Starting phenix.real_space_refine on Mon Feb 19 02:49:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/02_2024/6ryu_10059_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/02_2024/6ryu_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_10059/02_2024/6ryu_10059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/02_2024/6ryu_10059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/02_2024/6ryu_10059_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryu_10059/02_2024/6ryu_10059_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 17.84, 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: 11.02 Conformation dependent library (CDL) restraints added in 5.0 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: 12.95 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: 13.03 Time building geometry restraints manager: 11.78 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: 12658 35.84 - 71.68: 1377 71.68 - 107.52: 54 107.52 - 143.36: 2 143.36 - 179.20: 2 Dihedral angle restraints: 14093 sinusoidal: 7739 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 14090 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.050 Check model and map are aligned: 1.030 Set scattering table: 0.000 Process input model: 88.580 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.340 ------------------------------------------------------------------------------- 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 : 23.190 179.204 9989 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 % Allowed : 5.97 % Favored : 92.39 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP W 488 HIS 0.014 0.002 HIS V 914 PHE 0.029 0.003 PHE V1072 TYR 0.023 0.003 TYR H 80 ARG 0.023 0.001 ARG W1159 *********************** 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 : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8893 (tt0) cc_final: 0.8692 (tt0) REVERT: B 88 TYR cc_start: 0.7989 (m-10) cc_final: 0.7480 (m-80) REVERT: C 38 ASN cc_start: 0.8543 (m-40) cc_final: 0.7957 (p0) REVERT: D 68 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7263 (tm-30) REVERT: G 61 GLU cc_start: 0.7451 (tp30) cc_final: 0.7203 (tp30) REVERT: H 40 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8794 (mttm) REVERT: H 51 ILE cc_start: 0.9155 (tt) cc_final: 0.8942 (tt) REVERT: H 65 ASP cc_start: 0.8249 (t0) cc_final: 0.7908 (t0) REVERT: W 550 MET cc_start: 0.6267 (mtt) cc_final: 0.5898 (mtm) REVERT: W 608 MET cc_start: 0.7792 (mmm) cc_final: 0.7291 (tpp) REVERT: W 1123 LEU cc_start: 0.8758 (mt) cc_final: 0.8556 (mp) REVERT: W 1135 LEU cc_start: 0.8166 (mt) cc_final: 0.7929 (mt) REVERT: V 470 SER cc_start: 0.3408 (OUTLIER) cc_final: 0.0567 (t) REVERT: V 504 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8246 (ttpp) REVERT: V 608 MET cc_start: 0.3331 (mmm) cc_final: 0.2388 (mmt) REVERT: V 731 MET cc_start: 0.6653 (mmm) cc_final: 0.6037 (tpp) REVERT: V 764 PHE cc_start: 0.8455 (t80) cc_final: 0.8230 (t80) REVERT: V 768 LEU cc_start: 0.8923 (mp) cc_final: 0.8554 (tt) REVERT: V 826 ASN cc_start: 0.2605 (OUTLIER) cc_final: 0.2256 (p0) REVERT: V 905 LEU cc_start: 0.8248 (mp) cc_final: 0.7840 (pt) REVERT: V 981 MET cc_start: 0.8699 (ttp) cc_final: 0.7256 (mpp) REVERT: V 1120 PHE cc_start: 0.5802 (t80) cc_final: 0.5479 (t80) REVERT: V 1140 THR cc_start: 0.6788 (m) cc_final: 0.6503 (p) REVERT: V 1155 GLN cc_start: 0.8384 (mm110) cc_final: 0.8051 (tp-100) REVERT: V 1186 GLN cc_start: 0.7364 (mm110) cc_final: 0.6456 (tt0) outliers start: 30 outliers final: 10 residues processed: 484 average time/residue: 0.4048 time to fit residues: 288.8656 Evaluate side-chains 258 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 246 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain W residue 489 LEU Chi-restraints excluded: chain W residue 494 THR Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1179 SER Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 460 GLU Chi-restraints excluded: chain V residue 470 SER Chi-restraints excluded: chain V residue 826 ASN Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1179 SER 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: 0.0070 chunk 140 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 overall best weight: 2.