Model: "" Number of chains: 30 Chain: "h" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "l" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 107, 'PCIS': 2} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "R" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 98, 'PCIS': 1} Chain: "Q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "D" 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 breaks: 1 Chain: "C" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 107, 'PCIS': 2} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "r" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 98, 'PCIS': 1} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "d" 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 breaks: 1 Chain: "c" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "7" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "8" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "6" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 98, 'PCIS': 1} Chain: "5" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "1" 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 breaks: 1 Chain: "2" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "3" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "4" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 107, 'PCIS': 2} Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 92 Unusual residues: {'BMA': 2, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 833 Unusual residues: {'BMA': 11, 'NAG': 32, 'MAN': 24} Classifications: {'undetermined': 67} Link IDs: {None: 66} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 67 Chain: "d" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 92 Unusual residues: {'BMA': 2, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 833 Unusual residues: {'BMA': 11, 'NAG': 32, 'MAN': 24} Classifications: {'undetermined': 67} Link IDs: {None: 66} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 67 Chain: "1" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 92 Unusual residues: {'BMA': 2, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 7 Chain: "2" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 833 Unusual residues: {'BMA': 11, 'NAG': 32, 'MAN': 24} Classifications: {'undetermined': 67} Link IDs: {None: 66} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 67 Time building chain proxies: 18.36, per 1000 atoms: 0.56 Number of scatterers: 32973 At special positions: 0 Unit cell: (163.24, 159, 154.76, 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 177 16.00 O 6816 8.00 N 5319 7.00 C 20661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.13 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.09 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.19 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 87 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100A" distance=2.16 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.34 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.13 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.09 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 95 " distance=2.25 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 87 " distance=2.05 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.16 Simple disulfide: pdb=" SG CYS d 598 " - pdb=" SG CYS d 604 " distance=2.02 Simple disulfide: pdb=" SG CYS d 605 " - pdb=" SG CYS c 501 " distance=2.03 Simple disulfide: pdb=" SG CYS c 54 " - pdb=" SG CYS c 74 " distance=2.27 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 126 " - pdb=" SG CYS c 196 " distance=2.02 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.03 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.02 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.03 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.02 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.03 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 22 " - pdb=" SG CYS 7 95 " distance=2.40 Simple disulfide: pdb=" SG CYS 8 23 " - pdb=" SG CYS 8 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 87 " distance=2.05 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 98 " - pdb=" SG CYS 5 100A" distance=2.17 Simple disulfide: pdb=" SG CYS 1 598 " - pdb=" SG CYS 1 604 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 605 " - pdb=" SG CYS 2 501 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.42 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.13 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM31510 O5 NAG c 624 .*. O " rejected from bonding due to valence issues. Atom "HETATM32435 O5 NAG 2 624 .*. O " rejected from bonding due to valence issues. Atom "HETATM30585 O5 NAG C 624 .*. O " rejected from bonding due to valence issues. Atom "HETATM31333 O5 NAG c 609 .*. O " rejected from bonding due to valence issues. Atom "HETATM30408 O5 NAG C 609 .*. O " rejected from bonding due to valence issues. Atom "HETATM32258 O5 NAG 2 609 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN 2 612 " - " MAN 2 614 " " MAN 2 619 " - " MAN 2 621 " " MAN 2 621 " - " MAN 2 623 " " MAN 2 634 " - " MAN 2 636 " " MAN 2 637 " - " MAN 2 638 " " MAN 2 647 " - " MAN 2 649 " " MAN 2 650 " - " MAN 2 652 " " MAN C 612 " - " MAN C 614 " " MAN C 619 " - " MAN C 621 " " MAN C 621 " - " MAN C 623 " " MAN C 634 " - " MAN C 636 " " MAN C 637 " - " MAN C 638 " " MAN C 647 " - " MAN C 649 " " MAN C 650 " - " MAN C 652 " " MAN c 612 " - " MAN c 614 " " MAN c 619 " - " MAN c 621 " " MAN c 621 " - " MAN c 623 " " MAN c 634 " - " MAN c 636 " " MAN c 637 " - " MAN c 638 " " MAN c 647 " - " MAN c 649 " " MAN c 650 " - " MAN c 652 " ALPHA1-3 " BMA 2 607 " - " MAN 2 608 " " BMA 2 611 " - " MAN 2 612 " " BMA 2 618 " - " MAN 2 619 " " MAN 2 620 " - " MAN 2 622 " " BMA 2 628 " - " MAN 2 629 " " BMA 2 633 " - " MAN 2 634 " " MAN 2 635 " - " MAN 2 637 " " BMA 2 646 " - " MAN 2 647 " " MAN 2 648 " - " MAN 2 650 " " BMA C 607 " - " MAN C 608 " " BMA C 611 " - " MAN C 612 " " BMA C 