Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 17:26:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/04_2023/6ryu_10059_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/04_2023/6ryu_10059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/04_2023/6ryu_10059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/04_2023/6ryu_10059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/04_2023/6ryu_10059_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/04_2023/6ryu_10059_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 303 5.49 5 Mg 2 5.21 5 S 100 5.16 5 C 13996 2.51 5 N 4285 2.21 5 O 4908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "W GLU 450": "OE1" <-> "OE2" Residue "W ASP 465": "OD1" <-> "OD2" Residue "W TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 541": "NH1" <-> "NH2" Residue "W PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 576": "NH1" <-> "NH2" Residue "W ASP 581": "OD1" <-> "OD2" Residue "W ASP 602": "OD1" <-> "OD2" Residue "W ARG 611": "NH1" <-> "NH2" Residue "W TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 791": "OE1" <-> "OE2" Residue "W GLU 853": "OE1" <-> "OE2" Residue "W GLU 910": "OE1" <-> "OE2" Residue "W PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 975": "NH1" <-> "NH2" Residue "W ASP 1041": "OD1" <-> "OD2" Residue "W ARG 1047": "NH1" <-> "NH2" Residue "W PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1094": "OE1" <-> "OE2" Residue "W PHE 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 1147": "OD1" <-> "OD2" Residue "W PHE 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 1159": "NH1" <-> "NH2" Residue "W GLU 1181": "OE1" <-> "OE2" Residue "W ARG 1183": "NH1" <-> "NH2" Residue "V GLU 450": "OE1" <-> "OE2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 541": "NH1" <-> "NH2" Residue "V PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 576": "NH1" <-> "NH2" Residue "V ASP 581": "OD1" <-> "OD2" Residue "V ASP 602": "OD1" <-> "OD2" Residue "V ARG 611": "NH1" <-> "NH2" Residue "V TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 791": "OE1" <-> "OE2" Residue "V GLU 853": "OE1" <-> "OE2" Residue "V GLU 910": "OE1" <-> "OE2" Residue "V PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 975": "NH1" <-> "NH2" Residue "V ASP 1041": "OD1" <-> "OD2" Residue "V ARG 1047": "NH1" <-> "NH2" Residue "V PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 1094": "OE1" <-> "OE2" Residue "V PHE 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 1147": "OD1" <-> "OD2" Residue "V PHE 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 1159": "NH1" <-> "NH2" Residue "V GLU 1181": "OE1" <-> "OE2" Residue "V ARG 1183": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23598 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3036 Classifications: {'DNA': 149} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3070 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "W" Number of atoms: 5668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 708, 5662 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 676} Chain breaks: 4 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 12, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 Conformer: "B" Number of residues, atoms: 708, 5662 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 676} Chain breaks: 4 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 12, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 bond proxies already assigned to first conformer: 5795 Chain: "V" Number of atoms: 5672 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 708, 5666 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 676} Chain breaks: 4 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 12, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Conformer: "B" Number of residues, atoms: 708, 5666 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 676} Chain breaks: 4 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 12, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 bond proxies already assigned to first conformer: 5799 Chain: "W" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ANP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ANP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12252 SG CYS W 452 79.094 105.559 50.583 1.00203.58 S ATOM 12276 SG CYS W 455 82.408 105.779 52.056 1.00206.12 S ATOM 12424 SG CYS W 475 82.423 106.747 48.289 1.00191.46 S ATOM 12338 SG CYS W 464 66.270 106.662 46.592 1.00212.42 S ATOM 12359 SG CYS W 467 66.545 103.209 48.025 1.00226.17 S ATOM 12542 SG CYS W 490 69.262 103.711 45.366 1.00221.82 S ATOM 12566 SG CYS W 493 65.846 103.680 44.560 1.00214.26 S ATOM 17920 SG CYS V 452 43.731 120.941 114.187 1.00236.99 S ATOM 17944 SG CYS V 455 40.424 120.483 112.755 1.00241.92 S ATOM 18092 SG CYS V 475 40.405 123.059 115.669 1.00244.27 S ATOM 18006 SG CYS V 464 56.552 123.671 117.314 1.00237.47 S ATOM 18027 SG CYS V 467 56.256 119.946 117.606 1.00245.21 S ATOM 18210 SG CYS V 490 53.535 121.617 119.730 1.00254.04 S ATOM 18234 SG CYS V 493 56.948 121.937 120.482 1.00246.60 S Time building chain proxies: 17.95, per 1000 atoms: 0.76 Number of scatterers: 23598 At special positions: 0 Unit cell: (123.9, 147, 194.