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS C 82 HIS C 104 GLN G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 826 ASN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 914 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24702 Z= 0.282 Angle : 0.720 10.093 34660 Z= 0.397 Chirality : 0.043 0.157 3823 Planarity : 0.006 0.061 3367 Dihedral : 26.416 177.807 5730 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.41 % Allowed : 14.29 % Favored : 83.31 % 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: -3.62 (0.15), residues: 2126 helix: -2.36 (0.13), residues: 962 sheet: -2.20 (0.35), residues: 184 loop : -2.39 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP V 736 HIS 0.012 0.001 HIS B 18 PHE 0.020 0.002 PHE V1122 TYR 0.028 0.002 TYR V 613 ARG 0.011 0.001 ARG V1047 *********************** 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 298 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 254 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8099 (m-10) cc_final: 0.7522 (m-80) REVERT: C 38 ASN cc_start: 0.8468 (m-40) cc_final: 0.7987 (p0) REVERT: D 56 MET cc_start: 0.8566 (tpp) cc_final: 0.8313 (tpp) REVERT: D 68 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7494 (tm-30) REVERT: E 60 LEU cc_start: 0.8578 (mm) cc_final: 0.8297 (mp) REVERT: E 120 MET cc_start: 0.8138 (mtp) cc_final: 0.7828 (mtp) REVERT: F 88 TYR cc_start: 0.7470 (m-80) cc_final: 0.7101 (m-80) REVERT: H 40 LYS cc_start: 0.9196 (mtpt) cc_final: 0.8928 (mttm) REVERT: H 51 ILE cc_start: 0.9216 (tt) cc_final: 0.9007 (tt) REVERT: W 471 TYR cc_start: 0.4918 (m-80) cc_final: 0.4666 (m-80) REVERT: W 550 MET cc_start: 0.6363 (mtt) cc_final: 0.5942 (mtm) REVERT: W 1075 MET cc_start: 0.8304 (mtm) cc_final: 0.8046 (mtp) REVERT: V 645 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6947 (mtm-85) REVERT: V 731 MET cc_start: 0.6841 (mmm) cc_final: 0.6244 (tpp) REVERT: V 905 LEU cc_start: 0.8465 (mp) cc_final: 0.8027 (pt) REVERT: V 956 ARG cc_start: 0.7125 (tpt-90) cc_final: 0.6658 (pmt-80) REVERT: V 1013 MET cc_start: 0.8460 (tpp) cc_final: 0.8131 (tpp) REVERT: V 1039 MET cc_start: 0.6862 (mmt) cc_final: 0.6085 (mmt) REVERT: V 1131 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6134 (pp) REVERT: V 1155 GLN cc_start: 0.8097 (mm110) cc_final: 0.7786 (tp-100) REVERT: V 1186 GLN cc_start: 0.7338 (mm110) cc_final: 0.6463 (tt0) outliers start: 44 outliers final: 26 residues processed: 289 average time/residue: 0.3461 time to fit residues: 156.6437 Evaluate side-chains 235 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 494 THR Chi-restraints excluded: chain W residue 605 PHE Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG Chi-restraints excluded: chain V residue 825 ASP Chi-restraints excluded: chain V residue 844 LYS Chi-restraints excluded: chain V residue 903 THR Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1131 LEU Chi-restraints excluded: chain V residue 1166 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 0.0770 chunk 74 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 overall best weight: 1.