618 " - " MAN C 619 " " MAN C 620 " - " MAN C 622 " " BMA C 628 " - " MAN C 629 " " BMA C 633 " - " MAN C 634 " " MAN C 635 " - " MAN C 637 " " BMA C 646 " - " MAN C 647 " " MAN C 648 " - " MAN C 650 " " BMA c 607 " - " MAN c 608 " " BMA c 611 " - " MAN c 612 " " BMA c 618 " - " MAN c 619 " " MAN c 620 " - " MAN c 622 " " BMA c 628 " - " MAN c 629 " " BMA c 633 " - " MAN c 634 " " MAN c 635 " - " MAN c 637 " " BMA c 646 " - " MAN c 647 " " MAN c 648 " - " MAN c 650 " ALPHA1-6 " BMA 2 611 " - " MAN 2 613 " " BMA 2 618 " - " MAN 2 620 " " BMA 2 628 " - " MAN 2 630 " " BMA 2 633 " - " MAN 2 635 " " BMA 2 646 " - " MAN 2 648 " " MAN 2 648 " - " MAN 2 651 " " BMA 2 660 " - " MAN 2 661 " " BMA C 611 " - " MAN C 613 " " BMA C 618 " - " MAN C 620 " " BMA C 628 " - " MAN C 630 " " BMA C 633 " - " MAN C 635 " " BMA C 646 " - " MAN C 648 " " MAN C 648 " - " MAN C 651 " " BMA C 660 " - " MAN C 661 " " BMA c 611 " - " MAN c 613 " " BMA c 618 " - " MAN c 620 " " BMA c 628 " - " MAN c 630 " " BMA c 633 " - " MAN c 635 " " BMA c 646 " - " MAN c 648 " " MAN c 648 " - " MAN c 651 " " BMA c 660 " - " MAN c 661 " BETA1-4 " NAG 1 702 " - " NAG 1 703 " " NAG 1 703 " - " BMA 1 704 " " NAG 1 705 " - " NAG 1 706 " " NAG 1 706 " - " BMA 1 707 " " NAG 2 601 " - " NAG 2 602 " " NAG 2 603 " - " NAG 2 604 " " NAG 2 605 " - " NAG 2 606 " " NAG 2 606 " - " BMA 2 607 " " NAG 2 609 " - " NAG 2 610 " " NAG 2 610 " - " BMA 2 611 " " NAG 2 616 " - " NAG 2 617 " " NAG 2 617 " - " BMA 2 618 " " NAG 2 624 " - " NAG 2 625 " " NAG 2 626 " - " NAG 2 627 " " NAG 2 627 " - " BMA 2 628 " " NAG 2 631 " - " NAG 2 632 " " NAG 2 632 " - " BMA 2 633 " " NAG 2 639 " - " NAG 2 640 " " NAG 2 641 " - " NAG 2 642 " " NAG 2 642 " - " BMA 2 643 " " NAG 2 644 " - " NAG 2 645 " " NAG 2 645 " - " BMA 2 646 " " NAG 2 655 " - " NAG 2 656 " " NAG 2 656 " - " BMA 2 657 " " NAG 2 658 " - " NAG 2 659 " " NAG 2 659 " - " BMA 2 660 " " NAG 2 662 " - " NAG 2 663 " " NAG 2 663 " - " BMA 2 664 " " NAG 2 665 " - " NAG 2 666 " " NAG 2 666 " - " BMA 2 667 " " NAG C 601 " - " NAG C 602 " " NAG C 603 " - " NAG C 604 " " NAG C 605 " - " NAG C 606 " " NAG C 606 " - " BMA C 607 " " NAG C 609 " - " NAG C 610 " " NAG C 610 " - " BMA C 611 " " NAG C 616 " - " NAG C 617 " " NAG C 617 " - " BMA C 618 " " NAG C 624 " - " NAG C 625 " " NAG C 626 " - " NAG C 627 " " NAG C 627 " - " BMA C 628 " " NAG C 631 " - " NAG C 632 " " NAG C 632 " - " BMA C 633 " " NAG C 639 " - " NAG C 640 " " NAG C 641 " - " NAG C 642 " " NAG C 642 " - " BMA C 643 " " NAG C 644 " - " NAG C 645 " " NAG C 645 " - " BMA C 646 " " NAG C 655 " - " NAG C 656 " " NAG C 656 " - " BMA C 657 " " NAG C 658 " - " NAG C 659 " " NAG C 659 " - " BMA C 660 " " NAG C 662 " - " NAG C 663 " " NAG C 663 " - " BMA C 664 " " NAG C 665 " - " NAG C 666 " " NAG C 666 " - " BMA C 667 " " NAG D 702 " - " NAG D 703 " " NAG D 703 " - " BMA D 704 " " NAG D 705 " - " NAG D 706 " " NAG D 706 " - " BMA D 707 " " NAG c 601 " - " NAG c 602 " " NAG c 603 " - " NAG c 604 " " NAG c 605 " - " NAG c 606 " " NAG c 606 " - " BMA c 607 " " NAG c 609 " - " NAG c 610 " " NAG c 610 " - " BMA c 611 " " NAG c 616 " - " NAG c 617 " " NAG c 617 " - " BMA c 618 " " NAG c 624 " - " NAG c 625 " " NAG c 626 " - " NAG c 627 " " NAG c 627 " - " BMA c 628 " " NAG c 631 " - " NAG c 632 " " NAG c 632 " - " BMA c 633 " " NAG c 639 " - " NAG c 640 " " NAG c 641 " - " NAG c 642 " " NAG c 642 " - " BMA c 643 " " NAG c 644 " - " NAG c 645 " " NAG c 645 " - " BMA c 646 " " NAG c 655 " - " NAG c 656 " " NAG c 656 " - " BMA c 657 " " NAG c 658 " - " NAG c 659 " " NAG c 659 " - " BMA c 660 " " NAG c 662 " - " NAG c 663 " " NAG c 663 " - " BMA c 664 " " NAG c 665 " - " NAG c 666 " " NAG c 666 " - " BMA c 667 " " NAG d 702 " - " NAG d 703 " " NAG d 703 " - " BMA d 704 " " NAG d 705 " - " NAG d 706 " " NAG d 706 " - " BMA d 707 " NAG-ASN " NAG 1 701 " - " ASN 1 618 " " NAG 1 702 " - " ASN 1 637 " " NAG 1 705 " - " ASN 1 611 " " NAG 2 601 " - " ASN 2 88 " " NAG 2 603 " - " ASN 2 133 " " NAG 2 605 " - " ASN 2 137 " " NAG 2 609 " - " ASN 2 156 " " NAG 2 616 " - " ASN 2 160 " " NAG 2 624 " - " ASN 2 197 " " NAG 2 626 " - " ASN 2 234 " " NAG 2 631 " - " ASN 2 262 " " NAG 2 639 " - " ASN 2 295 " " NAG 2 641 " - " ASN 2 301 " " NAG 2 644 " - " ASN 2 332 " " NAG 2 653 " - " ASN 2 339 " " NAG 2 654 " - " ASN 2 355 " " NAG 2 655 " - " ASN 2 363 " " NAG 2 658 " - " ASN 2 386 " " NAG 2 662 " - " ASN 2 392 " " NAG 2 665 " - " ASN 2 448 " " NAG C 601 " - " ASN C 88 " " NAG C 603 " - " ASN C 133 " " NAG C 605 " - " ASN C 137 " " NAG C 609 " - " ASN C 156 " " NAG C 616 " - " ASN C 160 " " NAG C 624 " - " ASN C 197 " " NAG C 626 " - " ASN C 234 " " NAG C 631 " - " ASN C 262 " " NAG C 639 " - " ASN C 295 " " NAG C 641 " - " ASN C 301 " " NAG C 644 " - " ASN C 332 " " NAG C 653 " - " ASN C 339 " " NAG C 654 " - " ASN C 355 " " NAG C 655 " - " ASN C 363 " " NAG C 658 " - " ASN C 386 " " NAG C 662 " - " ASN C 392 " " NAG C 665 " - " ASN C 448 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 637 " " NAG D 705 " - " ASN D 611 " " NAG c 601 " - " ASN c 88 " " NAG c 603 " - " ASN c 133 " " NAG c 605 " - " ASN c 137 " " NAG c 609 " - " ASN c 156 " " NAG c 616 " - " ASN c 160 " " NAG c 624 " - " ASN c 197 " " NAG c 626 " - " ASN c 234 " " NAG c 631 " - " ASN c 262 " " NAG c 639 " - " ASN c 295 " " NAG c 641 " - " ASN c 301 " " NAG c 644 " - " ASN c 332 " " NAG c 653 " - " ASN c 339 " " NAG c 654 " - " ASN c 355 " " NAG c 655 " - " ASN c 363 " " NAG c 658 " - " ASN c 386 " " NAG c 662 " - " ASN c 392 " " NAG c 665 " - " ASN c 448 " " NAG d 701 " - " ASN d 618 " " NAG d 702 " - " ASN d 637 " " NAG d 705 " - " ASN d 611 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.77 Conformation dependent library (CDL) restraints added in 4.6 seconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 84 sheets defined 13.