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 100 16.00 P 303 15.00 Mg 2 11.99 O 4908 8.00 N 4285 7.00 C 13996 6.00 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: 11.70 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN V2203 " pdb="ZN ZN V2203 " - pdb=" SG CYS V 455 " pdb="ZN ZN V2203 " - pdb=" SG CYS V 452 " pdb="ZN ZN V2203 " - pdb=" SG CYS V 475 " pdb=" ZN V2204 " pdb="ZN ZN V2204 " - pdb=" SG CYS V 467 " pdb="ZN ZN V2204 " - pdb=" SG CYS V 493 " pdb="ZN ZN V2204 " - pdb=" SG CYS V 490 " pdb="ZN ZN V2204 " - pdb=" SG CYS V 464 " pdb=" ZN W2203 " pdb="ZN ZN W2203 " - pdb=" SG CYS W 455 " pdb="ZN ZN W2203 " - pdb=" SG CYS W 452 " pdb="ZN ZN W2203 " - pdb=" SG CYS W 475 " pdb=" ZN W2204 " pdb="ZN ZN W2204 " - pdb=" SG CYS W 467 " pdb="ZN ZN W2204 " - pdb=" SG CYS W 493 " pdb="ZN ZN W2204 " - pdb=" SG CYS W 490 " pdb="ZN ZN W2204 " - pdb=" SG CYS W 464 " Number of angles added : 12 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 14 sheets defined 41.8% alpha, 6.2% beta 126 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 9.28 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.604A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 106 removed outlier: 3.511A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.903A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 54 through 75 removed outlier: 4.002A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 removed outlier: 4.214A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 35 removed outlier: 3.623A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.358A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.691A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.901A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 96' Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.559A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 removed outlier: 3.630A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.596A pdb=" N GLN D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.943A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 54 removed outlier: 3.882A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 88 through 94 removed outlier: 3.786A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 113 removed outlier: 4.335A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 130 removed outlier: 3.567A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 54 through 75 removed outlier: 4.001A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 90 removed outlier: 4.213A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 28 through 35 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.644A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'G' and resid 91 through 94 No H-bonds generated for 'chain 'G' and resid 91 through 94' Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.551A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.828A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE H 67 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 98 removed outlier: 3.697A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG H 96 " --> pdb=" O GLN H 92 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 119 removed outlier: 3.541A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 560 through 563 No H-bonds generated for 'chain 'W' and resid 560 through 563' Processing helix chain 'W' and resid 568 through 577 removed outlier: 3.648A pdb=" N ARG W 576 " --> pdb=" O ARG W 572 " (cutoff:3.500A) Processing helix chain 'W' and resid 599 through 601 No H-bonds generated for 'chain 'W' and resid 599 through 601' Processing helix chain 'W' and resid 603 through 611 removed outlier: 4.015A pdb=" N GLU W 610 " --> pdb=" O ALA W 606 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG W 611 " --> pdb=" O GLU W 607 " (cutoff:3.500A) Processing helix chain 'W' and resid 619 through 622 No H-bonds generated for 'chain 'W' and resid 619 through 622' Processing helix chain 'W' and resid 649 through 651 No H-bonds generated for 