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 568 GLN W 760 GLN ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 826 ASN ** 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: 0.7903 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24702 Z= 0.225 Angle : 0.656 10.984 34660 Z= 0.358 Chirality : 0.040 0.171 3823 Planarity : 0.005 0.056 3367 Dihedral : 26.417 174.812 5720 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.41 % Allowed : 17.13 % Favored : 80.46 % 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: -2.57 (0.17), residues: 2126 helix: -1.30 (0.15), residues: 951 sheet: -1.56 (0.40), residues: 152 loop : -2.09 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP V 797 HIS 0.006 0.001 HIS V1088 PHE 0.013 0.001 PHE B 100 TYR 0.021 0.002 TYR H 37 ARG 0.007 0.000 ARG V 645 *********************** 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 279 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 53 GLU cc_start: 0.8027 (tp30) cc_final: 0.7614 (tp30) REVERT: C 89 ASN cc_start: 0.8008 (m-40) cc_final: 0.7652 (t0) REVERT: D 56 MET cc_start: 0.8563 (tpp) cc_final: 0.8253 (tpp) REVERT: D 68 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7617 (tm-30) REVERT: E 59 GLU cc_start: 0.7673 (pm20) cc_final: 0.7471 (pm20) REVERT: E 120 MET cc_start: 0.8017 (mtp) cc_final: 0.7810 (mtp) REVERT: F 88 TYR cc_start: 0.7518 (m-80) cc_final: 0.7091 (m-80) REVERT: H 40 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8851 (mttm) REVERT: H 51 ILE cc_start: 0.9200 (tt) cc_final: 0.8988 (tt) REVERT: W 550 MET cc_start: 0.6374 (mtt) cc_final: 0.5446 (mpp) REVERT: W 608 MET cc_start: 0.7174 (tpp) cc_final: 0.6835 (tpt) REVERT: W 1192 MET cc_start: 0.7371 (mtp) cc_final: 0.7127 (ttm) REVERT: V 623 MET cc_start: 0.8086 (tpp) cc_final: 0.7853 (tpp) REVERT: V 731 MET cc_start: 0.6936 (mmm) cc_final: 0.6331 (tpp) REVERT: V 905 LEU cc_start: 0.8556 (mp) cc_final: 0.8138 (pt) REVERT: V 1013 MET cc_start: 0.8357 (tpp) cc_final: 0.8084 (tpp) REVERT: V 1131 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6218 (pp) REVERT: V 1155 GLN cc_start: 0.8061 (mm110) cc_final: 0.7697 (tp-100) outliers start: 44 outliers final: 32 residues processed: 268 average time/residue: 0.3657 time to fit residues: 156.5481 Evaluate side-chains 237 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 494 THR Chi-restraints excluded: chain W residue 569 VAL Chi-restraints excluded: chain W residue 605 PHE Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 794 PHE Chi-restraints excluded: chain V residue 844 LYS Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1131 LEU Chi-restraints excluded: chain V residue 1142 ILE Chi-restraints excluded: chain V residue 1143 ILE Chi-restraints excluded: chain V residue 1166 ASN Chi-restraints excluded: chain V residue 1194 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 231 optimal weight: 0.0000 chunk 114 optimal weight: 10.0000 chunk 207 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24702 Z= 0.193 Angle : 0.626 13.120 34660 Z= 0.336 Chirality : 0.039 0.148 3823 Planarity : 0.004 0.054 3367 Dihedral : 26.221 175.830 5719 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.46 % Allowed : 18.39 % Favored : 79.15 % 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: -2.08 (0.17), residues: 2126 helix: -0.68 (0.16), residues: 949 sheet: -1.50 (0.38), residues: 164 loop : -2.02 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP V 797 HIS 0.014 0.001 HIS V1021 PHE 0.012 0.001 PHE B 100 TYR 0.027 0.001 TYR H 37 ARG 0.004 0.000 ARG V1159 *********************** 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 269 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 53 GLU cc_start: 0.7991 (tp30) cc_final: 0.7617 (tp30) REVERT: C 89 ASN cc_start: 0.7981 (m-40) cc_final: 0.7680 (t0) REVERT: D 56 MET cc_start: 0.8495 (tpp) cc_final: 0.8259 (tpp) REVERT: D 68 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7707 (tm-30) REVERT: E 120 MET cc_start: 0.7917 (mtp) cc_final: 