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'M' and resid 86 through 90 removed outlier: 3.511A pdb=" N ASP M 89 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER M 90 " --> pdb=" O ALA M 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 86 through 90' Processing helix chain 'M' and resid 107 through 111 Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.684A pdb=" N GLN Q 64 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.678A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.798A pdb=" N PHE D 519 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.214A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 4.113A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.855A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 627 through 633 Processing helix chain 'D' and resid 638 through 663 removed outlier: 4.039A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.693A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.438A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.824A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'm' and resid 86 through 90 removed outlier: 3.511A pdb=" N ASP m 89 " --> pdb=" O THR m 86 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER m 90 " --> pdb=" O ALA m 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 86 through 90' Processing helix chain 'm' and resid 107 through 111 Processing helix chain 'q' and resid 61 through 64 removed outlier: 3.685A pdb=" N GLN q 64 " --> pdb=" O ARG q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 61 through 64' Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.678A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 515 through 520 removed outlier: 3.798A pdb=" N PHE d 519 " --> pdb=" O ILE d 515 " (cutoff:3.500A) Processing helix chain 'd' and resid 523 through 527 removed outlier: 4.213A pdb=" N GLY d 527 " --> pdb=" O GLY d 524 " (cutoff:3.500A) Processing helix chain 'd' and resid 529 through 534 removed outlier: 4.113A pdb=" N SER d 534 " --> pdb=" O MET d 530 " (cutoff:3.500A) Processing helix chain 'd' and resid 537 through 543 removed outlier: 3.854A pdb=" N ALA d 541 " --> pdb=" O LEU d 537 " (cutoff:3.500A) Processing helix chain 'd' and resid 570 through 595 Processing helix chain 'd' and resid 620 through 625 Processing helix chain 'd' and resid 627 through 633 Processing helix chain 'd' and resid 638 through 663 removed outlier: 4.038A pdb=" N LEU d 663 " --> pdb=" O ASP d 659 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 63 Processing helix chain 'c' and resid 99 through 115 removed outlier: 3.693A pdb=" N ILE c 109 " --> pdb=" O HIS c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 177 through 179 No H-bonds generated for 'chain 'c' and resid 177 through 179' Processing helix chain 'c' and resid 195 through 198 Processing helix chain 'c' and resid 335 through 354 removed outlier: 4.439A pdb=" N LYS c 351 " --> pdb=" O LYS c 347 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS c 352 " --> pdb=" O GLN c 348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE c 353 " --> pdb=" O LEU c 349 " (cutoff:3.500A) Processing helix chain 'c' and resid 368 through 373 removed outlier: 3.824A pdb=" N THR c 372 " --> pdb=" O ASP c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 476 through 481 Processing helix chain '7' and resid 86 through 90 removed outlier: 3.511A pdb=" N ASP 7 89 " --> pdb=" O THR 7 86 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER 7 90 " --> pdb=" O ALA 7 87 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 86 through 90' Processing helix chain '7' and resid 107 through 111 Processing helix chain '5' and resid 61 through 64 removed outlier: 3.684A pdb=" N GLN 5 64 " --> pdb=" O ARG 5 61 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 61 through 64' Processing helix chain '5' and resid 83 through 87 removed outlier: 3.678A pdb=" N THR 5 87 " --> pdb=" O PRO 5 84 " (cutoff:3.500A) Processing helix chain '1' and resid 515 through 520 removed outlier: 3.798A pdb=" N PHE 1 519 " --> pdb=" O ILE 1 515 " (cutoff:3.500A) Processing helix chain '1' and resid 523 through 527 removed outlier: 4.214A pdb=" N GLY 1 527 " --> pdb=" O GLY 1 524 " (cutoff:3.500A) Processing helix chain '1' and resid 529 through 534 removed outlier: 4.112A pdb=" N SER 1 534 " --> pdb=" O MET 1 530 " (cutoff:3.500A) Processing helix chain '1' and resid 537 through 543 removed outlier: 3.855A pdb=" N ALA 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 570 through 595 Processing helix chain '1' and resid 620 through 625 Processing helix chain '1' and resid 627 through 633 Processing helix chain '1' and resid 638 through 663 removed outlier: 4.038A pdb=" N LEU 1 663 " --> pdb=" O ASP 1 659 " (cutoff:3.500A) Processing helix chain '2' and resid 58 through 63 Processing helix chain '2' and resid 99 through 115 removed outlier: 3.693A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 177 through 179 No H-bonds generated for 'chain '2' and resid 177 through 179' Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 354 removed outlier: 4.437A pdb=" N LYS 2 351 " --> pdb=" O LYS 2 347 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS 2 352 " --> pdb=" O GLN 2 348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE 2 353 " --> pdb=" O LEU 2 349 " (cutoff:3.500A) Processing helix chain '2' and resid 368 through 373 removed outlier: 3.824A pdb=" N THR 2 372 " --> pdb=" O ASP 2 368 " (cutoff:3.500A) Processing helix chain '2' and resid 476 through 481 Processing sheet with id=AA1, first strand: chain 'h' and resid 10 through 11 removed outlier: 6.540A pdb=" N ASP h 10 " --> pdb=" O THR h 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'h' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'h' and resid 44 through 51 removed outlier: 6.581A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET h 34 " --> pdb=" O ALA h 50 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER h 93 " --> pdb=" O HIS h 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG h 94 " --> pdb=" O ASP h 