'chain 'W' and resid 649 through 651' Processing helix chain 'W' and resid 665 through 677 Processing helix chain 'W' and resid 720 through 722 No H-bonds generated for 'chain 'W' and resid 720 through 722' Processing helix chain 'W' and resid 728 through 743 removed outlier: 4.427A pdb=" N GLU W 732 " --> pdb=" O TYR W 729 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY W 733 " --> pdb=" O GLN W 730 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU W 737 " --> pdb=" O LEU W 734 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE W 739 " --> pdb=" O TRP W 736 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP W 741 " --> pdb=" O ARG W 738 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA W 742 " --> pdb=" O PHE W 739 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN W 743 " --> pdb=" O SER W 740 " (cutoff:3.500A) Processing helix chain 'W' and resid 759 through 770 Processing helix chain 'W' and resid 787 through 797 Processing helix chain 'W' and resid 810 through 819 removed outlier: 3.991A pdb=" N ARG W 817 " --> pdb=" O ARG W 813 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU W 818 " --> pdb=" O ALA W 814 " (cutoff:3.500A) Processing helix chain 'W' and resid 853 through 857 Processing helix chain 'W' and resid 875 through 879 removed outlier: 3.600A pdb=" N LYS W 879 " --> pdb=" O HIS W 876 " (cutoff:3.500A) Processing helix chain 'W' and resid 884 through 890 removed outlier: 3.753A pdb=" N LEU W 889 " --> pdb=" O PHE W 885 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN W 890 " --> pdb=" O PHE W 886 " (cutoff:3.500A) Processing helix chain 'W' and resid 910 through 919 removed outlier: 3.503A pdb=" N HIS W 914 " --> pdb=" O GLU W 910 " (cutoff:3.500A) Processing helix chain 'W' and resid 927 through 932 Processing helix chain 'W' and resid 944 through 947 No H-bonds generated for 'chain 'W' and resid 944 through 947' Processing helix chain 'W' and resid 951 through 953 No H-bonds generated for 'chain 'W' and resid 951 through 953' Processing helix chain 'W' and resid 980 through 990 removed outlier: 3.635A pdb=" N LEU W 990 " --> pdb=" O TYR W 986 " (cutoff:3.500A) Processing helix chain 'W' and resid 1011 through 1014 No H-bonds generated for 'chain 'W' and resid 1011 through 1014' Processing helix chain 'W' and resid 1022 through 1024 No H-bonds generated for 'chain 'W' and resid 1022 through 1024' Processing helix chain 'W' and resid 1026 through 1029 No H-bonds generated for 'chain 'W' and resid 1026 through 1029' Processing helix chain 'W' and resid 1044 through 1048 Processing helix chain 'W' and resid 1051 through 1064 removed outlier: 3.798A pdb=" N GLN W1056 " --> pdb=" O LEU W1052 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS W1057 " --> pdb=" O LEU W1053 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN W1061 " --> pdb=" O LYS W1057 " (cutoff:3.500A) Processing helix chain 'W' and resid 1076 through 1089 removed outlier: 3.515A pdb=" N LEU W1081 " --> pdb=" O LYS W1077 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS W1088 " --> pdb=" O ASP W1084 " (cutoff:3.500A) Processing helix chain 'W' and resid 1102 through 1112 removed outlier: 4.099A pdb=" N GLN W1106 " --> pdb=" O GLY W1102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU W1107 " --> pdb=" O ASN W1103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE W1109 " --> pdb=" O ARG W1105 " (cutoff:3.500A) Processing helix chain 'W' and resid 1150 through 1159 removed outlier: 3.663A pdb=" N ILE W1154 " --> pdb=" O HIS W1151 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN W1155 " --> pdb=" O ASN W1152 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE W1157 " --> pdb=" O ILE W1154 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER W1158 " --> pdb=" O GLN W1155 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG W1159 " --> pdb=" O ALA W1156 " (cutoff:3.500A) Processing helix chain 'W' and resid 1180 through 1190 removed outlier: 3.732A pdb=" N ILE W1184 " --> pdb=" O GLU W1181 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR W1185 " --> pdb=" O GLU W1182 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL W1187 " --> pdb=" O ILE W1184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS W1190 " --> pdb=" O VAL W1187 " (cutoff:3.500A) Processing helix chain 'W' and resid 1197 through 1199 No H-bonds generated for 'chain 'W' and resid 1197 through 1199' Processing helix chain 'W' and resid 1408 through 1413 Processing helix chain 'V' and resid 560 through 563 No H-bonds generated for 'chain 'V' and resid 560 through 563' Processing helix chain 'V' and resid 568 