Starting phenix.real_space_refine on Fri Feb 16 22:28:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdt_31925/02_2024/7vdt_31925_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdt_31925/02_2024/7vdt_31925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdt_31925/02_2024/7vdt_31925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdt_31925/02_2024/7vdt_31925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdt_31925/02_2024/7vdt_31925_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdt_31925/02_2024/7vdt_31925_updated.pdb" } resolution = 2.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 20 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians P 274 5.49 5 Mg 1 5.21 5 S 39 5.16 5 Be 1 3.05 5 C 9682 2.51 5 N 3077 2.21 5 O 3627 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 740": "OE1" <-> "OE2" Residue "A TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 801": "NH1" <-> "NH2" Residue "A TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 849": "NH1" <-> "NH2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A ARG 874": "NH1" <-> "NH2" Residue "A TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 955": "OD1" <-> "OD2" Residue "A ARG 966": "NH1" <-> "NH2" Residue "A ARG 967": "NH1" <-> "NH2" Residue "A ARG 973": "NH1" <-> "NH2" Residue "A PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A TYR 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1119": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "A ARG 1189": "NH1" <-> "NH2" Residue "A ARG 1192": "NH1" <-> "NH2" Residue "A ARG 1200": "NH1" <-> "NH2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A TYR 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1260": "OE1" <-> "OE2" Residue "A GLU 1279": "OE1" <-> "OE2" Residue "A PHE 1283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1292": "NH1" <-> "NH2" Residue "A ARG 1303": "NH1" <-> "NH2" Residue "A GLU 1307": "OE1" <-> "OE2" Residue "A PHE 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1336": "NH1" <-> "NH2" Residue "A ARG 1341": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K ASP 106": "OD1" <-> "OD2" Residue "K GLU 133": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16704 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 5057 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 20, 'TRANS': 596} Chain breaks: 3 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2752 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Chain: "J" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2827 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.93, per 1000 atoms: 0.53 Number of scatterers: 16704 At special positions: 0 Unit cell: (132.065, 116.91, 150.467, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 39 16.00 P 274 15.00 Mg 1 11.99 F 3 9.00 O 3627 8.00 N 3077 7.00 C 9682 6.00 Be 1 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.81 Conformation dependent library (CDL) restraints added in 2.0 seconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2614 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 2 sheets defined 55.1% alpha, 2.5% beta 118 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 8.68 Creating SS restraints... Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.544A pdb=" N ASP A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 735 No H-bonds generated for 'chain 'A' and resid 732 through 735' Processing helix chain 'A' and resid 756 through 770 removed outlier: 3.518A pdb=" N LYS A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 Processing helix chain 'A' and resid 812 through 825 removed outlier: 4.373A pdb=" N SER A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP A 818 " --> pdb=" O LEU A 815 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP A 825 " --> pdb=" O PHE A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 843 removed outlier: 3.589A pdb=" N ALA A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 860 through 865 removed outlier: 3.752A pdb=" N ILE A 864 " --> pdb=" O TYR A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 870 No H-bonds generated for 'chain 'A' and resid 867 through 870' Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 919 through 928 Processing helix chain 'A' and resid 963 through 971 removed outlier: 3.605A pdb=" N LEU A 968 " --> pdb=" O ILE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 984 No H-bonds generated for 'chain 'A' and resid 981 through 984' Processing helix chain 'A' and resid 1002 through 1013 Processing helix chain 'A' and resid 1038 through 1047 Processing helix chain 'A' and resid 1049 through 1052 removed outlier: 4.079A pdb=" N PHE A1052 " --> pdb=" O PRO A1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1049 through 1052' Processing helix chain 'A' and resid 1055 through 1062 Processing helix chain 'A' and resid 1073 through 1078 Processing helix chain 'A' and resid 1080 through 1094 removed outlier: 3.514A pdb=" N ARG A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 3.644A pdb=" N ILE