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'l' and resid 5 through 7 removed outlier: 4.152A pdb=" N THR l 5 " --> pdb=" O LYS l 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS l 24 " --> pdb=" O THR l 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'l' and resid 33 through 38 removed outlier: 4.422A pdb=" N GLY l 84 " --> pdb=" O LEU l 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU l 104 " --> pdb=" O GLY l 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL M 12 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL M 128 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA M 91 " --> pdb=" O VAL M 128 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL M 12 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL M 128 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA M 91 " --> pdb=" O VAL M 128 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR M 33 " --> pdb=" O THR M 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA M 96 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 13 removed outlier: 5.736A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'N' and resid 19 through 22 Processing sheet with id=AB2, first strand: chain 'N' and resid 31 through 38 removed outlier: 3.882A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 5 through 7 removed outlier: 3.579A pdb=" N ASP R 69 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU R 11 " --> pdb=" O GLU R 100 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP R 34 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU R 11 " --> pdb=" O GLU R 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AB7, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.664A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE Q 45 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.984A pdb=" N TYR Q 102 " --> pdb=" O ARG Q 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.532A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.875A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.513A pdb=" N THR C 244 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.127A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.198A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.385A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.531A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.790A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 304 through 312 removed outlier: 7.058A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.539A pdb=" N ASP H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AD4, first strand: chain 'H' and resid 44 through 51 removed outlier: 6.579A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.153A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 33 through 38 removed outlier: 4.422A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.507A pdb=" N VAL m 12 " --> pdb=" O THR m 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL m 128 " --> pdb=" O ALA m 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA m 91 " --> pdb=" O VAL m 128 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.507A pdb=" N VAL m 12 " --> pdb=" O THR m 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL m 128 " --> pdb=" O ALA m 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA m 91 " --> pdb=" O VAL m 128 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR m 33 " --> pdb=" O THR m 98 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA m 96 " --> pdb=" O SER m 35 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'm' and resid 71 through 72 Processing sheet with id=AE1, first strand: chain 'n' and resid 11 through 13 removed outlier: 5.743A pdb=" N VAL n 11 " --> pdb=" O ILE n 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'n' and resid 19 through 22 Processing sheet with id=AE3, first strand: chain 'n' and resid 31 through 38 removed outlier: 3.882A pdb=" N TYR n 87 " --> pdb=" O TYR n 36 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'r' and resid 5 through 7 removed outlier: 3.580A pdb=" N ASP r 69 " --> pdb=" O SER r 66 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU r 11 " --> pdb=" O GLU r 100 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU r 11 " --> pdb=" O GLU r 100 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'q' and resid 3 through 5 Processing sheet with id=AE8, first strand: chain 'q' and resid 10 through 11 removed outlier: 3.664A pdb=" N GLY q 49 " --> pdb=" O TRP q 36 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'q' and resid 10 through 11 removed outlier: 3.983A pdb=" N TYR q 102 " --> pdb=" O ARG q 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 35 through 40 Processing sheet with id=AF2, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.532A pdb=" N LYS c 487 " --> pdb=" O LEU c 226 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 75 through 76 removed outlier: 3.875A pdb=" N VAL c 75 " --> pdb=" O CYS c 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE c 53 " --> pdb=" O CYS c 218 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 84 through 85 removed outlier: 3.514A pdb=" N THR c 244 " --> pdb=" O ILE c 84 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 91 through 94 removed outlier: 4.127A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 130 through 133 Processing sheet with id=AF7, first strand: chain 'c' and resid 181 through 183 Processing sheet with id=AF8, first strand: chain 'c' and resid 202 through 203 removed outlier: 7.198A pdb=" N THR c 202 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 271 through 273 removed outlier: 7.385A pdb=" N THR c 450 " --> pdb=" O PHE c 288 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N THR c 290 " --> pdb=" O ASN c 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN c 448 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N VAL c 292 " --> pdb=" O VAL c 446 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N VAL c 446 " --> pdb=" O VAL