through 577 removed outlier: 3.648A pdb=" N ARG V 576 " --> pdb=" O ARG V 572 " (cutoff:3.500A) Processing helix chain 'V' and resid 599 through 601 No H-bonds generated for 'chain 'V' and resid 599 through 601' Processing helix chain 'V' and resid 603 through 611 removed outlier: 4.015A pdb=" N GLU V 610 " --> pdb=" O ALA V 606 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG V 611 " --> pdb=" O GLU V 607 " (cutoff:3.500A) Processing helix chain 'V' and resid 619 through 622 No H-bonds generated for 'chain 'V' and resid 619 through 622' Processing helix chain 'V' and resid 649 through 651 No H-bonds generated for 'chain 'V' and resid 649 through 651' Processing helix chain 'V' and resid 665 through 677 Processing helix chain 'V' and resid 720 through 722 No H-bonds generated for 'chain 'V' and resid 720 through 722' Processing helix chain 'V' and resid 728 through 743 removed outlier: 4.428A pdb=" N GLU V 732 " --> pdb=" O TYR V 729 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY V 733 " --> pdb=" O GLN V 730 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU V 737 " --> pdb=" O LEU V 734 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE V 739 " --> pdb=" O TRP V 736 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP V 741 " --> pdb=" O ARG V 738 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA V 742 " --> pdb=" O PHE V 739 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN V 743 " --> pdb=" O SER V 740 " (cutoff:3.500A) Processing helix chain 'V' and resid 759 through 770 Processing helix chain 'V' and resid 787 through 797 Processing helix chain 'V' and resid 810 through 819 removed outlier: 3.991A pdb=" N ARG V 817 " --> pdb=" O ARG V 813 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU V 818 " --> pdb=" O ALA V 814 " (cutoff:3.500A) Processing helix chain 'V' and resid 853 through 857 Processing helix chain 'V' and resid 875 through 879 removed outlier: 3.600A pdb=" N LYS V 879 " --> pdb=" O HIS V 876 " (cutoff:3.500A) Processing helix chain 'V' and resid 884 through 890 removed outlier: 3.753A pdb=" N LEU V 889 " --> pdb=" O PHE V 885 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN V 890 " --> pdb=" O PHE V 886 " (cutoff:3.500A) Processing helix chain 'V' and resid 910 through 919 removed outlier: 3.504A pdb=" N HIS V 914 " --> pdb=" O GLU V 910 " (cutoff:3.500A) Processing helix chain 'V' and resid 927 through 932 Processing helix chain 'V' and resid 944 through 947 No H-bonds generated for 'chain 'V' and resid 944 through 947' Processing helix chain 'V' and resid 951 through 953 No H-bonds generated for 'chain 'V' and resid 951 through 953' Processing helix chain 'V' and resid 980 through 990 removed outlier: 3.635A pdb=" N LEU V 990 " --> pdb=" O TYR V 986 " (cutoff:3.500A) Processing helix chain 'V' and resid 1011 through 1014 No H-bonds generated for 'chain 'V' and resid 1011 through 1014' Processing helix chain 'V' and resid 1022 through 1024 No H-bonds generated for 'chain 'V' and resid 1022 through 1024' Processing helix chain 'V' and resid 1026 through 1029 No H-bonds generated for 'chain 'V' and resid 1026 through 1029' Processing helix chain 'V' and resid 1044 through 1048 Processing helix chain 'V' and resid 1051 through 1064 removed outlier: 3.797A pdb=" N GLN V1056 " --> pdb=" O LEU V1052 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS V1057 " --> pdb=" O LEU V1053 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN V1061 " --> pdb=" O LYS V1057 " (cutoff:3.500A) Processing helix chain 'V' and resid 1076 through 1089 removed outlier: 3.515A pdb=" N LEU V1081 " --> pdb=" O LYS V1077 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS V1088 " --> pdb=" O ASP V1084 " (cutoff:3.500A) Processing helix chain 'V' and resid 1102 through 1112 removed outlier: 4.100A pdb=" N GLN V1106 " --> pdb=" O GLY V1102 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU V1107 " --> pdb=" O ASN V1103 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE V1109 " --> pdb=" O ARG V1105 " (cutoff:3.500A) Processing helix chain 'V' and resid 1150 through 1159 removed outlier: 3.663A pdb=" N ILE V1154 " --> pdb=" O HIS V1151 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN V1155 " --> pdb=" O ASN V1152 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE V1157 " --> pdb=" O ILE V1154 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER V1158 " --> pdb=" O GLN V1155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG V1159 " --> pdb=" O ALA V1156 " (cutoff:3.500A) Processing helix chain 'V' and resid 1180 through 1190 removed outlier: 3.733A pdb=" N ILE