Starting phenix.real_space_refine (version: dev) on Tue May 17 15:12:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/05_2022/7en1_31199_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/05_2022/7en1_31199.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/05_2022/7en1_31199_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/05_2022/7en1_31199_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/05_2022/7en1_31199_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/05_2022/7en1_31199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/05_2022/7en1_31199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/05_2022/7en1_31199_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/05_2022/7en1_31199_neut_trim_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 374": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 944": "OD1" <-> "OD2" Residue "A GLU 958": "OE1" <-> "OE2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A GLU 1117": "OE1" <-> "OE2" Residue "A PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A PHE 1200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1234": "OE1" <-> "OE2" Residue "A GLU 1310": "OE1" <-> "OE2" Residue "A GLU 1356": "OE1" <-> "OE2" Residue "A GLU 1361": "OE1" <-> "OE2" Residue "A ARG 1372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1375": "OE1" <-> "OE2" Residue "A PHE 1379": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1399": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 530": "OD1" <-> "OD2" Residue "B TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B GLU 831": "OE1" <-> "OE2" Residue "B ARG 901": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 914": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1015": "OE1" <-> "OE2" Residue "B ASP 1034": "OD1" <-> "OD2" Residue "B GLU 1159": "OE1" <-> "OE2" Residue "B PHE 1200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1207": "OE1" <-> "OE2" Residue "B ASP 1291": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 40862 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 20280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 20280 Classifications: {'peptide': 1320} Link IDs: {'PTRANS': 83, 'TRANS': 1235, 'PCIS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 20444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 20444 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 84, 'TRANS': 1248, 'PCIS': 1} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 71 Unusual residues: {'J9F': 1, 'PNS': 1, ' MG': 1} Classifications: {'undetermined': 3, 'RNA': 1, 'peptide': 1} Modifications used: {'NH1NOTPRO': 1, 'rna2p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Planarities with less than four sites: {'J9F:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'PNS': 1, ' MG': 1, 'SAL': 1} Classifications: {'undetermined': 3, 'RNA': 1, 'peptide': 1} Modifications used: {'NH1NOTPRO': 1, 'COO': 1, 'rna2p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Planarities with less than four sites: {'SAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C28 PNS A1501 " occ=0.00 ... (19 atoms not shown) pdb=" S44 PNS A1501 " occ=0.00 residue: pdb=" C1 SAL B1502 " occ=0.00 ... (7 atoms not shown) pdb=" O2 SAL B1502 " occ=0.00 Time building chain proxies: 18.64, per 1000 atoms: 0.46 Number of scatterers: 40862 At special positions: 0 Unit cell: (133, 148, 137, 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) S 69 16.00 P 4 15.00 Mg 2 11.99 O 3716 8.00 N 3772 7.00 C 12880 6.00 H 20419 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 36.99 Conformation dependent library (CDL) restraints added in 3.5 seconds 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4906 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 117 helices and 28 sheets defined 40.6% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 189 through 205 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 241 through 256 removed outlier: 4.135A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.948A pdb=" N ALA A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 404 through 423 removed outlier: 4.016A pdb=" N ASP A 420 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.723A pdb=" N ALA A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 521 Processing helix chain 'A' and resid 535 through 545 Processing helix chain 'A' and resid 558 through 566 Processing helix chain 'A' and resid 582 through 598 Processing helix chain 'A' and resid 615 through 626 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 711 through 725 removed outlier: 4.319A pdb=" N LEU A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 removed outlier: 3.702A pdb=" N LEU A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 749 " --> pdb=" O PHE A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 769 through 779 Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 943 through 945 No H-bonds generated for 'chain 'A' and resid 943 through 945' Processing helix chain 'A' and resid 956 through 964 