c 292 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ILE c 294 " --> pdb=" O ARG c 444 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ARG c 444 " --> pdb=" O ILE c 294 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE c 358 " --> pdb=" O GLU c 466 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE c 468 " --> pdb=" O ILE c 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG c 360 " --> pdb=" O PHE c 468 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 271 through 273 removed outlier: 6.790A pdb=" N GLN c 293 " --> pdb=" O SER c 334 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER c 334 " --> pdb=" O GLN c 293 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS c 330 " --> pdb=" O THR c 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE c 376 " --> pdb=" O PHE c 383 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'c' and resid 304 through 312 removed outlier: 7.068A pdb=" N GLN c 315 " --> pdb=" O ILE c 309 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '7' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL 7 12 " --> pdb=" O THR 7 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 7 128 " --> pdb=" O ALA 7 91 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 7 91 " --> pdb=" O VAL 7 128 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP 7 34 " --> pdb=" O TYR 7 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR 7 50 " --> pdb=" O TRP 7 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP 7 36 " --> pdb=" O ILE 7 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '7' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL 7 12 " --> pdb=" O THR 7 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 7 128 " --> pdb=" O ALA 7 91 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 7 91 " --> pdb=" O VAL 7 128 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR 7 33 " --> pdb=" O THR 7 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA 7 96 " --> pdb=" O SER 7 35 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '7' and resid 71 through 72 Processing sheet with id=AG6, first strand: chain '8' and resid 11 through 13 removed outlier: 5.730A pdb=" N VAL 8 11 " --> pdb=" O ILE 8 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain '8' and resid 19 through 22 Processing sheet with id=AG8, first strand: chain '8' and resid 31 through 38 removed outlier: 3.881A pdb=" N TYR 8 87 " --> pdb=" O TYR 8 36 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '6' and resid 5 through 7 removed outlier: 3.579A pdb=" N ASP 6 69 " --> pdb=" O SER 6 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '6' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU 6 11 " --> pdb=" O GLU 6 100 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP 6 34 " --> pdb=" O LEU 6 46 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '6' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU 6 11 " --> pdb=" O GLU 6 100 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '5' and resid 3 through 5 Processing sheet with id=AH4, first strand: chain '5' and resid 10 through 11 removed outlier: 3.664A pdb=" N GLY 5 49 " --> pdb=" O TRP 5 36 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG 5 38 " --> pdb=" O TRP 5 47 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP 5 47 " --> pdb=" O ARG 5 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE 5 40 " --> pdb=" O PHE 5 45 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE 5 45 " --> pdb=" O ILE 5 40 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '5' and resid 10 through 11 removed outlier: 3.983A pdb=" N TYR 5 102 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '2' and resid 35 through 40 Processing sheet with id=AH7, first strand: chain '2' and resid 45 through 47 removed outlier: 3.532A pdb=" N LYS 2 487 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '2' and resid 75 through 76 removed outlier: 3.875A pdb=" N VAL 2 75 " --> pdb=" O CYS 2 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE 2 53 " --> pdb=" O CYS 2 218 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2' and resid 84 through 85 removed outlier: 3.513A pdb=" N THR 2 244 " --> pdb=" O ILE 2 84 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '2' and resid 91 through 94 removed outlier: 4.127A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain '2' and resid 130 through 133 Processing sheet with id=AI3, first strand: chain '2' and resid 181 through 183 Processing sheet with id=AI4, first strand: chain '2' and resid 202 through 203 removed outlier: 7.199A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain '2' and resid 271 through 273 removed outlier: 7.385A pdb=" N THR 2 450 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N THR 2 290 " --> pdb=" O ASN 2 448 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN 2 448 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N VAL 2 292 " --> pdb=" O VAL 2 446 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N VAL 2 446 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ILE 2 294 " --> pdb=" O ARG 2 444 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ARG 2 444 " --> pdb=" O ILE 2 294 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE 2 358 " --> pdb=" O GLU 2 466 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE 2 468 " --> pdb=" O ILE 2 358 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG 2 360 " --> pdb=" O PHE 2 468 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '2' and resid 271 through 273 removed outlier: 6.791A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS 2 330 " --> pdb=" O THR 2 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE 2 376 " --> pdb=" O PHE 2 383 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain '2' and resid 304 through 312 removed outlier: 7.058A pdb=" N GLN 2 315 " --> pdb=" O ILE 2 309 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain '3' and resid 10 through 11 removed outlier: 6.539A