Starting phenix.real_space_refine (version: dev) on Thu Dec 15 15:13:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktr_23027/12_2022/7ktr_23027_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktr_23027/12_2022/7ktr_23027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktr_23027/12_2022/7ktr_23027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktr_23027/12_2022/7ktr_23027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktr_23027/12_2022/7ktr_23027_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktr_23027/12_2022/7ktr_23027_trim_updated.pdb" } resolution = 2.93 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= 0.172 sd= 0.753 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 "A ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A PHE 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1210": "OE1" <-> "OE2" Residue "A GLU 1309": "OE1" <-> "OE2" Residue "A GLU 1343": "OE1" <-> "OE2" Residue "A GLU 1402": "OE1" <-> "OE2" Residue "A GLU 1524": "OE1" <-> "OE2" Residue "A GLU 1530": "OE1" <-> "OE2" Residue "A ARG 1660": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 1684": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2323": "OE1" <-> "OE2" Residue "A ARG 2451": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 2586": "OE1" <-> "OE2" Residue "A GLU 2773": "OE1" <-> "OE2" Residue "A ARG 2903": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 3068": "OE1" <-> "OE2" Residue "A TYR 3083": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 3107": "OE1" <-> "OE2" Residue "A PHE 3447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 3515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 3546": "OE1" <-> "OE2" Residue "A ARG 3603": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 3606": "OD1" <-> "OD2" Residue "A GLU 3629": "OE1" <-> "OE2" Residue "A TYR 3654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 3670": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 3718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 3821": "OE1" <-> "OE2" Residue "B TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 122": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 78998 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 45505 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3042, 45454 Classifications: {'peptide': 3042} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 326} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 119, 'TRANS': 2917} Chain breaks: 22 Unresolved non-hydrogen bonds: 652 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 326 Planarities with less than four sites: {'UNK:plan-1': 326} Unresolved non-hydrogen planarities: 326 Conformer: "B" Number of residues, atoms: 3042, 45454 Classifications: {'peptide': 3042} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 326} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 119, 'TRANS': 2917} Chain breaks: 22 Unresolved non-hydrogen bonds: 652 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 326 Planarities with less than four sites: {'UNK:plan-1': 326} Unresolved non-hydrogen planarities: 326 bond proxies already assigned to first conformer: 45845 Chain: "B" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8338 Classifications: {'peptide': 534} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 515} Chain breaks: 1 Chain: "C" Number of atoms: 6608 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 6591 Classifications: {'peptide': 407} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 383} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 407, 6591 Classifications: {'peptide': 407} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 383} Chain breaks: 2 bond proxies already assigned to first conformer: 6633 Chain: "D" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3107 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 209} Chain breaks: 3 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2013 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 13, 'TRANS': 110} Chain: "F" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2069 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "G" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1704 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1566 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain breaks: 1 Chain: "I" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3808 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3380 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 16, 'TRANS': 197} Chain breaks: 1 Chain: "N" Number of atoms: 864 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 53, 847 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Conformer: "B" Number of residues, atoms: 53, 847 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} bond proxies already assigned to first conformer: 841 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AHIS A 912 " occ=0.50 ... (32 atoms not shown) pdb=" HE2BHIS A 912 " occ=0.50 residue: pdb=" N AHIS A 981 " occ=0.50 ... (32 atoms not shown) pdb=" HE2BHIS A 981 " occ=0.50 residue: pdb=" N AHIS A2906 " occ=0.50 ... (32 atoms not shown) pdb=" HE2BHIS A2906 " occ=0.50 residue: pdb=" N AHIS C 331 " occ=0.50 ... (32 atoms not shown) pdb=" HE2BHIS C 331 " occ=0.50 residue: pdb=" N AHIS N 514 " occ=0.50 ... (32 atoms not shown) pdb=" HE2BHIS N 514 " occ=0.50 Time building chain proxies: 45.51, per 1000 atoms: 0.58 Number of scatterers: 78998 At special positions: 0 Unit cell: (174.489, 137.692, 235.026, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 253 16.00 P 6 15.00 O 7465 8.00 N 7081 7.00 C 25532 6.00 H 38661 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 53.60 Conformation dependent library (CDL) restraints added in 8.3 seconds 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9998 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 231 helices and 18 sheets defined 62.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.75 Creating SS restraints... Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 372 through 385 removed outlier: 3.801A pdb=" N SER A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 407 removed outlier: 3.768A pdb=" N LYS A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 434 removed outlier: 4.384A pdb=" N ASP A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 442 through 468 removed outlier: 4.051A pdb=" N LEU A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 564 removed outlier: 3.876A pdb=" N PHE A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 559 " --> pdb=" O CYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 603 removed outlier: 3.706A pdb=" N GLN A 597 " --> pdb=" O LYS A 593 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP A 600 " --> pdb=" O MET A 596 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE A 601 " --> pdb=" O GLN A 597 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLN A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 643 through 653 removed outlier: 4.040A pdb=" N THR A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.642A pdb=" N ILE A 669 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 673 