A1111 " --> pdb=" O SER A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1143 removed outlier: 4.263A pdb=" N GLY A1136 " --> pdb=" O ALA A1132 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1159 No H-bonds generated for 'chain 'A' and resid 1156 through 1159' Processing helix chain 'A' and resid 1180 through 1189 removed outlier: 3.518A pdb=" N ARG A1189 " --> pdb=" O GLN A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1228 removed outlier: 4.072A pdb=" N ASN A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP A1225 " --> pdb=" O LYS A1221 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1254 removed outlier: 3.600A pdb=" N ALA A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A1251 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A1252 " --> pdb=" O GLN A1248 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS A1253 " --> pdb=" O ALA A1249 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A1254 " --> pdb=" O ILE A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1273 Processing helix chain 'A' and resid 1277 through 1294 removed outlier: 3.841A pdb=" N ARG A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET A1286 " --> pdb=" O LEU A1282 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP A1287 " --> pdb=" O PHE A1283 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A1288 " --> pdb=" O MET A1284 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A1291 " --> pdb=" O ASP A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1315 Processing helix chain 'B' and resid 17 through 21 removed outlier: 3.897A pdb=" N VAL B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 21' Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 92 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 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.474A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.511A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.656A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.626A pdb=" N HIS D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 111 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR D 121 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 123 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.017A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.512A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 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 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.500A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.571A pdb=" N LYS H 108 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL H 111 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 115 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR H 119 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS H 120 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 53 removed outlier: 3.884A pdb=" N GLU K 50 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 78 removed outlier: 4.117A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 114 removed outlier: 3.628A pdb=" N LEU K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA K 114 " --> pdb=" O CYS K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 131 Processing sheet with id= A, first strand: chain 'A' and resid 906 through 908 removed outlier: 6.729A pdb=" N MET A 878 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 807 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 856 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL A 810 " --> pdb=" O LEU A 856 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR A 858 " --> pdb=" O VAL A 810 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 992 through 996 removed outlier: 3.514A pdb=" N PHE A1152 " --> pdb=" O VAL A1099 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A1155 " --> pdb=" O LEU A1126 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 284 hydrogen bonds 556 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 8.24 Time building geometry restraints manager: 8.37 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: 3336 1.33 - 1.45: 5072 1.45 - 1.57: 8536 1.57 - 1.69: 546 1.69 - 1.81: 72 Bond restraints: 17562 Sorted by residual: bond pdb=" BE BEF A1701 " pdb=" F2 BEF A1701 " ideal model delta sigma weight residual 1.476 1.711 -0.235 2.00e-02 2.50e+03 1.37e+02 bond pdb=" BE BEF A1701 " pdb=" F1 BEF A1701 " ideal model delta sigma weight residual 1.476 1.703 -0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" BE BEF A1701 " pdb=" F3 BEF A1701 " ideal model delta sigma weight residual 1.476 1.689 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CG1 ILE A1151 " pdb=" CD1 ILE A1151 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.29e+00 bond pdb=" CG LEU A1100 " pdb=" CD1 LEU A1100 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.82e+00 ... (remaining 17557 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.78: 1562 105.78 - 113.23: 9827 113.23 - 120.68: 8153 120.68 - 128.13: 4916 128.13 - 135.58: 421 Bond angle restraints: 24879 