pdb=" N ASP 3 10 " --> pdb=" O THR 3 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain '3' and resid 21 through 23 Processing sheet with id=AJ1, first strand: chain '3' and resid 44 through 51 removed outlier: 6.580A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA 3 50 " --> pdb=" O MET 3 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET 3 34 " --> pdb=" O ALA 3 50 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER 3 93 " --> pdb=" O HIS 3 35 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG 3 94 " --> pdb=" O ASP 3 101 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain '4' and resid 5 through 7 removed outlier: 4.153A pdb=" N THR 4 5 " --> pdb=" O LYS 4 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS 4 24 " --> pdb=" O THR 4 5 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain '4' and resid 33 through 38 removed outlier: 4.422A pdb=" N GLY 4 84 " --> pdb=" O LEU 4 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU 4 104 " --> pdb=" O GLY 4 84 " (cutoff:3.500A) 882 hydrogen bonds defined for protein. 2223 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: 13.07 Time building geometry restraints manager: 17.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9936 1.34 - 1.46: 9053 1.46 - 1.59: 14446 1.59 - 1.71: 0 1.71 - 1.83: 240 Bond restraints: 33675 Sorted by residual: bond pdb=" CA GLY C 263 " pdb=" C GLY C 263 " ideal model delta sigma weight residual 1.520 1.501 0.019 7.30e-03 1.88e+04 6.65e+00 bond pdb=" CA GLY c 263 " pdb=" C GLY c 263 " ideal model delta sigma weight residual 1.520 1.503 0.018 7.30e-03 1.88e+04 5.78e+00 bond pdb=" CA GLY 2 263 " pdb=" C GLY 2 263 " ideal model delta sigma weight residual 1.520 1.503 0.017 7.30e-03 1.88e+04 5.70e+00 bond pdb=" CB ASN 1 611 " pdb=" CG ASN 1 611 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 5.05e+00 bond pdb=" CB ASN D 611 " pdb=" CG ASN D 611 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 5.02e+00 ... (remaining 33670 not shown) Histogram of bond angle deviations from ideal: 95.80 - 103.46: 363 103.46 - 111.11: 14026 111.11 - 118.77: 13693 118.77 - 126.43: 16996 126.43 - 134.08: 654 Bond angle restraints: 45732 Sorted by residual: angle pdb=" N GLN R 89 " pdb=" CA GLN R 89 " pdb=" C GLN R 89 " ideal model delta sigma weight residual 108.41 98.37 10.04 1.63e+00 3.76e-01 3.80e+01 angle pdb=" C SER 1 615 " pdb=" N ASN 1 616 " pdb=" CA ASN 1 616 " ideal model delta sigma weight residual 122.46 129.36 -6.90 1.41e+00 5.03e-01 2.39e+01 angle pdb=" C SER D 615 " pdb=" N ASN D 616 " pdb=" CA ASN D 616 " ideal model delta sigma weight residual 122.46 129.35 -6.89 1.41e+00 5.03e-01 2.39e+01 angle pdb=" C SER d 615 " pdb=" N ASN d 616 " pdb=" CA ASN d 616 " ideal model delta sigma weight residual 122.46 129.34 -6.88 1.41e+00 5.03e-01 2.38e+01 angle pdb=" N PHE Q 100D" pdb=" CA PHE Q 100D" pdb=" C PHE Q 100D" ideal model delta sigma weight residual 109.81 120.28 -10.47 2.21e+00 2.05e-01 2.24e+01 ... (remaining 45727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.86: 19421 19.86 - 39.72: 550 39.72 - 59.58: 108 59.58 - 79.45: 31 79.45 - 99.31: 8 Dihedral angle restraints: 20118 sinusoidal: 9099 harmonic: 11019 Sorted by residual: dihedral pdb=" CB CYS 2 54 " pdb=" SG CYS 2 54 " pdb=" SG CYS 2 74 " pdb=" CB CYS 2 74 " ideal model delta sinusoidal sigma weight residual -86.00 -171.53 85.53 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS c 54 " pdb=" SG CYS c 54 " pdb=" SG CYS c 74 " pdb=" CB CYS c 74 " ideal model delta sinusoidal sigma weight residual -86.00 -169.43 83.43 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -156.77 70.77 1 1.00e+01 1.00e-02 6.44e+01 ... (remaining 20115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.327: 5688 0.327 - 0.653: 18 0.653 - 0.980: 9 0.980 - 1.307: 9 1.307 - 1.633: 6 Chirality restraints: 5730 Sorted by residual: chirality pdb=" C1 NAG C 644 " pdb=" ND2 ASN C 332 " pdb=" C2 NAG C 644 " pdb=" O5 NAG C 644 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-01 2.50e+01 6.67e+01 chirality pdb=" C1 NAG c 644 " pdb=" ND2 ASN c 332 " pdb=" C2 NAG c 644 " pdb=" O5 NAG c 644 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-01 2.50e+01 6.66e+01 chirality pdb=" C1 NAG 2 644 " pdb=" ND2 ASN 2 332 " pdb=" C2 NAG 2 644 " pdb=" O5 NAG 2 644 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-01 2.50e+01 6.65e+01 ... (remaining 5727 not shown) Planarity restraints: 5529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN c 392 " -0.073 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" CG ASN c 392 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN c 392 " -0.193 2.00e-02 2.50e+03 pdb=" ND2 ASN c 392 " 0.519 2.00e-02 2.50e+03 pdb=" C1 NAG c 662 " -0.344 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 392 " 0.073 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" CG ASN C 392 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 392 " 0.193 2.00e-02 2.50e+03 pdb=" ND2 ASN C 392 " -0.519 2.00e-02 2.50e+03 pdb=" C1 NAG C 662 " 0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 2 392 " 0.073 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" CG ASN 2 392 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN 2 392 " 0.193 2.00e-02 2.50e+03 pdb=" ND2 ASN 2 392 " -0.518 2.00e-02 2.50e+03 pdb=" C1 NAG 2 662 " 0.343 2.00e-02 2.50e+03 ... (remaining 5526 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 47 2.30 - 2.95: 15387 2.95 - 3.60: 42730 3.60 - 4.25: 71011 4.25 - 4.90: 116013 Nonbonded interactions: 245188 Sorted by model distance: nonbonded pdb=" O GLY 2 263 " pdb=" CG2 THR 2 450 " model vdw 1.655 3.460 nonbonded pdb=" O GLY C 263 " pdb=" CG2 THR C 450 " model vdw 1.664 3.460 nonbonded pdb=" O GLY c 263 " pdb=" CG2 THR c 450 " model vdw 1.664 3.460 nonbonded pdb=" O LYS c 502 " pdb=" CD2 LEU 1 661 " model vdw 1.865 3.460 nonbonded pdb=" CD2 LEU D 661 " pdb=" O LYS 2 502 " model vdw 1.918 3.460 ... (remaining 245183 