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 694 removed outlier: 3.597A pdb=" N ASP A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 722 removed outlier: 3.832A pdb=" N LEU A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.836A pdb=" N GLU A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN A 729 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) Proline residue: A 733 - end of helix removed outlier: 5.237A pdb=" N HIS A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYS A 737 " --> pdb=" O PRO A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 767 Processing helix chain 'A' and resid 773 through 794 removed outlier: 3.595A pdb=" N GLU A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Proline residue: A 780 - end of helix Proline residue: A 783 - end of helix removed outlier: 3.574A pdb=" N GLN A 787 " --> pdb=" O PRO A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 820 through 835 Proline residue: A 824 - end of helix removed outlier: 5.167A pdb=" N ASP A 828 " --> pdb=" O MET A 825 " (cutoff:3.500A) Proline residue: A 829 - end of helix Processing helix chain 'A' and resid 838 through 854 Processing helix chain 'A' and resid 857 through 880 removed outlier: 3.582A pdb=" N HIS A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Proline residue: A 866 - end of helix removed outlier: 5.540A pdb=" N ALA A 869 " --> pdb=" O GLN A 865 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU A 870 " --> pdb=" O PRO A 866 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG A 880 " --> pdb=" O TRP A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 897 removed outlier: 4.476A pdb=" N VAL A 889 " --> pdb=" O SER A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 901 No H-bonds generated for 'chain 'A' and resid 899 through 901' Processing helix chain 'A' and resid 939 through 950 Processing helix chain 'A' and resid 956 through 972 Processing helix chain 'A' and resid 980 through 987 removed outlier: 3.735A pdb=" N TYR A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 994 Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1012 through 1029 Processing helix chain 'A' and resid 1034 through 1056 Proline residue: A1039 - end of helix Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.628A pdb=" N LEU A1091 " --> pdb=" O PRO A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1125 Processing helix chain 'A' and resid 1128 through 1133 removed outlier: 4.001A pdb=" N GLN A1133 " --> pdb=" O GLU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1149 removed outlier: 4.021A pdb=" N CYS A1147 " --> pdb=" O ARG A1143 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR A1149 " --> pdb=" O CYS A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1169 Processing helix chain 'A' and resid 1172 through 1192 removed outlier: 4.897A pdb=" N GLN A1180 " --> pdb=" O LEU A1176 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N THR A1181 " --> pdb=" O GLN A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1217 Processing helix chain 'A' and resid 1227 through 1249 removed outlier: 4.676A pdb=" N THR A1249 " --> pdb=" O VAL A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1270 Processing helix chain 'A' and resid 1274 through 1284 Proline residue: A1280 - end of helix removed outlier: 5.059A pdb=" N GLU A1283 " --> pdb=" O GLU A1279 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A1284 " --> pdb=" O PRO A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1301 through 1314 Processing helix chain 'A' and resid 1329 through 1343 Processing helix chain 'A' and resid 1346 through 1350 Processing helix chain 'A' and resid 1362 through 1373 Processing helix chain 'A' and resid 1379 through 1381 No H-bonds generated for 'chain 'A' and resid 1379 through 1381' Processing helix chain 'A' and resid 1383 through 1393 Processing helix chain 'A' and resid 1398 through 1414 removed outlier: 3.714A pdb=" N GLU A1413 " --> pdb=" O ARG A1409 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLY A1414 " --> pdb=" O LYS A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1430 Proline residue: A1428 - end of helix Processing helix chain 'A' and resid 1441 through 1453 Processing helix chain 'A' and resid 1460 through 1483 removed outlier: 3.653A pdb=" N GLY A1483 " --> pdb=" O ILE A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1504 removed outlier: 4.107A pdb=" N PHE A1502 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS A1503 " --> pdb=" O ILE A1499 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A1504 " --> pdb=" O ASN A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1527 Processing helix chain 'A' and resid 1536 through 1545 removed outlier: 3.632A pdb=" N LYS A1541 " --> pdb=" O GLU A1537 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A1542 " --> pdb=" O PRO A1538 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG A1545 " --> pdb=" O LYS A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1554 removed outlier: 3.825A pdb=" N LEU A1553 " --> pdb=" O GLN A1549 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A1554 " --> pdb=" O THR A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1560 No H-bonds generated for 'chain 'A' and resid 1557 through 1560' Processing helix chain 'A' and resid 1563 through 1573 Processing helix chain 'A' and resid 1579 through 1586 Processing helix chain 'A' and resid 1590 through 1595 removed outlier: 4.071A pdb=" N THR A1594 " --> pdb=" O ASN A1590 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1595 " --> pdb=" O ARG A1591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1590 through 1595' Processing helix chain 'A' and resid 1618 through 1634 removed outlier: 4.090A pdb=" N ILE A1627 " --> pdb=" O ILE A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1640 No H-bonds generated for 'chain 'A' and resid 1638 through 1640' Processing helix chain 'A' and resid 1642 through 1653 removed outlier: 4.360A pdb=" N SER A1646 " --> pdb=" O HIS A1642 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLN A1647 " --> pdb=" O SER A1643 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A1649 " --> pdb=" O VAL A1645 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP A1652 " --> pdb=" O LEU A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1661 removed outlier: 3.552A pdb=" N ARG A1660 " --> pdb=" O ASN A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1687 removed outlier: 3.508A pdb=" N TYR A1684 " --> pdb=" O CYS A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1700 removed outlier: 4.551A pdb=" N UNK A1700 " --> pdb=" O UNK A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1716 Processing helix chain 'A' and resid 1730 through 1744 removed outlier: 3.840A pdb=" N UNK A1743 " --> pdb=" O UNK A1739 " (cutoff:3.500A) Processing helix chain 'A' and resid 1755 through 1765 removed outlier: 5.734A pdb=" N UNK A1760 " --> pdb=" O UNK A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1798 Processing helix chain 'A' and resid 1807 through 1820 Processing helix chain 'A' and resid 1840 through 1846 Processing helix chain 'A' and resid 1961 through 1972 removed outlier: 4.038A pdb=" N UNK A1965 " --> pdb=" O