Sorted by residual: angle pdb=" F1 BEF A1701 " pdb=" BE BEF A1701 " pdb=" F3 BEF A1701 " ideal model delta sigma weight residual 120.12 98.85 21.27 3.00e+00 1.11e-01 5.03e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.47 108.01 5.46 1.01e+00 9.80e-01 2.93e+01 angle pdb=" F2 BEF A1701 " pdb=" BE BEF A1701 " pdb=" F3 BEF A1701 " ideal model delta sigma weight residual 119.96 105.59 14.37 3.00e+00 1.11e-01 2.29e+01 angle pdb=" CA LYS A1301 " pdb=" C LYS A1301 " pdb=" N PRO A1302 " ideal model delta sigma weight residual 120.77 116.52 4.25 9.70e-01 1.06e+00 1.92e+01 angle pdb=" CA MET A 749 " pdb=" CB MET A 749 " pdb=" CG MET A 749 " ideal model delta sigma weight residual 114.10 121.41 -7.31 2.00e+00 2.50e-01 1.34e+01 ... (remaining 24874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 8648 35.61 - 71.22: 1235 71.22 - 106.83: 10 106.83 - 142.44: 3 142.44 - 178.05: 2 Dihedral angle restraints: 9898 sinusoidal: 5860 harmonic: 4038 Sorted by residual: dihedral pdb=" O2A ADP A1703 " pdb=" O3A ADP A1703 " pdb=" PA ADP A1703 " pdb=" PB ADP A1703 " ideal model delta sinusoidal sigma weight residual 300.00 121.95 178.05 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP A1703 " pdb=" O3A ADP A1703 " pdb=" PB ADP A1703 " pdb=" PA ADP A1703 " ideal model delta sinusoidal sigma weight residual -60.00 65.55 -125.55 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP A1703 " pdb=" O5' ADP A1703 " pdb=" PA ADP A1703 " pdb=" O2A ADP A1703 " ideal model delta sinusoidal sigma weight residual -60.00 -151.03 91.03 1 2.00e+01 2.50e-03 2.44e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1848 0.036 - 0.073: 768 0.073 - 0.109: 147 0.109 - 0.146: 43 0.146 - 0.182: 6 Chirality restraints: 2812 Sorted by residual: chirality pdb=" CA MET A 749 " pdb=" N MET A 749 " pdb=" C MET A 749 " pdb=" CB MET A 749 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CB VAL B 43 " pdb=" CA VAL B 43 " pdb=" CG1 VAL B 43 " pdb=" CG2 VAL B 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" C3' ADP A1703 " pdb=" C2' ADP A1703 " pdb=" C4' ADP A1703 " pdb=" O3' ADP A1703 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2809 not shown) Planarity restraints: 2210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1152 " 0.020 2.00e-02 2.50e+03 2.11e-02 7.81e+00 pdb=" CG PHE A1152 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A1152 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A1152 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A1152 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A1152 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A1152 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 804 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO A 805 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 77 " -0.040 9.50e-02 1.11e+02 2.32e-02 2.95e+00 pdb=" NE ARG G 77 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG G 77 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG G 77 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG G 77 " 0.008 2.00e-02 2.50e+03 ... (remaining 2207 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 8 2.02 - 2.74: 1846 2.74 - 3.46: 21884 3.46 - 4.18: 46084 4.18 - 4.90: 73050 Nonbonded interactions: 142872 Sorted by model distance: nonbonded pdb=" O LEU A 550 " pdb=" CD2 LEU A 554 " model vdw 1.303 3.460 nonbonded pdb=" O ALA A 551 " pdb=" NE2 GLN A 555 " model vdw 1.368 2.520 nonbonded pdb=" NE2 GLN A 556 " pdb=" CG2 ILE A 932 " model vdw 1.544 3.540 nonbonded pdb=" OH TYR A1076 " pdb=" NZ LYS A1301 " model vdw 1.722 2.520 nonbonded pdb=" O ALA A 551 " pdb=" CD GLN A 555 " model vdw 1.743 3.270 ... (remaining 142867 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 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or (resid 118 and (name N or \ name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 40 through 134) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 9.970 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 53.450 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.235 17562 Z= 0.395 Angle : 0.704 21.266 24879 Z= 0.399 Chirality : 0.041 0.182 2812 Planarity : 0.004 0.057 2210 Dihedral : 23.616 178.049 7284 Min Nonbonded Distance : 1.303 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 0.34 % Allowed : 0.42 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1360 helix: -0.00 (0.18), residues: 778 sheet: -0.31 (0.73), residues: 63 loop : -1.49 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1313 HIS 0.005 0.001 HIS F 75 PHE 0.048 0.002 PHE A1152 TYR 0.025 0.002 TYR C 57 ARG 0.029 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 215 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1051 MET cc_start: 0.9168 (mtp) cc_final: 0.8799 (mtp) REVERT: A 1308 ASP cc_start: 0.7876 (m-30) cc_final: 0.7641 (p0) REVERT: B 79 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8807 (mtpt) REVERT: K 80 THR cc_start: 0.9116 (p) cc_final: 0.8541 (p) REVERT: K 115 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8509 (mttp) outliers start: 4 outliers final: 2 residues processed: 218 average time/residue: 1.8800 time to fit residues: 441.2197 Evaluate side-chains 180 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 555 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN A 555 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17562 Z= 0.206 Angle : 0.619 11.778 24879 Z= 0.349 Chirality : 0.038 0.144 2812 Planarity : 0.004 0.049 2210 Dihedral : 27.918 177.049 4516 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.61 % Allowed : 9.35 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1360 helix: 0.98 (0.18), residues: 805 sheet: -0.26 (0.71), residues: 65 loop : -1.45 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 922 HIS 0.008 0.001 HIS A 969 PHE 0.024 0.002 PHE A1152 TYR 0.052 0.002 TYR A 552 ARG 0.009 0.001 ARG A1296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 1.703 Fit side-chains REVERT: A 874 ARG cc_start: 0.6784 (ptt180) cc_final: 0.6384 (ptt90) REVERT: A 905 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7485 (mtp85) REVERT: A 949 MET cc_start: -0.0683 (ppp) cc_final: -0.1397 (ptt) REVERT: A 1051 MET cc_start: 0.9127 (mtp) cc_final: 0.8757 (mtp) REVERT: A 1284 MET cc_start: 0.7326 (mmm) cc_final: 0.7123 (mmm) REVERT: A 1308 ASP cc_start: 0.7781 (m-30) cc_final: 0.7542 (p0) REVERT: B 84 MET cc_start: 0.8553 (mmm) cc_final: 0.8333 (mmm) REVERT: C 91 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: D 68 ASP cc_start: 0.9014 (t0) cc_final: 0.8744 (t0) REVERT: K 106 ASP cc_start: 0.8407 (m-30) cc_final: 0.8108 (m-30) REVERT: K 115 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8512 (mttp) outliers start: 19 outliers final: 3 residues processed: 205 average time/residue: 1.7576 time to fit residues: 389.7914 Evaluate side-chains 182 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 0.0050 chunk 98 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN A1241 HIS D 63 ASN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17562 Z= 0.184 Angle : 0.558 9.876 24879 Z= 0.317 Chirality : 0.036 0.139 2812 Planarity : 0.004 0.048 2210 Dihedral : 27.666 178.391 4511 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.78 % Allowed : 12.66 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1360 helix: 1.37 (0.19), residues: 808 sheet: -0.17 (0.71), residues: 64 loop : -1.32 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 922 HIS 0.006 0.001 HIS A1241 PHE 0.024 0.002 PHE A1065 TYR 0.046 0.001 TYR A 552 ARG 0.006 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 874 ARG cc_start: 0.6713 (ptt180) cc_final: 0.6392 (ptt90) REVERT: A 949 MET cc_start: -0.0968 (ppp) cc_final: -0.1679 (ptt) REVERT: A 975 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8290 (p90) REVERT: A 1051 MET cc_start: 0.9112 (mtp) cc_final: 0.8730 (mtp) REVERT: B 22 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6555 (mm) REVERT: D 68 ASP cc_start: 0.8974 (t0) cc_final: 0.8720 (t0) REVERT: F 93 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8515 (mp10) REVERT: H 57 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8030 (mmmm) REVERT: K 106 ASP cc_start: 0.8485 (m-30) cc_final: 0.8172 (m-30) REVERT: K 115 LYS cc_start: 0.8795 (mmtm) cc_final: 0.8560 (mttp) outliers start: 21 outliers final: 8 residues processed: 196 average time/residue: 1.8450 time to fit residues: 391.6636 Evaluate side-chains 187 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17562 Z= 0.382 Angle : 0.638 10.322 24879 Z= 0.359 Chirality : 0.042 0.165 2812 Planarity : 0.005 0.053 2210 Dihedral : 28.078 178.796 4511 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.23 % Allowed : 13.59 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1360 helix: 1.29 (0.19), residues: 804 sheet: -0.13 (0.69), residues: 65 loop : -1.50 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 942 HIS 0.009 0.001 HIS A1241 PHE 0.033 0.002 PHE A1152 TYR 0.053 0.002 TYR A 552 ARG 0.008 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 874 ARG cc_start: 0.6762 (ptt180) cc_final: 0.6467 (ptt90) REVERT: A 949 MET cc_start: -0.0813 (ppp) cc_final: -0.1561 (ptt) REVERT: A 975 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8467 (p90) REVERT: A 1100 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8888 (pp) REVERT: B 22 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6606 (mm) REVERT: B 84 MET cc_start: 0.8581 (mmm) cc_final: 0.8375 (mmm) REVERT: D 68 ASP cc_start: 0.9038 (t0) cc_final: 0.8784 (t0) REVERT: F 93 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8518 (mp10) REVERT: G 116 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8479 (pp) REVERT: H 57 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8154 (mmmm) REVERT: K 106 ASP cc_start: 0.8576 (m-30) cc_final: 0.8234 (m-30) REVERT: K 115 LYS cc_start: 0.8781 (mmtm) cc_final: 0.8547 (mttp) outliers start: 38 outliers final: 17 residues processed: 194 average time/residue: 1.7100 time to fit residues: 359.9899 Evaluate side-chains 196 