Processing helix chain 'A' and resid 1009 through 1032 removed outlier: 4.168A pdb=" N ALA A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'A' and resid 1035 through 1047 removed outlier: 4.367A pdb=" N ALA A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1067 through 1082 Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1108 through 1116 Processing helix chain 'A' and resid 1120 through 1124 Processing helix chain 'A' and resid 1139 through 1147 removed outlier: 3.522A pdb=" N GLY A1144 " --> pdb=" O TRP A1140 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER A1147 " --> pdb=" O GLN A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1171 removed outlier: 3.728A pdb=" N ALA A1167 " --> pdb=" O VAL A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1188 through 1190 No H-bonds generated for 'chain 'A' and resid 1188 through 1190' Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1236 through 1245 Processing helix chain 'A' and resid 1249 through 1251 No H-bonds generated for 'chain 'A' and resid 1249 through 1251' Processing helix chain 'A' and resid 1255 through 1264 Processing helix chain 'A' and resid 1292 through 1302 Processing helix chain 'A' and resid 1305 through 1307 No H-bonds generated for 'chain 'A' and resid 1305 through 1307' Processing helix chain 'A' and resid 1328 through 1338 Processing helix chain 'A' and resid 1354 through 1367 Processing helix chain 'A' and resid 1378 through 1381 No H-bonds generated for 'chain 'A' and resid 1378 through 1381' Processing helix chain 'A' and resid 1385 through 1398 removed outlier: 3.589A pdb=" N ARG A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1410 Processing helix chain 'A' and resid 1414 through 1422 removed outlier: 4.667A pdb=" N HIS A1420 " --> pdb=" O GLY A1416 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A1421 " --> pdb=" O LEU A1417 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 22 Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.692A pdb=" N CYS B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 142 through 155 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.525A pdb=" N HIS B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 241 through 256 Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 269 through 297 removed outlier: 4.781A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 327 through 339 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 404 through 423 removed outlier: 4.381A pdb=" N ASP B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 458 through 461 No H-bonds generated for 'chain 'B' and resid 458 through 461' Processing helix chain 'B' and resid 505 through 522 Processing helix chain 'B' and resid 535 through 545 Processing helix chain 'B' and resid 558 through 566 Processing helix chain 'B' and resid 582 through 598 Processing helix chain 'B' and resid 615 through 626 Processing helix chain 'B' and resid 640 through 649 Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 711 through 725 removed outlier: 3.898A pdb=" N LEU B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 749 removed outlier: 3.693A pdb=" N LEU B 748 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B 749 " --> pdb=" O PHE B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 769 through 779 Processing helix chain 'B' and resid 788 through 796 Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 907 through 913 Processing helix chain 'B' and resid 956 through 964 Processing helix chain 'B' and resid 1009 through 1028 removed outlier: 3.842A pdb=" N GLU B1028 " --> pdb=" O GLY B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1032 No H-bonds generated for 'chain 'B' and resid 1030 through 1032' Processing helix chain 'B' and resid 1035 through 1047 removed outlier: 3.589A pdb=" N ASP B1043 " --> pdb=" O ARG B1039 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1063 Processing helix chain 'B' and resid 1067 through 1082 Processing helix chain 'B' and resid 1088 through 1092 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1108 through 1115 removed outlier: 3.897A pdb=" N ARG B1114 " --> pdb=" O GLU B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1124 No H-bonds generated for 'chain 'B' and resid 1121 through 1124' Processing helix chain 'B' and resid 1141 through 1143 No H-bonds generated for 'chain 'B' and resid 1141 through 1143' Processing helix chain 'B' and resid 1145 through 1148 No H-bonds generated for 'chain 'B' and resid 1145 through 1148' Processing helix chain 'B' and resid 1162 through 1169 Processing helix chain 'B' and resid 1182 through 1184 No H-bonds generated for 'chain 'B' and resid 1182 through 1184' Processing helix chain 'B' and resid 1188 through 1190 No H-bonds generated for 'chain 'B' and resid 1188 through 1190' Processing helix chain 'B' and resid 1203 through 1205 No H-bonds generated for 'chain 'B' and resid 1203 through 1205' Processing helix chain 'B' and resid 1209 through 1219 Processing helix chain 'B' and resid 1236 