0.7677 (mtp) REVERT: F 88 TYR cc_start: 0.7463 (m-80) cc_final: 0.7073 (m-80) REVERT: W 550 MET cc_start: 0.6368 (mtt) cc_final: 0.5420 (mpp) REVERT: W 608 MET cc_start: 0.7259 (tpp) cc_final: 0.6854 (tpt) REVERT: W 1083 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: V 623 MET cc_start: 0.8102 (tpp) cc_final: 0.7885 (tpp) REVERT: V 712 TYR cc_start: 0.5321 (m-10) cc_final: 0.5042 (m-10) REVERT: V 731 MET cc_start: 0.7015 (mmm) cc_final: 0.6399 (tpp) REVERT: V 764 PHE cc_start: 0.8781 (t80) cc_final: 0.8509 (t80) REVERT: V 905 LEU cc_start: 0.8553 (mp) cc_final: 0.8053 (pt) REVERT: V 1013 MET cc_start: 0.8295 (tpp) cc_final: 0.8018 (tpp) REVERT: V 1080 ASP cc_start: 0.7793 (m-30) cc_final: 0.7478 (t0) REVERT: V 1131 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6218 (pp) REVERT: V 1155 GLN cc_start: 0.8136 (mm110) cc_final: 0.7776 (tp-100) REVERT: V 1186 GLN cc_start: 0.7724 (mm110) cc_final: 0.6316 (tt0) REVERT: V 1190 LYS cc_start: 0.6831 (mmpt) cc_final: 0.6481 (tppt) outliers start: 45 outliers final: 30 residues processed: 260 average time/residue: 0.3314 time to fit residues: 138.1302 Evaluate side-chains 232 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain W residue 494 THR Chi-restraints excluded: chain W residue 569 VAL Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 825 ASP Chi-restraints excluded: chain V residue 844 LYS Chi-restraints excluded: chain V residue 908 ASN Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Chi-restraints excluded: chain V residue 1131 LEU Chi-restraints excluded: chain V residue 1166 ASN Chi-restraints excluded: chain V residue 1194 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 715 GLN V 743 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: 0.7914 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24702 Z= 0.228 Angle : 0.631 12.121 34660 Z= 0.338 Chirality : 0.039 0.148 3823 Planarity : 0.004 0.052 3367 Dihedral : 26.228 175.017 5719 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.74 % Allowed : 19.10 % Favored : 78.16 % 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: -1.72 (0.17), residues: 2126 helix: -0.32 (0.16), residues: 959 sheet: -1.27 (0.40), residues: 148 loop : -1.92 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP V 797 HIS 0.006 0.001 HIS V1088 PHE 0.016 0.001 PHE V 821 TYR 0.022 0.001 TYR H 37 ARG 0.010 0.000 ARG A 49 *********************** 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 261 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 211 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7587 (mt-10) REVERT: B 16 LYS cc_start: 0.6282 (pptt) cc_final: 0.5617 (tptp) REVERT: B 53 GLU cc_start: 0.8027 (tp30) cc_final: 0.7819 (tp30) REVERT: D 56 MET cc_start: 0.8504 (tpp) cc_final: 0.8234 (tpp) REVERT: D 68 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7727 (tm-30) REVERT: F 88 TYR cc_start: 0.7629 (m-80) cc_final: 0.7346 (m-80) REVERT: F 93 GLN cc_start: 0.8136 (mt0) cc_final: 0.7934 (mt0) REVERT: W 550 MET cc_start: 0.6477 (mtt) cc_final: 0.6126 (mtm) REVERT: W 608 MET cc_start: 0.7400 (tpp) cc_final: 0.6933 (tpt) REVERT: W 1083 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: V 623 MET cc_start: 0.8218 (tpp) cc_final: 0.7988 (tpp) REVERT: V 731 MET cc_start: 0.7178 (mmm) cc_final: 0.6837 (tpp) REVERT: V 905 LEU cc_start: 0.8513 (mp) cc_final: 0.8034 (pt) REVERT: V 1013 MET cc_start: 0.8328 (tpp) cc_final: 0.8020 (tpp) REVERT: V 1131 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6293 (pp) REVERT: V 1155 GLN cc_start: 0.8128 (mm110) cc_final: 0.7756 (tp-100) REVERT: V 1186 GLN cc_start: 0.7904 (mm110) cc_final: 0.7618 (mm110) REVERT: V 1190 LYS cc_start: 0.6938 (mmpt) cc_final: 0.6484 (tppt) outliers start: 50 outliers final: 36 residues processed: 255 