V1184 " --> pdb=" O GLU V1181 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR V1185 " --> pdb=" O GLU V1182 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL V1187 " --> pdb=" O ILE V1184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS V1190 " --> pdb=" O VAL V1187 " (cutoff:3.500A) Processing helix chain 'V' and resid 1197 through 1199 No H-bonds generated for 'chain 'V' and resid 1197 through 1199' Processing helix chain 'V' and resid 1408 through 1413 Processing sheet with id= A, first strand: chain 'W' and resid 507 through 511 Processing sheet with id= B, first strand: chain 'W' and resid 629 through 631 removed outlier: 3.516A pdb=" N ASN W 629 " --> pdb=" O LEU W 641 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'W' and resid 747 through 750 removed outlier: 3.728A pdb=" N THR W 901 " --> pdb=" O LEU W 749 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'W' and resid 869 through 872 Processing sheet with id= E, first strand: chain 'W' and resid 969 through 976 removed outlier: 6.970A pdb=" N VAL W1169 " --> pdb=" O THR W 970 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LEU W 972 " --> pdb=" O VAL W1169 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE W1171 " --> pdb=" O LEU W 972 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL W 974 " --> pdb=" O ILE W1171 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG W1173 " --> pdb=" O VAL W 974 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL W 976 " --> pdb=" O ARG W1173 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL W1175 " --> pdb=" O VAL W 976 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'W' and resid 502 through 505 removed outlier: 6.666A pdb=" N LYS W 546 " --> pdb=" O GLN W 503 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'W' and resid 624 through 627 removed outlier: 7.184A pdb=" N LYS W 643 " --> pdb=" O HIS W 625 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'V' and resid 507 through 511 Processing sheet with id= I, first strand: chain 'V' and resid 629 through 631 removed outlier: 3.516A pdb=" N ASN V 629 " --> pdb=" O LEU V 641 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'V' and resid 747 through 750 removed outlier: 3.728A pdb=" N THR V 901 " --> pdb=" O LEU V 749 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'V' and resid 869 through 872 Processing sheet with id= L, first strand: chain 'V' and resid 969 through 976 removed outlier: 6.970A pdb=" N VAL V1169 " --> pdb=" O THR V 970 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LEU V 972 " --> pdb=" O VAL V1169 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE V1171 " --> pdb=" O LEU V 972 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL V 974 " --> pdb=" O ILE V1171 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG V1173 " --> pdb=" O VAL V 974 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL V 976 " --> pdb=" O ARG V1173 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL V1175 " --> pdb=" O VAL V 976 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'V' and resid 502 through 505 removed outlier: 6.665A pdb=" N LYS V 546 " --> pdb=" O GLN V 503 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 624 through 627 removed outlier: 7.186A pdb=" N LYS V 643 " --> pdb=" O HIS V 625 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 616 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 11.83 Time building geometry restraints manager: 12.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5241 1.33 - 1.45: 6629 1.45 - 1.57: 12053 1.57 - 1.69: 611 1.69 - 1.81: 168 Bond restraints: 24702 Sorted by residual: bond pdb=" O3A ANP V2201 " pdb=" PB ANP V2201 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" O3A ANP W2201 " pdb=" PB ANP W2201 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" N3B ANP V2201 " pdb=" PG ANP V2201 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" N3B ANP W2201 " pdb=" PG ANP W2201 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CG LEU V 480 " pdb=" CD2 LEU V 480 " ideal model delta sigma weight residual 1.521 1.673 -0.152 3.30e-02 9.18e+02 2.13e+01 ... (remaining 24697 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.30: 1623 105.30 - 112.52: 12767 112.52 - 119.74: 8871 119.74 - 126.95: 10402 126.95 - 134.17: 997 Bond angle restraints: 34660 Sorted by residual: angle pdb=" CA ASN W 826 " pdb=" CB ASN W 826 " pdb=" CG ASN W 826 " ideal model delta sigma weight residual 112.60 119.26 -6.66 1.00e+00 1.00e+00 4.43e+01 angle pdb=" CA ASN V 826 " pdb=" CB ASN V 826 " pdb=" CG ASN V 826 " ideal model delta sigma weight residual 112.60 