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain 'D' selection = chain 'd' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'c' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '6' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '7' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '8' selection = chain 'N' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 177 5.16 5 C 20661 2.51 5 N 5319 2.21 5 O 6816 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.410 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: 0.020 Extract box with map and model: 14.680 Check model and map are aligned: 0.430 Convert atoms to be neutral: 0.290 Process input model: 87.110 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 33675 Z= 0.479 Angle : 0.942 11.145 45732 Z= 0.512 Chirality : 0.096 1.633 5730 Planarity : 0.006 0.067 5469 Dihedral : 9.910 99.308 12897 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.12), residues: 3774 helix: -2.28 (0.20), residues: 405 sheet: -1.48 (0.14), residues: 1221 loop : -2.67 (0.11), residues: 2148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 709 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 716 average time/residue: 0.5007 time to fit residues: 559.3119 Evaluate side-chains 336 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 332 time to evaluate : 3.936 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3100 time to fit residues: 7.2024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 340 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN N 50 ASN R 36 GLN D 543 ASN D 625 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 293 GLN L 38 GLN n 50 ASN d 543 ASN d 625 ASN ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 103 GLN c 293 GLN 8 50 ASN 1 543 ASN 1 625 ASN 2 293 GLN 2 478 ASN 3 61 GLN ** 4 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 93 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 33675 Z= 0.243 Angle : 0.651 7.724 45732 Z= 0.343 Chirality : 0.048 0.551 5730 Planarity : 0.005 0.050 5469 Dihedral : 7.154 106.534 5934 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.13), residues: 3774 helix: -0.57 (0.25), residues: 426 sheet: -1.23 (0.14), residues: 1302 loop : -2.29 (0.12), residues: 2046 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 430 time to evaluate : 4.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 34 residues processed: 474 average time/residue: 0.4383 time to fit residues: 341.4677 Evaluate side-chains 369 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 335 time to evaluate : 3.483 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2837 time to fit residues: 23.5083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 283 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 341 optimal weight: 3.9990 chunk 368 optimal weight: 20.0000 chunk 303 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 273 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 38 GLN l 42 GLN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN L 93 HIS r 36 GLN ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 36 GLN 1 543 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 33675 Z= 0.374 Angle : 0.665 14.741 45732 Z= 0.345 Chirality : 0.047 0.344 5730 Planarity : 0.004 0.039 5469 Dihedral : 6.945 107.968 5934 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.13), residues: 3774 helix: 0.16 (0.25), residues: 426 sheet: -0.96 (0.14), residues: 1254 loop : -2.08 (0.13), residues: 2094 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 367 time to evaluate : 3.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 29 residues processed: 409 average time/residue: 0.4430 time to fit residues: 297.5489 Evaluate side-chains 350 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 321 time to evaluate : 3.794 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.2912 time to fit residues: 21.2963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 0.8980 chunk 256 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 342 optimal weight: 0.9980 chunk 362 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 324 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN ** l 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 30 ASN 3 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 33675 Z= 0.284 Angle : 0.614 14.399 45732 Z= 0.315 Chirality : 0.045 0.304 5730 Planarity : 0.004 0.036 5469 Dihedral : 6.720 107.793 5934 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.13), residues: 3774 helix: 0.61 (0.26), residues: 426 sheet: -0.92 (0.14), residues: 1311 loop : -1.94 (0.13), residues: 2037 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 350 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 379 average time/residue: 0.4566 time to fit residues: 291.3655 Evaluate side-chains 324 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 308 time to evaluate : 3.791 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.3406 time to fit residues: 14.7123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 185 optimal weight: 0.7980 chunk 325 optimal weight: 0.0980 chunk 91 optimal weight: 7.