average time/residue: 0.3582 time to fit residues: 148.2431 Evaluate side-chains 234 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 569 VAL Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 818 GLU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1075 MET Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 570 MET Chi-restraints excluded: chain V residue 825 ASP Chi-restraints excluded: chain V residue 908 ASN Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Chi-restraints excluded: chain V residue 1131 LEU Chi-restraints excluded: chain V residue 1143 ILE Chi-restraints excluded: chain V residue 1166 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 0.0170 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 472 HIS V 819 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24702 Z= 0.191 Angle : 0.617 13.736 34660 Z= 0.328 Chirality : 0.039 0.314 3823 Planarity : 0.004 0.053 3367 Dihedral : 26.075 175.533 5718 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.68 % Allowed : 20.03 % Favored : 77.29 % 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: -1.37 (0.18), residues: 2126 helix: 0.01 (0.17), residues: 958 sheet: -1.24 (0.37), residues: 176 loop : -1.76 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 797 HIS 0.006 0.001 HIS V1021 PHE 0.016 0.001 PHE V 821 TYR 0.030 0.001 TYR V1023 ARG 0.003 0.000 ARG V1159 *********************** 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 260 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: B 16 LYS cc_start: 0.6108 (pptt) cc_final: 0.5575 (tptp) REVERT: B 53 GLU cc_start: 0.7978 (tp30) cc_final: 0.7692 (tp30) REVERT: D 56 MET cc_start: 0.8489 (tpp) cc_final: 0.8171 (tpp) REVERT: D 68 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7783 (tm-30) REVERT: F 88 TYR cc_start: 0.7570 (m-80) cc_final: 0.7368 (m-80) REVERT: W 550 MET cc_start: 0.6404 (mtt) cc_final: 0.6104 (mtm) REVERT: W 608 MET cc_start: 0.7373 (tpp) cc_final: 0.6889 (tpt) REVERT: W 981 MET cc_start: 0.5243 (mmp) cc_final: 0.4933 (mmm) REVERT: W 1083 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: V 731 MET cc_start: 0.7386 (mmm) cc_final: 0.6799 (tpp) REVERT: V 905 LEU cc_start: 0.8536 (mp) cc_final: 0.8040 (pt) REVERT: V 954 MET cc_start: 0.6992 (tmm) cc_final: 0.6594 (tmm) REVERT: V 1013 MET cc_start: 0.8319 (tpp) cc_final: 0.7990 (tpp) REVERT: V 1131 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6196 (pp) REVERT: V 1155 GLN cc_start: 0.8253 (mm110) cc_final: 0.7851 (tp-100) REVERT: V 1190 LYS cc_start: 0.6931 (mmpt) cc_final: 0.6468 (tppt) outliers start: 49 outliers final: 33 residues processed: 254 average time/residue: 0.3338 time to fit residues: 135.8792 Evaluate side-chains 226 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain W residue 569 VAL Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 818 GLU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 570 MET Chi-restraints excluded: chain V residue 825 ASP Chi-restraints excluded: chain V residue 908 ASN Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Chi-restraints excluded: chain V residue 1131 LEU Chi-restraints excluded: chain V residue 1166 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 0.1980 chunk 169 optimal weight: 30.0000 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 129 optimal weight: 0.0370 chunk 231 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 141 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7842 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24702 Z= 0.155 Angle : 0.603 11.936 34660 Z= 0.319 Chirality : 0.038 0.286 3823 Planarity : 0.004 0.055 3367 Dihedral : 25.834 174.936 5718 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.86 % Allowed : 21.07 % Favored : 77.07 % 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: -1.19 (0.18), residues: 2126 helix: 0.20 (0.17), residues: 984 sheet: -1.14 (0.37), residues: 176 loop : -1.76 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP W 488 HIS 0.010 0.001 HIS V 472 PHE 0.030 0.001 PHE H 67 TYR 0.026 0.001 TYR V1023 ARG 0.003 0.000 ARG V1111 *********************** 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 253 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6941 (tm-30) REVERT: B 53 GLU cc_start: 0.7881 (tp30) cc_final: 0.7405 (tp30) REVERT: C 38 ASN cc_start: 0.8355 (m-40) cc_final: 0.7941 (p0) REVERT: D 48 ASP cc_start: 0.7913 (p0) cc_final: 0.7530 (p0) REVERT: D 56 MET cc_start: 0.8465 (tpp) cc_final: 0.8107 (tpp) REVERT: D 68 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7821 (tm-30) REVERT: F 24 ASP cc_start: 0.7961 (t0) cc_final: 0.7723 (t0) REVERT: W 550 MET cc_start: 0.6298 (mtt) cc_final: 0.6083 (mtm) REVERT: W 608 MET cc_start: 0.7445 (tpp) cc_final: 0.6958 (tpt) REVERT: W 622 MET cc_start: 0.7828 (mmp) cc_final: 0.7600 (mmt) REVERT: W 642 ILE cc_start: 0.8136 (tt) cc_final: 0.7920 (mp) REVERT: W 981 MET cc_start: 0.5207 (mmp) cc_final: 0.4916 (mmm) REVERT: W 1083 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: W 1192 MET cc_start: 0.7312 (tpt) cc_final: 0.6183 (ttm) REVERT: V 449 MET cc_start: 0.4719 (pmm) cc_final: 0.4050 (ptp) REVERT: V 543 PHE cc_start: 0.6557 (m-80) cc_final: 0.6185 (m-80) REVERT: V 731 MET cc_start: 0.7372 (mmm) cc_final: 0.6873 (tpp) REVERT: V 874 GLU cc_start: 0.7839 (mp0) cc_final: 0.7118 (tt0) REVERT: V 905 LEU cc_start: 0.8500 (mp) cc_final: 0.8012 (pt) REVERT: V 1013 MET cc_start: 0.8318 (tpp) cc_final: 0.8069 (tpp) REVERT: V 1155 GLN cc_start: 0.8265 (mm110) cc_final: 0.7951 (tp-100) REVERT: V 1190 LYS cc_start: 0.6812 (mmpt) cc_final: 0.6518 (tmtt) outliers start: 34 outliers final: 27 residues processed: 249 average time/residue: 0.3346 time to fit residues: 134.3146 Evaluate side-chains 225 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain W residue 569 VAL Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 570 MET Chi-restraints excluded: chain V residue 825 ASP Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Chi-restraints excluded: chain V residue 1143 ILE Chi-restraints excluded: chain V residue 1166 ASN Chi-restraints excluded: chain V residue 1194 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 157 optimal weight: 0.2980 chunk 114 optimal weight: 0.0020 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4828 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= 0.170 Angle : 0.611 12.056 34660 Z= 0.322 Chirality : 0.038 0.281 3823 Planarity : 0.004 0.053 3367 Dihedral : 25.800 174.374 5718 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.97 % Allowed : 22.00 % Favored : 76.03 % 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: -1.02 (0.18), residues: 2126 helix: 0.33 (0.17), residues: 980 sheet: -1.21 (0.35), residues: 208 loop : -1.62 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP V 736 HIS 0.006 0.001 HIS V1088 PHE 0.021 0.001 PHE V 821 TYR 0.028 0.001 TYR V1023 ARG 0.004 0.000 ARG V1047 *********************** 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 246 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: C 38 ASN cc_start: 0.8370 (m-40) cc_final: 0.7949 (p0) REVERT: D 48 ASP cc_start: 0.7933 (p0) cc_final: 0.7552 (p0) REVERT: D 56 MET cc_start: 0.8477 (tpp) cc_final: 0.8120 (tpp) REVERT: D 68 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7743 (tm-30) REVERT: W 608 MET cc_start: 0.7392 (tpp) cc_final: 0.7152 (tpp) REVERT: W 622 MET cc_start: 0.7720 (mmp) cc_final: 0.7421 (mmt) REVERT: W 642 ILE cc_start: 0.8145 (tt) cc_final: 0.7928 (mp) REVERT: W 981 MET cc_start: 0.5215 (mmp) cc_final: 0.4913 (mmm) REVERT: W 1083 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7997 (tp30) REVERT: V 449 MET cc_start: 0.4684 (pmm) cc_final: 0.3966 (ptp) REVERT: V 543 PHE cc_start: 0.6512 (m-80) cc_final: 0.6209 (m-80) REVERT: V 731 MET cc_start: 0.7331 (mmm) cc_final: 0.6928 (tpp) REVERT: V 905 LEU cc_start: 0.8452 (mp) cc_final: 0.7997 (pt) REVERT: V 1013 MET cc_start: 0.8366 (tpp) cc_final: 0.8097 (tpp) REVERT: V 1155 GLN cc_start: 0.8262 (mm110) cc_final: 0.7884 (tp-100) REVERT: V 1190 LYS cc_start: 0.6791 (mmpt) cc_final: 0.6531 (tmtt) outliers start: 36 outliers final: 27 residues processed: 241 average time/residue: 0.3249 time to fit residues: 125.9884 Evaluate side-chains 229 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 200 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain W residue 569 VAL Chi-restraints excluded: chain W residue 624 ILE Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 624 ILE Chi-restraints excluded: chain V residue 825 ASP Chi-restraints excluded: chain V residue 908 ASN Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Chi-restraints excluded: chain V residue 1143 ILE Chi-restraints excluded: chain V residue 1166 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.1980 chunk 221 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 203 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 HIS ** W 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 890 ASN ** 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: 0.7893 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24702 Z= 0.220 Angle : 0.639 16.400 34660 Z= 0.336 Chirality : 0.039 0.269 3823 Planarity : 0.004 0.050 3367 Dihedral : 25.926 174.737 5718 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.08 % Allowed : 22.11 % Favored : 75.81 % 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: -0.91 (0.18), residues: 2126 helix: 0.46 (0.17), residues: 961 sheet: -1.18 (0.35), residues: 208 loop : -1.56 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP V 736 HIS 0.005 0.001 HIS V1088 PHE 0.018 0.001 PHE H 67 TYR 0.024 0.002 TYR V1023 ARG 0.003 0.000 ARG V1111 *********************** 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 233 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7231 (tm-30) REVERT: D 56 MET cc_start: 0.8483 (tpp) cc_final: 0.8121 (tpp) REVERT: D 68 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7753 (tm-30) REVERT: W 608 MET cc_start: 0.7366 (tpp) cc_final: 0.7129 (tpp) REVERT: W 642 ILE cc_start: 0.8194 (tt) cc_final: 0.7970 (mp) REVERT: W 981 MET cc_start: 0.5240 (mmp) cc_final: 0.4946 (mmm) REVERT: W 1013 MET cc_start: 0.8958 (tpp) cc_final: 0.8753 (tpp) REVERT: W 1083 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: V 449 MET cc_start: 0.4592 (pmm) cc_final: 0.3952 (ptp) REVERT: V 731 MET cc_start: 0.7447 (mmm) cc_final: 0.7050 (tpp) REVERT: V 797 TRP cc_start: 0.7088 (m-90) cc_final: 0.6748 (m-90) REVERT: V 905 LEU cc_start: 0.8427 (mp) cc_final: 0.7921 (pt) REVERT: V 1013 MET cc_start: 0.8358 (tpp) cc_final: 0.8072 (tpp) REVERT: V 1155 GLN cc_start: 0.8273 (mm110) cc_final: 0.7857 (tp-100) REVERT: V 1190 LYS cc_start: 0.6901 (mmpt) cc_final: 0.6496 (tmmt) REVERT: V 1192 MET cc_start: 0.6351 (mmp) cc_final: 0.5976 (mmt) outliers start: 38 outliers final: 33 residues processed: 228 average time/residue: 0.3347 time to fit residues: 122.0567 Evaluate side-chains 225 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain W residue 569 VAL Chi-restraints excluded: chain W residue 624 ILE Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 624 ILE Chi-restraints excluded: chain V residue 794 PHE Chi-restraints excluded: chain V residue 825 ASP Chi-restraints excluded: chain V residue 908 ASN Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Chi-restraints