UNK A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 2000 Processing helix chain 'A' and resid 2078 through 2087 Processing helix chain 'A' and resid 2104 through 2115 Processing helix chain 'A' and resid 2123 through 2126 Processing helix chain 'A' and resid 2132 through 2138 Processing helix chain 'A' and resid 2154 through 2161 Processing helix chain 'A' and resid 2168 through 2174 Processing helix chain 'A' and resid 2194 through 2205 Processing helix chain 'A' and resid 2220 through 2236 Processing helix chain 'A' and resid 2251 through 2259 removed outlier: 4.260A pdb=" N UNK A2258 " --> pdb=" O UNK A2254 " (cutoff:3.500A) Processing helix chain 'A' and resid 2265 through 2267 No H-bonds generated for 'chain 'A' and resid 2265 through 2267' Processing helix chain 'A' and resid 2274 through 2285 Processing helix chain 'A' and resid 2301 through 2315 removed outlier: 3.608A pdb=" N VAL A2306 " --> pdb=" O SER A2303 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A2311 " --> pdb=" O LEU A2308 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A2312 " --> pdb=" O SER A2309 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A2315 " --> pdb=" O LEU A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2322 through 2339 removed outlier: 4.192A pdb=" N LEU A2333 " --> pdb=" O ILE A2329 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A2334 " --> pdb=" O GLN A2330 " (cutoff:3.500A) Processing helix chain 'A' and resid 2343 through 2357 Processing helix chain 'A' and resid 2364 through 2366 No H-bonds generated for 'chain 'A' and resid 2364 through 2366' Processing helix chain 'A' and resid 2371 through 2388 removed outlier: 4.955A pdb=" N GLU A2386 " --> pdb=" O MET A2382 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A2387 " --> pdb=" O THR A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2393 through 2408 Processing helix chain 'A' and resid 2417 through 2430 removed outlier: 3.809A pdb=" N GLU A2422 " --> pdb=" O ALA A2419 " (cutoff:3.500A) Proline residue: A2423 - end of helix Processing helix chain 'A' and resid 2434 through 2446 removed outlier: 3.657A pdb=" N VAL A2443 " --> pdb=" O LYS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2452 through 2460 Processing helix chain 'A' and resid 2466 through 2468 No H-bonds generated for 'chain 'A' and resid 2466 through 2468' Processing helix chain 'A' and resid 2474 through 2483 Processing helix chain 'A' and resid 2505 through 2509 Processing helix chain 'A' and resid 2512 through 2520 removed outlier: 3.804A pdb=" N ALA A2517 " --> pdb=" O HIS A2513 " (cutoff:3.500A) Processing helix chain 'A' and resid 2568 through 2586 removed outlier: 3.943A pdb=" N GLU A2586 " --> pdb=" O ASP A2582 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2600 removed outlier: 3.784A pdb=" N ALA A2595 " --> pdb=" O ALA A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2604 through 2621 Proline residue: A2616 - end of helix removed outlier: 3.662A pdb=" N ILE A2621 " --> pdb=" O ARG A2617 " (cutoff:3.500A) Processing helix chain 'A' and resid 2624 through 2638 removed outlier: 3.912A pdb=" N SER A2635 " --> pdb=" O ALA A2631 " (cutoff:3.500A) Proline residue: A2636 - end of helix Processing helix chain 'A' and resid 2641 through 2646 removed outlier: 3.653A pdb=" N GLN A2644 " --> pdb=" O GLY A2641 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A2645 " --> pdb=" O SER A2642 " (cutoff:3.500A) Processing helix chain 'A' and resid 2653 through 2663 removed outlier: 4.071A pdb=" N GLN A2663 " --> pdb=" O GLU A2659 " (cutoff:3.500A) Processing helix chain 'A' and resid 2672 through 2681 Processing helix chain 'A' and resid 2685 through 2696 Processing helix chain 'A' and resid 2710 through 2712 No H-bonds generated for 'chain 'A' and resid 2710 through 2712' Processing helix chain 'A' and resid 2724 through 2737 Processing helix chain 'A' and resid 2740 through 2750 removed outlier: 3.557A pdb=" N LYS A2749 " --> pdb=" O GLY A2745 " (cutoff:3.500A) Processing helix chain 'A' and resid 2754 through 2765 removed outlier: 3.797A pdb=" N HIS A2765 " --> pdb=" O ALA A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2768 through 2788 removed outlier: 3.607A pdb=" N GLU A2773 " --> pdb=" O GLU A2769 " (cutoff:3.500A) Processing helix chain 'A' and resid 2793 through 2813 removed outlier: 3.560A pdb=" N PHE A2796 " --> pdb=" O PRO A2793 " (cutoff:3.500A) Proline residue: A2797 - end of helix removed outlier: 3.501A pdb=" N TRP A2806 " --> pdb=" O GLU A2803 " (cutoff:3.500A) Processing helix chain 'A' and resid 2816 through 2823 Processing helix chain 'A' and resid 2831 through 2841 removed outlier: 4.777A pdb=" N TRP A2839 " --> pdb=" O LEU A2835 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ARG A2840 " --> pdb=" O GLU A2836 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A2841 " --> pdb=" O CYS A2837 " (cutoff:3.500A) Processing helix chain 'A' and resid 2844 through 2854 Processing helix chain 'A' and resid 2860 through 2876 removed outlier: 4.931A pdb=" N TRP A2864 " --> pdb=" O GLU A2861 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A2865 " --> pdb=" O MET A2862 " (cutoff:3.500A) Processing helix chain 'A' and resid 2886 through 2903 removed outlier: 3.730A pdb=" N ARG A2903 " --> pdb=" O ARG A2899 " (cutoff:3.500A) Processing helix chain 'A' and resid 2910 through 2934 Proline residue: A2914 - end of helix removed outlier: 3.527A pdb=" N ALA A2919 " --> pdb=" O LEU A2916 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A2922 " --> pdb=" O ALA A2919 " (cutoff:3.500A) Processing helix chain 'A' and resid 2937 through 2939 No H-bonds generated for 'chain 'A' and resid 2937 through 2939' Processing helix chain 'A' and resid 2943 through 2958 removed outlier: 3.611A pdb=" N ASN A2958 " --> pdb=" O LYS A2954 " (cutoff:3.500A) Processing helix chain 'A' and resid 2967 through 2991 removed outlier: 3.963A pdb=" N TRP A2976 " --> pdb=" O SER A2972 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS A2980 " --> pdb=" O TRP A2976 " (cutoff:3.500A) Processing helix chain 'A' and resid 2999 through 3022 Processing helix chain 'A' and resid 3025 through 3037 removed outlier: 3.772A pdb=" N ARG A3034 " --> pdb=" O ASP A3030 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE A3035 " --> pdb=" O ILE A3031 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N HIS A3036 " --> pdb=" O LEU A3032 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR A3037 " --> pdb=" O SER A3033 " (cutoff:3.500A) Processing helix chain 'A' and resid 3043 through 3062 removed outlier: 4.490A pdb=" N GLY A3062 " --> pdb=" O LEU A3058 " (cutoff:3.500A) Processing helix chain 'A' and resid 3066 through 3077 Processing helix chain 'A' and resid 3086 through 3102 Processing helix chain 'A' and resid 3106 through 3119 Processing helix chain 'A' and resid 3124 through 3141 removed outlier: 3.993A pdb=" N LYS A3140 " --> pdb=" O ASN A3136 " (cutoff:3.500A) Processing helix chain 'A' and resid 3144 through 3159 removed outlier: 3.525A pdb=" N VAL A3148 " --> pdb=" O LEU A3144 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER A3149 " --> pdb=" O HIS A3145 " (cutoff:3.500A) Processing helix chain 'A' and resid 3167 through 3179 removed outlier: 3.676A pdb=" N LEU A3177 " --> pdb=" O VAL A3173 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N SER A3178 " --> pdb=" O LEU A3174 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE A3179 " --> pdb=" O TRP A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3185 through 3193 Processing helix chain 'A' and resid 3199 through 3202 Processing helix chain 'A' and resid 3206 through 3213 Processing helix chain 'A' and resid 3216 through 3231 removed outlier: 3.834A pdb=" N LYS A3219 " --> pdb=" O SER A3216 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A3221 " --> pdb=" O GLY A3218 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A3222 " --> pdb=" O LYS A3219 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN A3223 " --> pdb=" O LEU A3220 " (cutoff:3.500A) Processing helix chain 'A' and resid 3233 through 3254 removed outlier: 4.561A pdb=" N PHE A3238 " --> pdb=" O GLN A3234 " (cutoff:3.500A) Proline residue: A3239 - end of helix Processing helix chain 'A' and resid 3284 through 3299 removed outlier: 3.614A pdb=" N LEU A3299 " --> pdb=" O MET A3295 " (cutoff:3.500A) Processing helix chain 'A' and resid 3301 through 3317 removed outlier: 4.254A pdb=" N VAL A3315 " --> pdb=" O VAL A3311 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TRP A3316 " --> pdb=" O ASP A3312 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3321 through 3343 removed outlier: 3.564A pdb=" N LEU A3326 " --> pdb=" O HIS A3322 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A3342 " --> pdb=" O SER A3338 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A3343 " --> pdb=" O VAL A3339 " (cutoff:3.500A) Processing helix chain 'A' and resid 3354 through 3365 Processing helix chain 'A' and resid 3385 through 3398 removed outlier: 3.889A pdb=" N GLN A3398 " --> pdb=" O GLN A3394 " (cutoff:3.500A) Processing helix chain 'A' and resid 3400 through 3412 Processing helix chain 'A' and resid 3423 through 3443 removed outlier: 3.810A pdb=" N LYS A3442 " --> pdb=" O GLU A3438 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLN A3443 " --> pdb=" O ALA A3439 " (cutoff:3.500A) Processing helix chain 'A' and resid 3455 through 3459 Processing helix chain 'A' and resid 3525 through 3546 removed outlier: 3.837A pdb=" N ARG A3529 " --> pdb=" O LEU A3525 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A3530 " --> pdb=" O THR A3526 " (cutoff:3.500A) Proline residue: A3543 - end of helix removed outlier: 4.535A pdb=" N GLU A3546 " --> pdb=" O ASN A3542 " (cutoff:3.500A) Processing helix chain 'A' and resid 3551 through 3554 No H-bonds generated for 'chain 'A' and resid 3551 through 3554' Processing helix chain 'A' and resid 3582 through 3593 Processing helix chain 'A' and resid 3599 through 3614 removed outlier: 4.035A pdb=" N ARG A3614 " --> pdb=" O THR A3610 " (cutoff:3.500A) Processing helix chain 'A' and resid 3620 through 3633 removed outlier: 3.593A pdb=" N ASN A3633 " --> pdb=" O GLU A3629 " (cutoff:3.500A) Processing helix chain 'A' and resid 3639 through 3647 Processing helix chain 'A' and resid 3651 through 3674 Processing helix chain 'A' and resid 3682 through 3684 No H-bonds generated for 'chain 'A' and resid 3682 through 3684' Processing helix chain 'A' and resid 3722 through 3728 Processing helix chain 'A' and resid 3730 through 3734 Processing helix chain 'A' and resid 3736 through 3748 removed outlier: 3.647A pdb=" N MET A3741 " --> pdb=" O LEU A3737 " (cutoff:3.500A) Processing helix chain 'A' and resid 3755 through 3778 removed outlier: 4.066A pdb=" N ASP A3765 " --> pdb=" O THR A3761 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A3766 " --> pdb=" O VAL A3762 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A3777 " --> pdb=" O LYS A3773 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR A3778 " --> pdb=" O THR A3774 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3789 No H-bonds generated for 'chain 'A' and resid 3787 through 3789' Processing helix chain 'A' and resid 3793 through 3815 removed outlier: 4.138A pdb=" N VAL A3797 " --> pdb=" O SER A3793 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A3814 " --> pdb=" O ARG A3810 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3820 No H-bonds generated for 'chain 'A' and resid 3818 through 3820' Processing helix chain 'A' and resid 3823 through 3831 Processing helix chain 'A' and resid 3834 through 3837 No H-bonds generated for 'chain 'A' and resid 3834 through 3837' Processing helix chain 'A' and resid 3842 through 3844 No H-bonds generated for 'chain 'A' and resid 3842 through 3844' Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.757A pdb=" N GLN B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 50 Processing helix chain 'B' and resid 67 through 83 removed outlier: 3.983A pdb=" N GLN B 73 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 83 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.576A pdb=" N GLU B 91 " --> pdb=" O GLN B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 94 through 109 removed outlier: 3.612A pdb=" N TYR B 97 " --> pdb=" O PRO B 94 " (cutoff:3.500A) Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 113 through 123 removed outlier: 4.024A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.989A pdb=" N GLN B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.654A pdb=" N LEU B 150 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 151 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.771A pdb=" N PHE B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 181 removed outlier: 3.577A pdb=" N TYR B 178 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'C' and resid 2 through 21 Processing helix chain 'C' and resid 36 through 49 removed outlier: 3.716A pdb=" N GLU C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 69 removed outlier: 4.296A pdb=" N MET C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.779A pdb=" N TYR C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 130 removed outlier: 3.740A pdb=" N ASP C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 182 removed outlier: 3.644A pdb=" N SER C 182 " --> pdb=" O HIS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 Processing helix chain 'C' and resid 214 through 226 Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.687A pdb=" N TYR C 241 " --> pdb=" O CYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 254 removed outlier: 3.925A pdb=" N ASP C 251 " --> pdb=" O ASN C 247 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 253 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N HIS C 254 " --> pdb=" O GLN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 271 Processing helix chain 'C' and resid 399 through 417 Processing helix chain 'D' and resid 58 through 86 Processing helix chain 'D' and resid 113 through 116 No H-bonds generated for 'chain 'D' and resid 113 through 116' Processing helix chain 'D' and resid 137 through 140 No H-bonds generated for 'chain 'D' and resid 137 through 140' Processing helix chain 'D' and resid 151 through 169 removed outlier: 3.649A pdb=" N GLN D 156 " --> pdb=" O