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.3980 chunk 2 optimal weight: 0.0370 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 868 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17562 Z= 0.192 Angle : 0.587 13.073 24879 Z= 0.329 Chirality : 0.037 0.152 2812 Planarity : 0.004 0.057 2210 Dihedral : 27.990 178.646 4511 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.72 % Allowed : 14.95 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1360 helix: 1.42 (0.19), residues: 805 sheet: -0.10 (0.71), residues: 64 loop : -1.45 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 922 HIS 0.005 0.001 HIS A 969 PHE 0.019 0.002 PHE A1152 TYR 0.057 0.002 TYR A 552 ARG 0.006 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 178 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 874 ARG cc_start: 0.6747 (ptt180) cc_final: 0.6384 (ptt90) REVERT: A 949 MET cc_start: -0.0783 (OUTLIER) cc_final: -0.1517 (ptt) REVERT: A 1100 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8795 (pp) REVERT: B 22 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6556 (mm) REVERT: D 68 ASP cc_start: 0.8992 (t0) cc_final: 0.8751 (t0) REVERT: F 93 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8514 (mp10) REVERT: G 116 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8423 (pp) REVERT: H 57 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8051 (mmmm) REVERT: K 115 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8542 (mttp) outliers start: 32 outliers final: 9 residues processed: 199 average time/residue: 1.7488 time to fit residues: 377.0195 Evaluate side-chains 188 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 6.9990 chunk 30 optimal weight: 0.0070 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17562 Z= 0.215 Angle : 0.578 11.853 24879 Z= 0.326 Chirality : 0.036 0.177 2812 Planarity : 0.004 0.060 2210 Dihedral : 27.867 179.885 4511 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.89 % Allowed : 15.38 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.23), residues: 1360 helix: 1.51 (0.19), residues: 805 sheet: -0.12 (0.70), residues: 64 loop : -1.40 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 922 HIS 0.004 0.001 HIS A 969 PHE 0.018 0.001 PHE A1152 TYR 0.053 0.002 TYR A 552 ARG 0.006 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.611 Fit side-chains REVERT: A 874 ARG cc_start: 0.6705 (ptt180) cc_final: 0.6426 (ptt90) REVERT: A 949 MET cc_start: -0.0819 (OUTLIER) cc_final: -0.1486 (ptt) REVERT: A 1100 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 22 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6527 (mm) REVERT: B 93 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: C 91 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: D 68 ASP cc_start: 0.8984 (t0) cc_final: 0.8686 (t0) REVERT: F 93 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: H 57 LYS cc_start: 0.8344 (mmmt) cc_final: 0.8023 (mmmm) REVERT: K 115 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8544 (mttp) outliers start: 34 outliers final: 16 residues processed: 197 average time/residue: 1.6580 time to fit residues: 355.1608 Evaluate side-chains 194 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 48 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17562 Z= 0.204 Angle : 0.582 13.851 24879 Z= 0.325 Chirality : 0.036 0.145 2812 Planarity : 0.004 0.065 2210 Dihedral : 27.847 179.760 4511 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.80 % Allowed : 15.63 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1360 helix: 1.54 (0.19), residues: 807 sheet: -0.06 (0.69), residues: 64 loop : -1.37 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 922 HIS 0.004 0.001 HIS D 109 PHE 0.016 0.001 PHE A1152 TYR 0.062 0.002 TYR A 552 ARG 0.006 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.653 Fit side-chains REVERT: A 874 ARG cc_start: 0.6693 (ptt180) cc_final: 0.6424 (ptt90) REVERT: A 949 MET cc_start: -0.0831 (OUTLIER) cc_final: -0.1492 (ptt) REVERT: A 1100 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8772 (pp) REVERT: B 22 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6533 (mm) REVERT: B 93 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7672 (mt0) REVERT: C 91 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: D 68 ASP cc_start: 0.8959 (t0) cc_final: 0.8652 (t0) REVERT: F 93 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: H 57 LYS cc_start: 0.8353 (mmmt) cc_final: 0.8033 (mmmm) REVERT: K 115 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8545 (mttp) outliers start: 33 outliers final: 18 residues processed: 198 average time/residue: 1.6891 time to fit residues: 363.0395 Evaluate side-chains 195 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 48 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17562 Z= 0.222 Angle : 0.587 13.046 24879 Z= 0.327 Chirality : 0.037 0.154 2812 Planarity : 0.004 0.065 2210 Dihedral : 27.854 179.399 4511 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.14 % Allowed : 16.06 