through 1245 Processing helix chain 'B' and resid 1249 through 1251 No H-bonds generated for 'chain 'B' and resid 1249 through 1251' Processing helix chain 'B' and resid 1255 through 1264 Processing helix chain 'B' and resid 1292 through 1302 Processing helix chain 'B' and resid 1328 through 1339 Processing sheet with id= A, first strand: chain 'A' and resid 469 through 472 Processing sheet with id= B, first strand: chain 'A' and resid 161 through 164 Processing sheet with id= C, first strand: chain 'A' and resid 318 through 325 removed outlier: 3.943A pdb=" N ARG A 485 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 364 through 372 Processing sheet with id= E, first strand: chain 'A' and resid 630 through 633 removed outlier: 6.814A pdb=" N LEU A 654 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.606A pdb=" N SER A 757 " --> pdb=" O LEU A 733 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 783 through 787 removed outlier: 7.021A pdb=" N ALA A 809 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N SER A 786 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 811 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 835 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 849 " --> pdb=" O GLY A 839 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 872 through 877 removed outlier: 3.615A pdb=" N GLY A 896 " --> pdb=" O ARG A 921 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG A 921 " --> pdb=" O GLY A 896 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 929 through 931 Processing sheet with id= J, first strand: chain 'A' and resid 946 through 949 removed outlier: 3.631A pdb=" N VAL A 947 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1311 through 1314 removed outlier: 3.668A pdb=" N ARG A1311 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 971 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1268 through 1273 removed outlier: 6.187A pdb=" N LEU A1280 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU A1159 " --> pdb=" O GLN A1179 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.599A pdb=" N VAL A 580 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.742A pdb=" N VAL A 709 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 694 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL A 707 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 469 through 471 Processing sheet with id= P, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= Q, first strand: chain 'B' and resid 318 through 325 Processing sheet with id= R, first strand: chain 'B' and resid 364 through 372 Processing sheet with id= S, first strand: chain 'B' and resid 732 through 734 removed outlier: 6.625A pdb=" N SER B 757 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 580 " --> pdb=" O ALA B 572 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 574 " --> pdb=" O GLN B 578 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.719A pdb=" N LEU B 654 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 783 through 787 removed outlier: 6.792A pdb=" N ALA B 809 " --> pdb=" O TRP B 784 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N SER B 786 " --> pdb=" O ALA B 809 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 811 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 849 " --> pdb=" O GLY B 839 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 872 through 877 Processing sheet with id= W, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= X, first strand: chain 'B' and resid 929 through 931 Processing sheet with id= Y, first strand: chain 'B' and resid 946 through 949 Processing sheet with id= Z, first strand: chain 'B' and resid 1311 through 1314 removed outlier: 3.793A pdb=" N ARG B1311 " --> pdb=" O LEU B 984 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 1153 through 1157 removed outlier: 6.101A pdb=" N LEU B1128 " --> pdb=" O GLU B1154 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N THR B1156 " --> pdb=" O LEU B1128 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B1130 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B1196 " --> pdb=" O ALA B1131 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG B1225 " --> pdb=" O VAL B1197 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER B1199 " --> pdb=" O ARG B1225 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B1227 " --> pdb=" O SER B1199 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B1230 " --> pdb=" O ALA B1279 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B1279 " --> pdb=" O ASP B1230 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B1282 " --> pdb=" O CYS B1271 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N CYS B1271 " --> pdb=" O GLU B1282 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B1284 " --> pdb=" O PRO B1269 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 691 through 697 removed outlier: 6.704A pdb=" N VAL B 709 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL B 694 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL B 707 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR B 696 " --> pdb=" O LYS B 705 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LYS B 705 " --> pdb=" O TYR B 696 " (cutoff:3.500A) 821 hydrogen bonds defined for protein. 