HIS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 207 removed outlier: 3.688A pdb=" N ASP D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 223 Processing helix chain 'D' and resid 228 through 238 removed outlier: 4.018A pdb=" N GLN D 232 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 261 Processing helix chain 'E' and resid 14 through 26 Processing helix chain 'E' and resid 33 through 60 Processing helix chain 'E' and resid 68 through 79 Processing helix chain 'E' and resid 89 through 99 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'F' and resid 14 through 24 removed outlier: 3.649A pdb=" N SER F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR F 24 " --> pdb=" O MET F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 57 removed outlier: 3.594A pdb=" N ALA F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS F 57 " --> pdb=" O GLN F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 109 through 113 Processing helix chain 'G' and resid 63 through 70 removed outlier: 3.643A pdb=" N GLU G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 106 removed outlier: 3.710A pdb=" N THR G 97 " --> pdb=" O GLU G 93 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG G 106 " --> pdb=" O LEU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 123 Processing helix chain 'G' and resid 146 through 160 Processing helix chain 'H' and resid 119 through 123 Processing helix chain 'H' and resid 132 through 141 Processing helix chain 'H' and resid 149 through 177 removed outlier: 3.633A pdb=" N ILE H 166 " --> pdb=" O PHE H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 207 Proline residue: H 202 - end of helix removed outlier: 3.532A pdb=" N GLU H 206 " --> pdb=" O PRO H 202 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR H 207 " --> pdb=" O ALA H 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 37 removed outlier: 4.150A pdb=" N TYR I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER I 36 " --> pdb=" O SER I 32 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU I 37 " --> pdb=" O MET I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 72 removed outlier: 4.063A pdb=" N LEU I 72 " --> pdb=" O GLU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 86 Processing helix chain 'I' and resid 91 through 111 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 149 through 155 removed outlier: 4.129A pdb=" N MET I 153 " --> pdb=" O GLU I 149 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE I 154 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU I 155 " --> pdb=" O LEU I 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 149 through 155' Processing helix chain 'I' and resid 175 through 178 No H-bonds generated for 'chain 'I' and resid 175 through 178' Processing helix chain 'I' and resid 188 through 204 Processing helix chain 'I' and resid 215 through 243 removed outlier: 4.071A pdb=" N GLU I 219 " --> pdb=" O VAL I 215 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE I 220 " --> pdb=" O VAL I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 257 removed outlier: 3.881A pdb=" N SER I 256 " --> pdb=" O SER I 252 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA I 257 " --> pdb=" O HIS I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 293 Processing helix chain 'J' and resid 106 through 108 No H-bonds generated for 'chain 'J' and resid 106 through 108' Processing helix chain 'J' and resid 148 through 162 removed outlier: 3.560A pdb=" N GLY J 153 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG J 154 " --> pdb=" O GLN J 150 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU J 161 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS J 162 " --> pdb=" O THR J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 193 removed outlier: 3.953A pdb=" N ARG J 193 " --> pdb=" O SER J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 219 through 229 removed outlier: 3.523A pdb=" N ASN J 226 " --> pdb=" O VAL J 222 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN J 227 " --> pdb=" O VAL J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 263 Processing helix chain 'J' and resid 277 through 286 Processing helix chain 'J' and resid 294 through 307 removed outlier: 3.683A pdb=" N GLU J 302 " --> pdb=" O ALA J 298 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 330 Processing helix chain 'N' and resid 541 through 556 Processing sheet with id= A, first strand: chain 'A' and resid 604 through 606 Processing sheet with id= B, first strand: chain 'A' and resid 922 through 927 removed outlier: 3.679A pdb=" N VAL A 925 " --> pdb=" O LEU A 934 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 932 " --> pdb=" O PHE A 927 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 3447 through 3449 removed outlier: 7.220A pdb=" N ARG A3491 " --> pdb=" O TYR A3506 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR A3506 " --> pdb=" O ARG A3491 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A3503 " --> pdb=" O VAL A3519 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A3571 " --> pdb=" O MET A3520 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A3572 " --> pdb=" O ALA A3565 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ALA A3565 " --> pdb=" O LEU A3572 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLU A3574 " --> pdb=" O VAL A3563 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A3563 " --> pdb=" O GLU A3574 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 3579 through 3581 Processing sheet with id= E, first strand: chain 'A' and resid 3485 through 3488 removed outlier: 6.625A pdb=" N ARG A3508 " --> pdb=" O ALA A3486 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 163 through 167 Processing sheet with id= G, first strand: chain 'B' and resid 258 through 260 Processing sheet with id= H, first strand: chain 'B' and resid 335 through 338 removed outlier: 3.677A pdb=" N THR B 273 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 345 through 350 removed outlier: 6.654A pdb=" N CYS B 360 " --> pdb=" O TYR B 346 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR B 348 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 358 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE B 350 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY B 356 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 378 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP B 370 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN B 376 " --> pdb=" O ASP B 370 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 399 through 402 removed outlier: 3.731A pdb=" N ALA B 408 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 420 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 429 through 434 removed outlier: 6.388A pdb=" N GLY B 444 " --> pdb=" O ASP B 430 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL B 432 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 442 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE B 434 " --> pdb=" O TYR B 440 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR B 440 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 450 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 462 