119.22 -6.62 1.00e+00 1.00e+00 4.39e+01 angle pdb=" C GLY W1003 " pdb=" N ASN W1004 " pdb=" CA ASN W1004 " ideal model delta sigma weight residual 121.70 133.35 -11.65 1.80e+00 3.09e-01 4.19e+01 angle pdb=" C GLY V1003 " pdb=" N ASN V1004 " pdb=" CA ASN V1004 " ideal model delta sigma weight residual 121.70 133.34 -11.64 1.80e+00 3.09e-01 4.19e+01 angle pdb=" C ASN V 826 " pdb=" CA ASN V 826 " pdb=" CB ASN V 826 " ideal model delta sigma weight residual 110.62 120.17 -9.55 1.51e+00 4.39e-01 4.00e+01 ... (remaining 34655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 12387 35.84 - 71.68: 1344 71.68 - 107.52: 40 107.52 - 143.36: 2 143.36 - 179.20: 2 Dihedral angle restraints: 13775 sinusoidal: 7421 harmonic: 6354 Sorted by residual: dihedral pdb=" CA ARG F 23 " pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta harmonic sigma weight residual -180.00 -149.08 -30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual -180.00 -149.18 -30.82 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA LYS V 832 " pdb=" C LYS V 832 " pdb=" N LYS V 833 " pdb=" CA LYS V 833 " ideal model delta harmonic sigma weight residual -180.00 -150.53 -29.47 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 13772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3428 0.085 - 0.169: 341 0.169 - 0.254: 39 0.254 - 0.339: 7 0.339 - 0.423: 8 Chirality restraints: 3823 Sorted by residual: chirality pdb=" CG LEU W 894 " pdb=" CB LEU W 894 " pdb=" CD1 LEU W 894 " pdb=" CD2 LEU W 894 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CG LEU V 894 " pdb=" CB LEU V 894 " pdb=" CD1 LEU V 894 " pdb=" CD2 LEU V 894 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB ILE W 937 " pdb=" CA ILE W 937 " pdb=" CG1 ILE W 937 " pdb=" CG2 ILE W 937 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 3820 not shown) Planarity restraints: 3367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN W 826 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.34e+01 pdb=" C ASN W 826 " -0.063 2.00e-02 2.50e+03 pdb=" O ASN W 826 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA W 827 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN V 826 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C ASN V 826 " -0.063 2.00e-02 2.50e+03 pdb=" O ASN V 826 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA V 827 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO G 80 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.050 5.00e-02 4.00e+02 ... (remaining 3364 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5230 2.79 - 3.32: 20058 3.32 - 3.85: 42449 3.85 - 4.37: 50084 4.37 - 4.90: 76169 Nonbonded interactions: 193990 Sorted by model distance: nonbonded pdb=" OG SER D 61 " pdb=" OXT GLY F 102 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR V 920 " pdb=" OE1 GLU V 922 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR W 920 " pdb=" OE1 GLU W 922 " model vdw 2.280 2.440 nonbonded pdb=" N ASP V 446 " pdb=" OD1 ASP V 446 " model vdw 2.290 2.520 nonbonded pdb=" N ASP W 446 " pdb=" OD1 ASP W 446 " model vdw 2.290 2.520 ... (remaining 193985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } ncs_group { reference = (chain 'V' and (resid 446 through 809 or resid 811 through 931 or (resid 932 thr \ ough 936 and (name N or name CA or name C or name O or name CB )) or resid 937 t \ hrough 1416 or resid 2201 through 2204)) selection = (chain 'W' and (resid 446 through 809 or resid 811 through 1416 or resid 2201 th \ rough 2204)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.820 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 82.020 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.152 24702 Z= 0.346 Angle : 1.057 18.714 34660 Z= 0.593 Chirality : 0.056 0.423 3823 Planarity : 0.007 0.091 3367 Dihedral : 22.935 179.204 9671 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.25 (0.13), residues: 2126 helix: -4.28 (0.07), residues: 952 sheet: -2.62 (0.36), residues: 180 loop : -2.68 (0.16), residues: 994 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 459 time to evaluate : 2.499 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 outliers start: 30 outliers final: 10 residues processed: 484 average time/residue: 0.4241 time to fit residues: 304.2242 Evaluate side-chains 245 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 2.607 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2218 time to fit residues: 7.4816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 0.4980 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 568 GLN W 575 GLN W 673 ASN W 715 GLN W 743 GLN W 846 HIS W 880 ASN W 882 GLN W 906 