2343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.94 Time building geometry restraints manager: 37.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.08: 7353 1.08 - 1.28: 16500 1.28 - 1.47: 7948 1.47 - 1.66: 9393 1.66 - 1.86: 94 Bond restraints: 41288 Sorted by residual: bond pdb=" C08 J9F A1502 " pdb=" N09 J9F A1502 " ideal model delta sigma weight residual 1.563 1.289 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C08 J9F A1502 " pdb=" S15 J9F A1502 " ideal model delta sigma weight residual 1.531 1.752 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C10 J9F A1502 " pdb=" C11 J9F A1502 " ideal model delta sigma weight residual 1.361 1.536 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C10 J9F A1502 " pdb=" C14 J9F A1502 " ideal model delta sigma weight residual 1.712 1.538 0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" N CYS A1505 " pdb=" H CYS A1505 " ideal model delta sigma weight residual 0.860 1.018 -0.158 2.00e-02 2.50e+03 6.24e+01 ... (remaining 41283 not shown) Histogram of bond angle deviations from ideal: 72.32 - 84.96: 3 84.96 - 97.60: 34 97.60 - 110.24: 37049 110.24 - 122.88: 34406 122.88 - 135.52: 3209 Bond angle restraints: 74701 Sorted by residual: angle pdb=" N GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 110.00 72.32 37.68 3.00e+00 1.11e-01 1.58e+02 angle pdb=" C GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 109.00 77.63 31.37 3.00e+00 1.11e-01 1.09e+02 angle pdb=" CB GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 109.00 78.51 30.49 3.00e+00 1.11e-01 1.03e+02 angle pdb=" CA PHE A 741 " pdb=" CB PHE A 741 " pdb=" CG PHE A 741 " ideal model delta sigma weight residual 113.80 122.27 -8.47 1.00e+00 1.00e+00 7.17e+01 angle pdb=" N PRO B 174 " pdb=" CA PRO B 174 " pdb=" CB PRO B 174 " ideal model delta sigma weight residual 103.22 107.09 -3.87 5.20e-01 3.70e+00 5.53e+01 ... (remaining 74696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 15107 21.16 - 42.33: 813 42.33 - 63.49: 292 63.49 - 84.65: 116 84.65 - 105.82: 8 Dihedral angle restraints: 16336 sinusoidal: 7776 harmonic: 8560 Sorted by residual: dihedral pdb=" CA VAL A 486 " pdb=" C VAL A 486 " pdb=" N GLY A 487 " pdb=" CA GLY A 487 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA VAL B 486 " pdb=" C VAL B 486 " pdb=" N GLY B 487 " pdb=" CA GLY B 487 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER B 813 " pdb=" C SER B 813 " pdb=" N GLY B 814 " pdb=" CA GLY B 814 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 16333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2114 0.094 - 0.189: 886 0.189 - 0.283: 146 0.283 - 0.377: 28 0.377 - 0.472: 5 Chirality restraints: 3179 Sorted by residual: chirality pdb=" CA GLN B 689 " pdb=" N GLN B 689 " pdb=" C GLN B 689 " pdb=" CB GLN B 689 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA ASP B 742 " pdb=" N ASP B 742 " pdb=" C ASP B 742 " pdb=" CB ASP B 742 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASP A1246 " pdb=" N ASP A1246 " pdb=" C ASP A1246 " pdb=" CB ASP A1246 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3176 not shown) Planarity restraints: 6264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 953 " 0.572 9.50e-02 1.11e+02 2.83e-01 1.02e+03 pdb=" NE ARG B 953 " 0.142 2.00e-02 2.50e+03 pdb=" CZ ARG B 953 " 0.126 2.00e-02 2.50e+03 pdb=" NH1 ARG B 953 " 0.176 2.00e-02 2.50e+03 pdb=" NH2 ARG B 953 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG B 953 " -0.486 2.00e-02 2.50e+03 pdb="HH12 ARG B 953 " 0.247 2.00e-02 2.50e+03 pdb="HH21 ARG B 953 " -0.156 2.00e-02 2.50e+03 pdb="HH22 ARG B 953 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.356 2.00e-02 2.50e+03 1.27e-01 6.43e+02 pdb=" CG TRP A 816 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.128 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.042 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " 0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " 0.057 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP A 816 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 816 " 0.116 2.00e-02 2.50e+03 pdb=" HE3 TRP A 816 " 0.141 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 816 " -0.138 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 816 " 0.059 2.00e-02 2.50e+03 pdb=" HH2 TRP A 816 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 602 " -0.285 9.50e-02 1.11e+02 1.79e-01 5.24e+02 pdb=" NE ARG A 602 " -0.117 2.00e-02 2.50e+03 pdb=" CZ ARG A 602 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 602 " 0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG A 602 " 0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 602 " 0.261 2.00e-02 2.50e+03 pdb="HH12 ARG A 602 " -0.316 2.00e-02 2.50e+03 pdb="HH21 ARG A 602 " 0.013 2.00e-02 2.50e+03 pdb="HH22 