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER B 454 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER B 460 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 471 through 476 removed outlier: 6.690A pdb=" N ALA B 486 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B 474 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA B 484 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE B 476 " --> pdb=" O TYR B 482 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TYR B 482 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP B 496 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU B 502 " --> pdb=" O ASP B 496 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 513 through 518 removed outlier: 6.442A pdb=" N ALA B 528 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU B 516 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 526 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE B 518 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 524 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 557 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP B 538 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 555 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 566 through 569 removed outlier: 6.489A pdb=" N THR B 580 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= P, first strand: chain 'C' and resid 350 through 356 removed outlier: 3.652A pdb=" N ASP C 336 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 340 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 363 through 365 Processing sheet with id= R, first strand: chain 'F' and resid 91 through 93 1960 hydrogen bonds defined for protein. 5283 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: 34.56 Time building geometry restraints manager: 56.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 38553 1.03 - 1.23: 137 1.23 - 1.42: 16863 1.42 - 1.62: 23828 1.62 - 1.81: 404 Bond restraints: 79785 Sorted by residual: bond pdb=" C ASN D 124 " pdb=" N ALA D 125 " ideal model delta sigma weight residual 1.331 1.368 -0.037 1.48e-02 4.57e+03 6.24e+00 bond pdb=" O15 IHP A4001 " pdb=" P5 IHP A4001 " ideal model delta sigma weight residual 1.675 1.643 0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C MET A3475 " pdb=" O MET A3475 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.42e+00 bond pdb=" CA PHE B 413 " pdb=" C PHE B 413 " ideal model delta sigma weight residual 1.522 1.496 0.026 1.72e-02 3.38e+03 2.22e+00 bond pdb=" O32 IHP A4001 " pdb=" P2 IHP A4001 " ideal model delta sigma weight residual 1.537 1.508 0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 79780 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.90: 1270 106.90 - 113.86: 95298 113.86 - 120.82: 29407 120.82 - 127.78: 17230 127.78 - 134.74: 425 Bond angle restraints: 143630 Sorted by residual: angle pdb=" C SER A2857 " pdb=" N CYS A2858 " pdb=" CA CYS A2858 " ideal model delta sigma weight residual 120.65 115.19 5.46 1.36e+00 5.41e-01 1.61e+01 angle pdb=" N GLY C 344 " pdb=" CA GLY C 344 " pdb=" C GLY C 344 " ideal model delta sigma weight residual 114.67 110.38 4.29 1.10e+00 8.26e-01 1.52e+01 angle pdb=" C HIS A 771 " pdb=" N ASP A 772 " pdb=" CA ASP A 772 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.17e+01 angle pdb=" N SER A3348 " pdb=" CA SER A3348 " pdb=" C SER A3348 " ideal model delta sigma weight residual 113.23 109.14 4.09 1.22e+00 6.72e-01 1.13e+01 angle pdb=" C VAL A 654 " pdb=" N PRO A 655 " pdb=" CA PRO A 655 " ideal model delta sigma weight residual 127.00 134.74 -7.74 2.40e+00 1.74e-01 1.04e+01 ... (remaining 143625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 30123 17.94 - 35.88: 2017 35.88 - 53.81: 293 53.81 - 71.75: 88 71.75 - 89.69: 59 Dihedral angle restraints: 32580 sinusoidal: 14970 harmonic: 17610 Sorted by residual: dihedral pdb=" CA VAL C 327 " pdb=" C VAL C 327 " pdb=" N TRP C 328 " pdb=" CA TRP C 328 " ideal model delta harmonic sigma weight residual -180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLN E 81 " pdb=" C GLN E 81 " pdb=" N SER E 82 " pdb=" CA SER E 82 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ILE G 128 " pdb=" C ILE G 128 " pdb=" N PRO G 129 " pdb=" CA PRO G 129 " ideal model delta harmonic sigma weight residual -180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 32577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.996: 6358 0.996 - 1.992: 0 1.992 - 2.988: 0 2.988 - 3.984: 0 3.984 - 4.980: 3 Chirality restraints: 6361 Sorted by residual: chirality pdb=" C4 IHP A4001 " pdb=" C3 IHP A4001 " pdb=" C5 IHP A4001 " pdb=" O14 IHP A4001 " both_signs ideal model delta sigma weight residual False 2.48 -2.50 4.98 2.00e-01 2.50e+01 6.20e+02 chirality pdb=" C2 IHP A4001 " pdb=" C1 IHP A4001 " pdb=" C3 IHP A4001 " pdb=" O12 IHP A4001 " both_signs ideal model delta sigma weight residual False -2.52 2.45 -4.97 2.00e-01 2.50e+01 6.17e+02 chirality pdb=" C1 IHP A4001 " pdb=" C2 IHP A4001 " pdb=" C6 IHP A4001 " pdb=" O11 IHP A4001 " both_signs ideal model delta sigma weight residual False 2.32 -2.47 4.78 2.00e-01 2.50e+01 5.72e+02 ... (remaining 6358 not shown) Planarity restraints: 11720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A3550 " -0.024 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C GLU A3550 " 0.082 2.00e-02 2.50e+03 pdb=" O GLU A3550 " -0.031 2.00e-02 2.50e+03 pdb=" N THR A3551 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A3729 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.07e+00 pdb=" C THR A3729 " -0.049 2.00e-02 2.50e+03 pdb=" O THR A3729 " 0.018 2.00e-02 2.50e+03 pdb=" N THR A3730 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 772 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C ASP A 772 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP A 772 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 773 " -0.016 2.00e-02 2.50e+03 ... (remaining 11717 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1917 2.15 - 2.76: 144738 2.76 - 3.37: 212945 3.37 - 3.99: 263699 3.99 - 4.60: 425023 Nonbonded interactions: 1048322 Sorted by model distance: nonbonded pdb=" H GLN B 144 " pdb=" OD2 ASP B 148 " model vdw 1.533 1.850 nonbonded pdb=" OE1 GLU I 46 " pdb=" H GLU I 46 " model vdw 1.540 1.850 nonbonded pdb=" OD1 ASP B 182 " pdb=" H ASN B 183 " model vdw 1.568 1.850 nonbonded pdb=" HE ARG E 34 " pdb=" O GLU F 87 " model vdw 1.586 1.850 nonbonded pdb=" OG SER A3106 " pdb=" HH TYR A3133 " model vdw 1.590 1.850 ... (remaining 1048317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 253 5.16 5 C 25532 2.51 5 N 7081 2.21 5 O 7465 1.98 5 H 38661 0.53 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.890 Extract box with map and model: 14.810 Check model and map are aligned: 1.280 Convert atoms to be neutral: 0.750 Process input model: 225.490 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 260.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 41124 Z= 0.255 Angle : 0.630 8.334 55737 Z= 0.375 Chirality : 0.113 4.980 6361 Planarity : 0.004 0.057 7167 Dihedral : 13.995 89.689 15149 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.23 % Favored : 94.72 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: 0.16 (0.12), residues: 4754 helix: 1.48 (0.10), residues: 2729 sheet: -1.26 (0.30), residues: 272 loop : -1.94 (0.14), residues: 1753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1243 time to evaluate : 5.