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 93 HIS ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 249 HIS 4 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 33675 Z= 0.262 Angle : 0.594 15.233 45732 Z= 0.303 Chirality : 0.044 0.306 5730 Planarity : 0.004 0.069 5469 Dihedral : 6.541 108.043 5934 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3774 helix: 0.86 (0.26), residues: 426 sheet: -0.82 (0.14), residues: 1320 loop : -1.84 (0.13), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 330 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 359 average time/residue: 0.4392 time to fit residues: 261.1558 Evaluate side-chains 323 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 305 time to evaluate : 3.869 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.3095 time to fit residues: 15.4096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 3.9990 chunk 326 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 362 optimal weight: 0.8980 chunk 301 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 575 GLN 8 50 ASN 2 478 ASN 4 27 GLN 4 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 33675 Z= 0.312 Angle : 0.605 16.282 45732 Z= 0.311 Chirality : 0.044 0.311 5730 Planarity : 0.004 0.062 5469 Dihedral : 6.487 108.002 5934 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3774 helix: 0.93 (0.26), residues: 426 sheet: -0.80 (0.14), residues: 1326 loop : -1.77 (0.13), residues: 2022 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 330 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 29 residues processed: 376 average time/residue: 0.4327 time to fit residues: 269.9533 Evaluate side-chains 331 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 302 time to evaluate : 3.856 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2920 time to fit residues: 20.9371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 264 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 305 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 361 optimal weight: 20.0000 chunk 226 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 27 GLN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS m 76 ASN 2 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 33675 Z= 0.301 Angle : 0.612 15.616 45732 Z= 0.310 Chirality : 0.044 0.308 5730 Planarity : 0.004 0.081 5469 Dihedral : 6.438 108.169 5934 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3774 helix: 1.17 (0.27), residues: 408 sheet: -0.69 (0.14), residues: 1314 loop : -1.72 (0.13), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 319 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 345 average time/residue: 0.4515 time to fit residues: 259.6753 Evaluate side-chains 308 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 294 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3332 time to fit residues: 13.6642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 284 optimal weight: 0.3980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 27 GLN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 33675 Z= 0.221 Angle : 0.589 16.268 45732 Z= 0.296 Chirality : 0.043 0.299 5730 Planarity : 0.004 0.091 5469 Dihedral : 6.288 108.413 5934 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3774 helix: 1.36 (0.27), residues: 408 sheet: -0.62 (0.14), residues: 1308 loop : -1.62 (0.13), residues: 2058 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 332 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 351 average time/residue: 0.4409 time to fit residues: 257.7558 Evaluate side-chains 306 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 297 time to evaluate : 3.714 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2884 time to fit residues: 9.9718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 4.9990 chunk 346 optimal weight: 0.6980 chunk 315 optimal weight: 6.9990 chunk 336 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 335 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 33675 Z= 0.299 Angle : 0.627 14.505 45732 Z= 0.318 Chirality : 0.050 1.274 5730 Planarity : 0.004 0.136 5469 Dihedral : 6.341 108.422 5934 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3774 helix: 1.34 (0.27), residues: 408 sheet: -0.52 (0.15), residues: 1266 loop : -1.61 (0.13), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 299 time to evaluate : 3.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 313 average time/residue: 0.4443 time to fit residues: 232.8701 Evaluate side-chains 297 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 286 time to evaluate : 3.849 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3155 time to fit residues: 11.8046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 1.9990 chunk 356 optimal weight: 8.9990 chunk 217 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 373 optimal weight: 7.9990 chunk 343 optimal weight: 1.9990 chunk 297 optimal weight: 0.0040 chunk 30 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 182 optimal weight: 0.0980 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 33675 Z= 0.207 Angle : 0.609 15.967 45732 Z= 0.304 Chirality : 0.049 1.163 5730 Planarity : 0.004 0.090 5469 Dihedral : 6.202 108.574 5934 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3774 helix: 1.53 (0.27), residues: 408 sheet: -0.46 (0.14), residues: 1293 loop : -1.55 (0.13), residues: 2073 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 324 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 329 average time/residue: 0.4648 time to fit residues: 252.4418 Evaluate side-chains 296 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 293 time to evaluate : 3.978 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3158 time to fit residues: 6.7949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 0.6980 chunk 316 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 274 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 297 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 305 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.067757 restraints weight = 85145.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.068327 restraints weight = 58485.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.068623 restraints weight = 46208.556| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 33675 Z= 0.196 Angle : 0.595 12.215 45732 Z= 0.296 Chirality : 0.047 1.033 5730 Planarity : 0.003 0.076 5469 Dihedral : 6.060 108.610 5934 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3774 helix: 1.65 (0.27), residues: 408 sheet: -0.41 (0.14), residues: 1293 loop : -1.49 (0.13), residues: 2073 =============================================================================== Job complete usr+sys time: 5952.36 seconds wall clock time: 111 minutes 6.61 seconds (6666.61 seconds total)