ARG A 602 " 0.149 2.00e-02 2.50e+03 ... (remaining 6261 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 3141 2.16 - 2.77: 75841 2.77 - 3.38: 130253 3.38 - 3.99: 173783 3.99 - 4.60: 254871 Nonbonded interactions: 637889 Sorted by model distance: nonbonded pdb=" OE2 GLU A 608 " pdb=" HG SER A 610 " model vdw 1.552 1.850 nonbonded pdb=" HG1 THR B 343 " pdb=" O26 PNS B1501 " model vdw 1.572 1.850 nonbonded pdb=" OE1 GLU B1015 " pdb=" HG SER B1235 " model vdw 1.580 1.850 nonbonded pdb=" HG SER A 472 " pdb=" OD2 ASP A 480 " model vdw 1.586 1.850 nonbonded pdb=" OD2 ASP B1134 " pdb=" HG SER B1199 " model vdw 1.593 1.850 ... (remaining 637884 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 99 through 1340 or resid 1501 or resid 1503 through 1505)) \ selection = (chain 'B' and (resid 99 through 1340 or resid 1501 or resid 1503 through 1504 o \ r (resid 1505 and (name N or name CA or name C or name O or name CB or name SG o \ r name H or name H2 or name HA or name HB2 or name HB3 or name HG )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 12880 2.51 5 N 3772 2.21 5 O 3716 1.98 5 H 20419 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.860 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: 0.620 Extract box with map and model: 7.010 Check model and map are aligned: 0.580 Convert atoms to be neutral: 0.340 Process input model: 131.030 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 : 0.013 0.274 20869 Z= 0.873 Angle : 1.971 21.372 28429 Z= 1.290 Chirality : 0.101 0.472 3179 Planarity : 0.022 0.206 3782 Dihedral : 15.035 105.818 7699 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.17 % Favored : 94.56 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 2648 helix: -1.68 (0.13), residues: 1092 sheet: -1.98 (0.24), residues: 422 loop : -0.97 (0.18), residues: 1134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 3.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 10 residues processed: 266 average time/residue: 1.0115 time to fit residues: 376.1677 Evaluate side-chains 142 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 3.203 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 10 average time/residue: 0.7725 time to fit residues: 15.8270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN B 449 ASN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 20869 Z= 0.263 Angle : 0.773 7.758 28429 Z= 0.397 Chirality : 0.042 0.418 3179 Planarity : 0.008 0.088 3782 Dihedral : 8.469 86.499 2994 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2648 helix: -0.56 (0.14), residues: 1107 sheet: -1.86 (0.23), residues: 429 loop : -0.73 (0.19), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 171 average time/residue: 0.9386 time to fit residues: 232.2529 Evaluate side-chains 134 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 3.176 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 14 average time/residue: 0.4907 time to fit residues: 16.2381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 241 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 20869 Z= 0.400 Angle : 0.699 7.912 28429 Z= 0.357 Chirality : 0.040 0.409 3179 Planarity : 0.005 0.068 3782 Dihedral : 7.712 80.898 2994 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2648 helix: -0.01 (0.15), residues: 1087 sheet: -2.03 (0.22), residues: 466 loop : -0.63 (0.20), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 128 average time/residue: 0.9551 time to fit residues: 177.8976 Evaluate side-chains 113 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 3.396 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.7099 time to fit residues: 13.2417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 241 optimal weight: 20.0000 chunk 256 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 20869 Z= 0.337 Angle : 0.652 8.224 28429 Z= 0.328 Chirality : 0.039 0.404 3179 Planarity : 0.005 0.060 3782 Dihedral : 7.250 75.024 2994 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.81 (0.16), residues: 2648 helix: 0.30 (0.16), residues: 1089 sheet: -1.98 (0.22), residues: 466 loop : -0.53 (0.20), residues: 1093 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 136 average time/residue: 0.9374 time to fit residues: 186.5246 Evaluate side-chains 114 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 3.165 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.6535 time to fit residues: 11.3108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 20869 Z= 0.367 Angle : 0.646 6.670 28429 Z= 0.325 Chirality : 0.039 0.400 3179 Planarity : 0.005 0.056 3782 Dihedral : 6.979 72.327 2994 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.74 (0.17), residues: 2648 helix: 0.43 (0.16), residues: 1100 sheet: -2.01 (0.22), residues: 474 loop : -0.54 (0.20), residues: 1074 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 118 average time/residue: 1.0165 time to fit residues: 173.6357 Evaluate side-chains 107 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 3.250 