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0 outliers final: 2 residues processed: 1243 average time/residue: 2.3229 time to fit residues: 3641.4583 Evaluate side-chains 926 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 924 time to evaluate : 4.998 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.7098 time to fit residues: 7.5105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 432 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 chunk 464 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 GLN A 668 GLN A 865 GLN A1665 ASN A2367 GLN A2655 ASN A2748 GLN A2764 GLN A2772 GLN A2921 GLN A2979 HIS A2982 GLN A3498 HIS A3617 GLN A3832 ASN B 69 GLN B 439 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 53 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN J 107 GLN J 220 ASN J 287 HIS N 558 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 41124 Z= 0.307 Angle : 0.620 11.234 55737 Z= 0.325 Chirality : 0.039 0.438 6361 Planarity : 0.005 0.067 7167 Dihedral : 4.727 80.997 5569 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.41 % Favored : 93.54 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: -0.00 (0.12), residues: 4754 helix: 1.25 (0.10), residues: 2731 sheet: -0.95 (0.31), residues: 272 loop : -1.91 (0.14), residues: 1751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 946 time to evaluate : 5.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 101 outliers final: 53 residues processed: 993 average time/residue: 2.3350 time to fit residues: 2946.4947 Evaluate side-chains 944 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 891 time to evaluate : 5.031 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 29 residues processed: 25 average time/residue: 0.9801 time to fit residues: 45.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 258 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 386 optimal weight: 2.9990 chunk 316 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 465 optimal weight: 4.9990 chunk 503 optimal weight: 2.9990 chunk 414 optimal weight: 1.9990 chunk 461 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 373 optimal weight: 0.0270 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1590 ASN A2396 ASN B 69 GLN B 133 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 254 HIS ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 53 GLN H 122 GLN J 107 GLN N 558 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 41124 Z= 0.219 Angle : 0.570 10.796 55737 Z= 0.294 Chirality : 0.037 0.292 6361 Planarity : 0.004 0.069 7167 Dihedral : 4.569 81.396 5569 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.68 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: 0.22 (0.12), residues: 4754 helix: 1.38 (0.10), residues: 2715 sheet: -0.76 (0.31), residues: 280 loop : -1.72 (0.15), residues: 1759 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 938 time to evaluate : 5.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 48 residues processed: 981 average time/residue: 2.2874 time to fit residues: 2861.7705 Evaluate side-chains 941 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 893 time to evaluate : 5.092 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 25 residues processed: 25 average time/residue: 0.8659 time to fit residues: 43.3443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 460 optimal weight: 2.9990 chunk 350 optimal weight: 4.9990 chunk 241 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 312 optimal weight: 3.9990 chunk 467 optimal weight: 3.9990 chunk 494 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 443 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1590 ASN A3053 GLN B 56 ASN B 69 GLN B 439 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 53 GLN I 310 ASN J 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 41124 Z= 0.290 Angle : 0.585 10.220 55737 Z= 0.304 Chirality : 0.038 0.359 6361 Planarity : 0.004 0.058 7167 Dihedral : 4.631 81.326 5569 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.63 % Favored : 93.35 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: 0.12 (0.12), residues: 4754 helix: 1.29 (0.10), residues: 2710 sheet: -0.72 (0.31), residues: 280 loop : -1.74 (0.15), residues: 1764 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 909 time to evaluate : 5.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 66 residues processed: 958 average time/residue: 2.2914 time to fit residues: 2804.0650 Evaluate side-chains 943 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 877 time to evaluate : 5.042 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 35 residues processed: 35 average time/residue: 0.9301 time to fit residues: 60.7029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 412 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 368 optimal weight: 0.7980 chunk 204 optimal weight: 0.6980 chunk 422 optimal weight: 1.9990 chunk 342 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 chunk 444 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 HIS A1590 ASN A3053 GLN B 56 ASN B 69 GLN C 153 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 41124 Z= 0.171 Angle : 0.544 9.344 55737 Z= 0.278 Chirality : 0.036 0.294 6361 Planarity : 0.004 0.056 7167 Dihedral : 4.427 81.010 5569 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.62 % Favored : 95.36 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: 0.51 (0.13), residues: 4754 helix: 1.60 (0.10), residues: 2706 sheet: -0.54 (0.32), residues: 277 loop : -1.55 (0.15), residues: 1771 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 925 time to evaluate : 4.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 50 residues processed: 966 average time/residue: 2.2661 time to fit residues: 2799.0204 Evaluate side-chains 926 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 876 time to evaluate : 5.044 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 31 residues processed: 22 average time/residue: 0.9010 time to fit residues: 40.0971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 166 optimal weight: 2.9990 chunk 445 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 290 optimal weight: 0.2980 chunk 122 optimal weight: 0.0980 chunk 495 optimal weight: 3.9990 chunk 411 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 HIS A1590 ASN A2748 GLN A2764 GLN B 56 ASN B 69 GLN B 439 ASN B 562 GLN E 101 GLN J 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 41124 Z= 0.172 Angle : 0.539 9.377 55737 Z= 0.273 Chirality : 0.036 0.270 6361 Planarity : 0.004 0.055 7167 Dihedral : 4.306 81.040 5569 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.02 % Favored : 94.96 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: 0.71 (0.13), residues: 4754 helix: 1.75 (0.10), residues: 2709 sheet: -0.46 (0.31), residues: 280 loop : -1.47 (0.15), residues: 1765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 915 time to evaluate : 5.