GLN W 908 ASN W 914 HIS ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1056 GLN V 575 GLN ** V 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 673 ASN V 715 GLN V 846 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 914 HIS V1155 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 24702 Z= 0.353 Angle : 0.760 9.586 34660 Z= 0.418 Chirality : 0.044 0.159 3823 Planarity : 0.006 0.061 3367 Dihedral : 26.678 178.130 5395 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.93 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.15), residues: 2126 helix: -2.40 (0.13), residues: 962 sheet: -2.30 (0.35), residues: 184 loop : -2.35 (0.17), residues: 980 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 26 residues processed: 268 average time/residue: 0.3538 time to fit residues: 149.9884 Evaluate side-chains 213 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 2.370 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2177 time to fit residues: 13.4761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 73 ASN H 60 ASN H 81 ASN W 760 GLN ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 743 GLN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 24702 Z= 0.198 Angle : 0.649 10.392 34660 Z= 0.353 Chirality : 0.039 0.171 3823 Planarity : 0.004 0.058 3367 Dihedral : 26.715 175.575 5395 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.16), residues: 2126 helix: -1.42 (0.15), residues: 960 sheet: -1.89 (0.38), residues: 164 loop : -2.20 (0.18), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 240 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 248 average time/residue: 0.3416 time to fit residues: 135.0484 Evaluate side-chains 204 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 197 time to evaluate : 2.303 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2544 time to fit residues: 6.0640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 0.0470 chunk 146 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS W 743 GLN ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1166 ASN V 669 GLN V 743 GLN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 24702 Z= 0.284 Angle : 0.687 11.712 34660 Z= 0.367 Chirality : 0.041 0.189 3823 Planarity : 0.005 0.053 3367 Dihedral : 26.847 175.505 5395 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.17), residues: 2126 helix: -0.84 (0.16), residues: 961 sheet: -1.50 (0.41), residues: 152 loop : -2.16 (0.18), residues: 1013 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 224 average time/residue: 0.3553 time to fit residues: 126.7879 Evaluate side-chains 193 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 2.394 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2274 time to fit residues: 7.7322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN E 93 GLN G 31 HIS ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 715 GLN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 998 ASN ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 24702 Z= 0.215 Angle : 0.644 10.862 34660 Z= 0.342 Chirality : 0.039 0.146 3823 Planarity : 0.004 0.053 3367 Dihedral : 26.776 175.838 5395 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.17), residues: 2126 helix: -0.46 (0.16), residues: 951 sheet: -1.22 (0.41), residues: 146 loop : -1.99 (0.18), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 217 average time/residue: 0.3455 time to fit residues: 121.8732 Evaluate side-chains 192 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 2.563 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2245 time to fit residues: 6.2295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS H 46 HIS ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 819 ASN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 998 ASN ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 24702 Z= 0.228 Angle : 0.645 12.094 34660 Z= 0.343 Chirality : 0.039 0.153 3823 Planarity : 0.004 0.052 3367 Dihedral : 26.694 175.501 5395 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 2126 helix: -0.24 (0.17), residues: 960 sheet: -1.18 (0.41), residues: 146 loop : -1.95 (0.18), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 202 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 218 average time/residue: 0.3570 time to fit residues: 124.7331 Evaluate side-chains 192 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 2.554 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2221 time to fit residues: 6.1812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.0370 chunk 26 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 169 optimal weight: 