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4871 time to fit residues: 8.5806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 8.9990 chunk 230 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 40.0000 chunk 21 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 20869 Z= 0.390 Angle : 0.645 7.208 28429 Z= 0.324 Chirality : 0.039 0.397 3179 Planarity : 0.005 0.054 3782 Dihedral : 6.807 73.323 2994 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.73 (0.17), residues: 2648 helix: 0.51 (0.16), residues: 1100 sheet: -2.10 (0.22), residues: 477 loop : -0.56 (0.20), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 115 average time/residue: 1.0415 time to fit residues: 173.3779 Evaluate side-chains 101 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 3.465 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4902 time to fit residues: 9.6070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 247 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 187 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 GLN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.139 20869 Z= 0.300 Angle : 0.617 6.713 28429 Z= 0.308 Chirality : 0.038 0.389 3179 Planarity : 0.005 0.106 3782 Dihedral : 6.653 73.499 2994 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.51 (0.17), residues: 2648 helix: 0.70 (0.16), residues: 1099 sheet: -2.01 (0.23), residues: 450 loop : -0.50 (0.20), residues: 1099 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 113 average time/residue: 1.0043 time to fit residues: 163.6333 Evaluate side-chains 100 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 3.266 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4617 time to fit residues: 4.8908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 20869 Z= 0.381 Angle : 0.634 6.310 28429 Z= 0.317 Chirality : 0.038 0.393 3179 Planarity : 0.005 0.080 3782 Dihedral : 6.656 73.702 2994 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.59 (0.17), residues: 2648 helix: 0.64 (0.16), residues: 1105 sheet: -2.06 (0.22), residues: 465 loop : -0.53 (0.20), residues: 1078 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 107 average time/residue: 1.0704 time to fit residues: 163.9112 Evaluate side-chains 98 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 3.208 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5471 time to fit residues: 5.9041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 232 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN B 421 HIS B 476 GLN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 20869 Z= 0.314 Angle : 0.609 5.990 28429 Z= 0.303 Chirality : 0.038 0.387 3179 Planarity : 0.005 0.063 3782 Dihedral : 6.540 73.069 2994 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.39 (0.17), residues: 2648 helix: 0.84 (0.16), residues: 1099 sheet: -1.94 (0.24), residues: 433 loop : -0.50 (0.20), residues: 1116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 1.0597 time to fit residues: 159.6402 Evaluate side-chains 100 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 3.128 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5124 time to fit residues: 5.7890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 20869 Z= 0.320 Angle : 0.612 6.809 28429 Z= 0.303 Chirality : 0.038 0.386 3179 Planarity : 0.005 0.063 3782 Dihedral : 6.478 73.488 2994 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.39 (0.17), residues: 2648 helix: 0.85 (0.16), residues: 1100 sheet: -1.96 (0.24), residues: 424 loop : -0.55 (0.19), residues: 1124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 1.0709 time to fit residues: 157.6275 Evaluate side-chains 97 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 210 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.086494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.061290 restraints weight = 189163.628| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.09 r_work: 0.3187 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work: 0.3157 rms_B_bonded: 2.88 restraints_weight: 0.1250 r_work: 0.3141 rms_B_bonded: 3.00 restraints_weight: 0.0625 r_work: 0.3124 rms_B_bonded: 3.16 restraints_weight: 0.0312 r_work: 0.3105 rms_B_bonded: 3.38 restraints_weight: 0.0156 r_work: 0.3084 rms_B_bonded: 3.66 restraints_weight: 0.0078 r_work: 0.3061 rms_B_bonded: 4.00 restraints_weight: 0.0039 r_work: 0.3035 rms_B_bonded: 4.42 restraints_weight: 0.0020 r_work: 0.3007 rms_B_bonded: 4.92 restraints_weight: 0.0010 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 20869 Z= 0.258 Angle : 0.591 6.008 28429 Z= 0.291 Chirality : 0.038 0.381 3179 Planarity : 0.005 0.059 3782 Dihedral : 6.390 72.760 2994 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.25 (0.17), residues: 2648 helix: 0.97 (0.16), residues: 1103 sheet: -1.85 (0.25), residues: 406 loop : -0.53 (0.19), residues: 1139 =============================================================================== Job complete usr+sys time: 6612.34 seconds wall clock time: 118 minutes 38.89 seconds (7118.89 seconds total)