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 54 residues processed: 954 average time/residue: 2.2418 time to fit residues: 2735.4199 Evaluate side-chains 930 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 876 time to evaluate : 5.040 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 31 residues processed: 25 average time/residue: 0.9020 time to fit residues: 44.2688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 477 optimal weight: 0.0050 chunk 55 optimal weight: 3.9990 chunk 282 optimal weight: 0.7980 chunk 361 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 417 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 chunk 493 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 HIS A1590 ASN A2748 GLN B 56 ASN B 69 GLN E 101 GLN J 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 41124 Z= 0.177 Angle : 0.538 8.784 55737 Z= 0.273 Chirality : 0.036 0.267 6361 Planarity : 0.004 0.044 7167 Dihedral : 4.237 80.904 5569 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.75 % Favored : 95.23 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: 0.80 (0.13), residues: 4754 helix: 1.84 (0.10), residues: 2697 sheet: -0.40 (0.31), residues: 280 loop : -1.42 (0.15), residues: 1777 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 909 time to evaluate : 5.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 50 residues processed: 947 average time/residue: 2.3267 time to fit residues: 2815.2077 Evaluate side-chains 923 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 873 time to evaluate : 4.995 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 30 residues processed: 21 average time/residue: 1.0127 time to fit residues: 40.3892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 305 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 313 optimal weight: 0.8980 chunk 336 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 387 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 HIS A1590 ASN A2748 GLN B 69 GLN B 439 ASN D 232 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 41124 Z= 0.262 Angle : 0.576 10.608 55737 Z= 0.295 Chirality : 0.037 0.273 6361 Planarity : 0.004 0.095 7167 Dihedral : 4.365 80.718 5569 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.10 % Favored : 93.88 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: 0.59 (0.13), residues: 4754 helix: 1.66 (0.10), residues: 2699 sheet: -0.50 (0.31), residues: 292 loop : -1.52 (0.15), residues: 1763 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 881 time to evaluate : 5.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 55 residues processed: 917 average time/residue: 2.2543 time to fit residues: 2647.9119 Evaluate side-chains 920 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 865 time to evaluate : 5.039 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 32 residues processed: 24 average time/residue: 1.0909 time to fit residues: 47.3225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 448 optimal weight: 0.9980 chunk 472 optimal weight: 0.8980 chunk 431 optimal weight: 2.9990 chunk 459 optimal weight: 4.9990 chunk 276 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 361 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 415 optimal weight: 0.7980 chunk 434 optimal weight: 3.9990 chunk 458 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 HIS A1590 ASN A2748 GLN B 69 GLN D 232 GLN E 101 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN J 107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 41124 Z= 0.173 Angle : 0.545 9.793 55737 Z= 0.276 Chirality : 0.035 0.246 6361 Planarity : 0.004 0.060 7167 Dihedral : 4.242 80.893 5569 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.45 % Favored : 95.53 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: 0.84 (0.13), residues: 4754 helix: 1.87 (0.10), residues: 2695 sheet: -0.43 (0.31), residues: 292 loop : -1.39 (0.15), residues: 1767 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 900 time to evaluate : 5.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 40 residues processed: 934 average time/residue: 2.2493 time to fit residues: 2692.3405 Evaluate side-chains 909 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 869 time to evaluate : 5.022 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 30 residues processed: 11 average time/residue: 1.1633 time to fit residues: 25.9109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 301 optimal weight: 2.9990 chunk 486 optimal weight: 2.9990 chunk 296 optimal weight: 0.8980 chunk 230 optimal weight: 0.6980 chunk 338 optimal weight: 3.9990 chunk 510 optimal weight: 1.9990 chunk 469 optimal weight: 1.9990 chunk 406 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 249 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 HIS A1590 ASN A2748 GLN A2764 GLN A3022 GLN B 69 GLN E 101 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 41124 Z= 0.185 Angle : 0.553 9.735 55737 Z= 0.280 Chirality : 0.036 0.250 6361 Planarity : 0.004 0.079 7167 Dihedral : 4.215 81.022 5569 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.25 % Favored : 94.72 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: 0.87 (0.13), residues: 4754 helix: 1.88 (0.10), residues: 2694 sheet: -0.37 (0.31), residues: 292 loop : -1.37 (0.15), residues: 1768 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9508 Ramachandran restraints generated. 4754 Oldfield, 0 Emsley, 4754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 885 time to evaluate : 5.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 47 outliers final: 38 residues processed: 917 average time/residue: 2.2799 time to fit residues: 2682.6872 Evaluate side-chains 904 residues out of total 4249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 866 time to evaluate : 4.984 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 30 residues processed: 9 average time/residue: 1.2033 time to fit residues: 22.6985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 322 optimal weight: 5.9990 chunk 432 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 406 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 417 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 HIS A1590 ASN A2748 GLN A3022 GLN A3251 GLN B 69 GLN D 232 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.096243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085773 restraints weight = 303847.826| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.79 r_work: 0.3216 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 41124 Z= 0.234 Angle : 0.570 10.216 55737 Z= 0.290 Chirality : 0.036 0.259 6361 Planarity : 0.004 0.066 7167 Dihedral : 4.301 81.002 5569 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.53 % Favored : 94.45 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % 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: 0.74 (0.13), residues: 4754 helix: 1.77 (0.10), residues: 2699 sheet: -0.40 (0.31), residues: 292 loop : -1.41 (0.15), residues: 1763 =============================================================================== Job complete usr+sys time: 35941.63 seconds wall clock time: 614 minutes 40.29 seconds (36880.29 seconds total)