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1360 helix: 1.55 (0.19), residues: 807 sheet: -0.01 (0.69), residues: 64 loop : -1.37 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 942 HIS 0.004 0.001 HIS A 969 PHE 0.017 0.001 PHE A1152 TYR 0.053 0.002 TYR A 552 ARG 0.007 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 175 time to evaluate : 1.563 Fit side-chains REVERT: A 874 ARG cc_start: 0.6687 (ptt180) cc_final: 0.6419 (ptt90) REVERT: A 949 MET cc_start: -0.1027 (OUTLIER) cc_final: -0.1631 (ptt) REVERT: B 22 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6532 (mm) REVERT: B 93 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: D 68 ASP cc_start: 0.8978 (t0) cc_final: 0.8681 (t0) REVERT: F 93 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8480 (mp10) REVERT: H 57 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8067 (mmmm) REVERT: K 115 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8559 (mttp) outliers start: 37 outliers final: 20 residues processed: 201 average time/residue: 1.7100 time to fit residues: 372.6468 Evaluate side-chains 197 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 151 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17562 Z= 0.193 Angle : 0.595 14.903 24879 Z= 0.328 Chirality : 0.036 0.173 2812 Planarity : 0.004 0.068 2210 Dihedral : 27.847 179.351 4511 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.55 % Allowed : 16.31 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.23), residues: 1360 helix: 1.57 (0.19), residues: 807 sheet: -0.06 (0.68), residues: 64 loop : -1.36 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 942 HIS 0.004 0.001 HIS A 969 PHE 0.020 0.001 PHE A1102 TYR 0.066 0.002 TYR A 552 ARG 0.007 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.542 Fit side-chains REVERT: A 874 ARG cc_start: 0.6683 (ptt180) cc_final: 0.6418 (ptt90) REVERT: A 949 MET cc_start: -0.1035 (OUTLIER) cc_final: -0.1635 (ptt) REVERT: A 1310 LEU cc_start: 0.6758 (mm) cc_final: 0.6529 (mm) REVERT: B 22 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6526 (mm) REVERT: B 93 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: D 68 ASP cc_start: 0.8976 (t0) cc_final: 0.8692 (t0) REVERT: F 93 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8484 (mp10) REVERT: H 57 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8058 (mmmm) REVERT: K 115 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8548 (mttp) outliers start: 30 outliers final: 19 residues processed: 196 average time/residue: 1.7161 time to fit residues: 366.0654 Evaluate side-chains 195 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 104 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 134 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17562 Z= 0.196 Angle : 0.592 15.259 24879 Z= 0.326 Chirality : 0.036 0.162 2812 Planarity : 0.004 0.069 2210 Dihedral : 27.817 179.149 4511 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.38 % Allowed : 16.74 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1360 helix: 1.59 (0.19), residues: 807 sheet: 0.05 (0.69), residues: 64 loop : -1.34 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 942 HIS 0.004 0.001 HIS F 75 PHE 0.014 0.001 PHE A1152 TYR 0.063 0.002 TYR A 552 ARG 0.008 0.000 ARG E 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.414 Fit side-chains REVERT: A 874 ARG cc_start: 0.6678 (ptt180) cc_final: 0.6412 (ptt90) REVERT: A 949 MET cc_start: -0.1042 (OUTLIER) cc_final: -0.1641 (ptt) REVERT: B 22 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6525 (mm) REVERT: B 93 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: D 68 ASP cc_start: 0.8970 (t0) cc_final: 0.8671 (t0) REVERT: F 93 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8494 (mp10) REVERT: H 57 LYS cc_start: 0.8332 (mmmt) cc_final: 0.8020 (mmmm) REVERT: K 115 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8557 (mttp) outliers start: 28 outliers final: 19 residues processed: 193 average time/residue: 1.7239 time to fit residues: 360.2329 Evaluate side-chains 194 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN A1062 HIS G 104 GLN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.111491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078333 restraints weight = 32205.642| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.88 r_work: 0.2981 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17562 Z= 0.203 Angle : 0.589 14.443 24879 Z= 0.325 Chirality : 0.036 0.163 2812 Planarity : 0.004 0.067 2210 Dihedral : 27.789 178.638 4511 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.38 % Allowed : 16.74 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1360 helix: 1.65 (0.19), residues: 804 sheet: 0.09 (0.70), residues: 64 loop : -1.34 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 942 HIS 0.006 0.001 HIS F 75 PHE 0.014 0.001 PHE A1152 TYR 0.057 0.002 TYR A 552 ARG 0.008 0.000 ARG E 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6483.51 seconds wall clock time: 115 minutes 12.46 seconds (6912.46 seconds total)