excluded: chain V residue 1166 ASN Chi-restraints excluded: chain V residue 1194 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.1980 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 220 optimal weight: 0.5980 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 773 HIS ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7861 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24702 Z= 0.177 Angle : 0.625 11.754 34660 Z= 0.328 Chirality : 0.038 0.271 3823 Planarity : 0.004 0.052 3367 Dihedral : 25.828 174.851 5718 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.70 % Allowed : 22.66 % Favored : 75.64 % 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: -0.93 (0.18), residues: 2126 helix: 0.42 (0.17), residues: 984 sheet: -1.22 (0.35), residues: 210 loop : -1.57 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP V 797 HIS 0.005 0.001 HIS V1088 PHE 0.019 0.001 PHE H 67 TYR 0.029 0.001 TYR V1023 ARG 0.006 0.000 ARG V1047 ********************** 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 236 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7157 (tm-30) REVERT: D 56 MET cc_start: 0.8484 (tpp) cc_final: 0.8053 (tpp) REVERT: D 68 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7779 (tm-30) REVERT: W 608 MET cc_start: 0.7371 (tpp) cc_final: 0.7128 (tpp) REVERT: W 642 ILE cc_start: 0.8151 (tt) cc_final: 0.7928 (mp) REVERT: W 981 MET cc_start: 0.5235 (mmp) cc_final: 0.4932 (mmm) REVERT: W 1083 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: V 449 MET cc_start: 0.4593 (pmm) cc_final: 0.3889 (ptp) REVERT: V 731 MET cc_start: 0.7384 (mmm) cc_final: 0.6963 (tpp) REVERT: V 905 LEU cc_start: 0.8462 (mp) cc_final: 0.7904 (pt) REVERT: V 1013 MET cc_start: 0.8354 (tpp) cc_final: 0.8107 (tpp) REVERT: V 1155 GLN cc_start: 0.8326 (mm110) cc_final: 0.7896 (tp-100) REVERT: V 1192 MET cc_start: 0.6294 (mmp) cc_final: 0.5967 (mmt) outliers start: 31 outliers final: 27 residues processed: 232 average time/residue: 0.3187 time to fit residues: 120.0138 Evaluate side-chains 224 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain W residue 569 VAL Chi-restraints excluded: chain W residue 624 ILE Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 624 ILE Chi-restraints excluded: chain V residue 825 ASP Chi-restraints excluded: chain V residue 908 ASN Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Chi-restraints excluded: chain V residue 1166 ASN Chi-restraints excluded: chain V residue 1194 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 202 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 HIS ** W1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.089527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069330 restraints weight = 206864.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.069902 restraints weight = 109390.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070391 restraints weight = 75955.876| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 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 = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24702 Z= 0.180 Angle : 0.626 11.965 34660 Z= 0.327 Chirality : 0.038 0.268 3823 Planarity : 0.004 0.051 3367 Dihedral : 25.746 174.651 5718 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.70 % Allowed : 23.10 % Favored : 75.21 % 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: -0.83 (0.18), residues: 2126 helix: 0.51 (0.17), residues: 977 sheet: -1.19 (0.35), residues: 208 loop : -1.52 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP V 736 HIS 0.005 0.001 HIS V1088 PHE 0.018 0.001 PHE H 67 TYR 0.034 0.001 TYR F 88 ARG 0.004 0.000 ARG V1047 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4153.19 seconds wall clock time: 77 minutes 5.98 seconds (4625.98 seconds total)