30.0000 chunk 131 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 472 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24702 Z= 0.172 Angle : 0.620 11.289 34660 Z= 0.329 Chirality : 0.038 0.158 3823 Planarity : 0.004 0.055 3367 Dihedral : 26.554 175.444 5395 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 2126 helix: -0.06 (0.17), residues: 992 sheet: -1.22 (0.38), residues: 174 loop : -1.94 (0.19), residues: 960 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 216 average time/residue: 0.3638 time to fit residues: 125.4345 Evaluate side-chains 192 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 2.453 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2146 time to fit residues: 5.2241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 157 optimal weight: 0.0050 chunk 114 optimal weight: 0.0570 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.8514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 743 GLN ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 630 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 998 ASN ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 24702 Z= 0.172 Angle : 0.625 11.343 34660 Z= 0.330 Chirality : 0.038 0.193 3823 Planarity : 0.004 0.055 3367 Dihedral : 26.411 174.809 5395 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2126 helix: 0.14 (0.17), residues: 979 sheet: -1.14 (0.38), residues: 174 loop : -1.78 (0.19), residues: 973 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 199 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 205 average time/residue: 0.3612 time to fit residues: 117.1718 Evaluate side-chains 190 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 2.655 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2256 time to fit residues: 5.8020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 202 optimal weight: 20.0000 chunk 215 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 HIS W 743 GLN ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 630 HIS V 890 ASN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 998 ASN ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 24702 Z= 0.285 Angle : 0.683 11.136 34660 Z= 0.361 Chirality : 0.041 0.328 3823 Planarity : 0.004 0.051 3367 Dihedral : 26.694 174.946 5395 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2126 helix: 0.08 (0.17), residues: 969 sheet: -1.17 (0.41), residues: 148 loop : -1.83 (0.18), residues: 1009 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 189 average time/residue: 0.3715 time to fit residues: 112.7293 Evaluate side-chains 182 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 2.351 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2306 time to fit residues: 4.3232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 0.0970 chunk 158 optimal weight: 8.9990 chunk 239 optimal weight: 0.0050 chunk 220 optimal weight: 0.7980 chunk 190 optimal weight: 0.0030 chunk 19 optimal weight: 0.2980 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 743 GLN V 630 HIS ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 24702 Z= 0.163 Angle : 0.638 11.474 34660 Z= 0.332 Chirality : 0.038 0.266 3823 Planarity : 0.004 0.057 3367 Dihedral : 26.437 175.273 5395 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2126 helix: 0.26 (0.17), residues: 977 sheet: -1.13 (0.38), residues: 176 loop : -1.69 (0.19), residues: 973 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.3518 time to fit residues: 120.3142 Evaluate side-chains 190 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.0030 chunk 202 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS W 743 GLN ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 876 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 998 ASN ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.088269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068498 restraints weight = 208273.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.069270 restraints weight = 111836.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.069799 restraints weight = 81330.550| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 24702 Z= 0.223 Angle : 0.653 11.143 34660 Z= 0.343 Chirality : 0.039 0.232 3823 Planarity : 0.004 0.053 3367 Dihedral : 26.466 174.816 5395 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2126 helix: 0.25 (0.17), residues: 983 sheet: -1.12 (0.38), residues: 176 loop : -1.72 (0.19), residues: 967 =============================================================================== Job complete usr+sys time: 3880.17 seconds wall clock time: 72 minutes 30.11 seconds (4350.11 seconds total)