Starting phenix.real_space_refine on Sat Mar 16 05:28:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qds_13925/03_2024/7qds_13925.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qds_13925/03_2024/7qds_13925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qds_13925/03_2024/7qds_13925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qds_13925/03_2024/7qds_13925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qds_13925/03_2024/7qds_13925.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qds_13925/03_2024/7qds_13925.pdb" } resolution = 3.8 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 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8774 2.51 5 N 2355 2.21 5 O 2609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 5": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 101": "OD1" <-> "OD2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 697": "OE1" <-> "OE2" Residue "B TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 781": "OD1" <-> "OD2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B ASP 915": "OD1" <-> "OD2" Residue "B ARG 918": "NH1" <-> "NH2" Residue "B ASP 943": "OD1" <-> "OD2" Residue "B TYR 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 974": "OE1" <-> "OE2" Residue "B GLU 1014": "OE1" <-> "OE2" Residue "B ASP 1037": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1075": "OE1" <-> "OE2" Residue "B ARG 1076": "NH1" <-> "NH2" Residue "B GLU 1098": "OE1" <-> "OE2" Residue "B TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1105": "OD1" <-> "OD2" Residue "B TYR 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1192": "OD1" <-> "OD2" Residue "B TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1250": "OD1" <-> "OD2" Residue "B ASP 1284": "OD1" <-> "OD2" Residue "B ASP 1298": "OD1" <-> "OD2" Residue "B ASP 1313": "OD1" <-> "OD2" Residue "B TYR 1320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1358": "OD1" <-> "OD2" Residue "B ARG 1367": "NH1" <-> "NH2" Residue "B GLU 1376": "OE1" <-> "OE2" Residue "B GLU 1388": "OE1" <-> "OE2" Residue "B ARG 1424": "NH1" <-> "NH2" Residue "B ASP 1461": "OD1" <-> "OD2" Residue "B GLU 1473": "OE1" <-> "OE2" Residue "B ARG 1503": "NH1" <-> "NH2" Residue "B ARG 1507": "NH1" <-> "NH2" Residue "B ARG 1523": "NH1" <-> "NH2" Residue "B ASP 1540": "OD1" <-> "OD2" Residue "B ARG 1553": "NH1" <-> "NH2" Residue "B ARG 1560": "NH1" <-> "NH2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 294": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13798 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1192 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 7860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7860 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 24, 'TRANS': 981} Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "D" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Time building chain proxies: 7.40, per 1000 atoms: 0.54 Number of scatterers: 13798 At special positions: 0 Unit cell: (145.502, 117.058, 122.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2609 8.00 N 2355 7.00 C 8774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 2.5 seconds 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 18 sheets defined 48.6% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.813A pdb=" N GLY A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.578A pdb=" N LEU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 577 removed outlier: 3.548A pdb=" N ARG B 569 " --> pdb=" O TRP B 565 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 597 through 611 removed outlier: 3.616A pdb=" N ARG B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.988A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 3.627A pdb=" N VAL B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.695A pdb=" N ALA B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 686 removed outlier: 3.580A pdb=" N ASP B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 removed outlier: 3.936A pdb=" N HIS B 709 " --> pdb=" O CYS B 705 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 726 removed outlier: 4.302A pdb=" N TRP B 717 " --> pdb=" O VAL B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 removed outlier: 3.586A pdb=" N LEU B 744 " --> pdb=" O GLY B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 773 removed outlier: 3.954A pdb=" N LEU B 772 " --> pdb=" O ARG B 768 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 796 Processing helix chain 'B' and resid 803 through 821 Processing helix chain 'B' and resid 824 through 836 removed outlier: 3.731A pdb=" N TRP B 828 " --> pdb=" O ASN B 824 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B 836 " --> pdb=" O GLY B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 857 Processing helix chain 'B' and resid 860 through 874 removed outlier: 3.819A pdb=" N TRP B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 894 through 908 removed outlier: 3.915A pdb=" N TRP B 898 " --> pdb=" O TYR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 925 removed outlier: 3.610A pdb=" N ASN B 924 " --> pdb=" O THR B 920 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET B 925 " --> pdb=" O THR B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 943 Processing helix chain 'B' and resid 951 through 960 Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.613A pdb=" N ALA B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 993 removed outlier: 3.803A pdb=" N PHE B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1011 removed outlier: 3.506A pdb=" N ALA B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1033 removed outlier: 3.591A pdb=" N THR B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1045 Processing helix chain 'B' and resid 1050 through 1065 Processing helix chain 'B' and resid 1066 through 1080 removed outlier: 3.738A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1101 removed outlier: 3.853A pdb=" N GLN B1101 " --> pdb=" O THR B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1116 removed outlier: 3.746A pdb=" N ALA B1107 " --> pdb=" O LYS B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1134 Processing helix chain 'B' and resid 1139 through 1152 removed outlier: 3.813A pdb=" N HIS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1172 removed outlier: 3.724A pdb=" N GLN B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1189 removed outlier: 3.557A pdb=" N LYS B1180 " --> pdb=" O VAL B1176 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1206 removed outlier: 3.853A pdb=" N TRP B1196 " --> pdb=" O ASP B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1224 Processing helix chain 'B' and resid 1228 through 1244 Processing helix chain 'B' and resid 1254 through 1266 Processing helix chain 'B' and resid 1269 through 1291 removed outlier: 4.494A pdb=" N TRP B1273 " --> pdb=" O ASP B1269 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B1274 " --> pdb=" O PRO B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1313 removed outlier: 4.126A pdb=" N ASP B1313 " --> pdb=" O ALA B1309 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1340 Processing helix chain 'B' and resid 1341 through 1356 removed outlier: 3.648A pdb=" N ASN B1356 " --> pdb=" O ASN B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1359 through 1371 removed outlier: 3.715A pdb=" N ILE B1363 " --> pdb=" O GLN B1359 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU B1364 " --> pdb=" O PRO B1360 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1396 Processing helix chain 'B' and resid 1399 through 1414 removed outlier: 3.844A pdb=" N TRP B1403 " --> pdb=" O SER B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1434 Processing helix chain 'B' and resid 1436 through 1456 removed outlier: 4.028A pdb=" N ALA B1456 " --> pdb=" O LYS B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1478 Processing helix chain 'B' and resid 1480 through 1494 Processing helix chain 'B' and resid 1499 through 1511 Processing helix chain 'B' and resid 1515 through 1533 Processing helix chain 'B' and resid 1535 through 1548 Processing helix chain 'B' and resid 1552 through 1563 removed outlier: 4.089A pdb=" N SER B1563 " --> pdb=" O GLN B1559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'B' and resid 737 through 739 Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 11 removed outlier: 7.039A pdb=" N ILE C 300 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS C 10 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 298 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 25 removed outlier: 6.563A pdb=" N VAL C 46 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.515A pdb=" N SER C 69 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 79 " --> pdb=" O TRP C 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.752A pdb=" N TYR C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLY C 134 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LYS C 140 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.630A pdb=" N GLY C 166 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE C 154 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 164 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 174 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 196 through 198 Processing sheet with id=AB1, first strand: chain 'C' and resid 213 through 217 removed outlier: 6.073A pdb=" N ILE C 214 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR C 227 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE C 216 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 235 through 240 removed outlier: 3.550A pdb=" N ASN C 237 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 268 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP C 260 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N CYS C 266 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.714A pdb=" N TRP D 58 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS D 48 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU D 56 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.506A pdb=" N SER D 69 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D 100 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AB6, first strand: chain 'D' and resid 163 through 166 removed outlier: 3.825A pdb=" N ILE D 174 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS D 184 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 195 through 197 removed outlier: 4.569A pdb=" N SER D 195 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 216 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY D 226 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 235 through 239 removed outlier: 6.835A pdb=" N SER D 250 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 238 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL D 248 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 256 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS D 268 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP D 260 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N CYS D 266 " --> pdb=" O ASP D 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 277 through 282 714 hydrogen bonds defined for protein. 2067 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: 4.64 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4467 1.34 - 1.46: 2215 1.46 - 1.58: 7327 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 14097 Sorted by residual: bond pdb=" CB VAL D 290 " pdb=" CG2 VAL D 290 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB ILE B 968 " pdb=" CG2 ILE B 968 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 bond pdb=" CB GLU A 31 " pdb=" CG GLU A 31 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CB CYS B 715 " pdb=" SG CYS B 715 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CG1 ILE B1007 " pdb=" CD1 ILE B1007 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.29e+00 ... (remaining 14092 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.68: 235 105.68 - 112.77: 7643 112.77 - 119.87: 4671 119.87 - 126.97: 6373 126.97 - 134.07: 219 Bond angle restraints: 19141 Sorted by residual: angle pdb=" C GLU A 31 " pdb=" CA GLU A 31 " pdb=" CB GLU A 31 " ideal model delta sigma weight residual 110.67 120.27 -9.60 2.23e+00 2.01e-01 1.85e+01 angle pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sigma weight residual 116.30 129.46 -13.16 3.50e+00 8.16e-02 1.41e+01 angle pdb=" CB MET A 194 " pdb=" CG MET A 194 " pdb=" SD MET A 194 " ideal model delta sigma weight residual 112.70 101.54 11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C GLU B1014 " pdb=" N ASP B1015 " pdb=" CA ASP B1015 " ideal model delta sigma weight residual 125.66 132.08 -6.42 1.85e+00 2.92e-01 1.20e+01 angle pdb=" N GLU A 31 " pdb=" CA GLU A 31 " pdb=" CB GLU A 31 " ideal model delta sigma weight residual 111.62 106.47 5.15 1.62e+00 3.81e-01 1.01e+01 ... (remaining 19136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 7445 17.33 - 34.65: 816 34.65 - 51.98: 112 51.98 - 69.31: 22 69.31 - 86.63: 18 Dihedral angle restraints: 8413 sinusoidal: 3260 harmonic: 5153 Sorted by residual: dihedral pdb=" CA ASP D 201 " pdb=" C ASP D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta harmonic sigma weight residual 180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ARG B 947 " pdb=" C ARG B 947 " pdb=" N GLU B 948 " pdb=" CA GLU B 948 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLY D 38 " pdb=" C GLY D 38 " pdb=" N SER D 39 " pdb=" CA SER D 39 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 8410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1406 0.042 - 0.084: 557 0.084 - 0.125: 161 0.125 - 0.167: 32 0.167 - 0.209: 6 Chirality restraints: 2162 Sorted by residual: chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA GLU A 31 " pdb=" N GLU A 31 " pdb=" C GLU A 31 " pdb=" CB GLU A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA ASN B1396 " pdb=" N ASN B1396 " pdb=" C ASN B1396 " pdb=" CB ASN B1396 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 2159 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B1119 " 0.092 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO B1120 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO B1120 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO B1120 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 105 " -0.048 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO C 106 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B1256 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C LEU B1256 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU B1256 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS B1257 " 0.017 2.00e-02 2.50e+03 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 207 2.63 - 3.20: 13015 3.20 - 3.77: 20682 3.77 - 4.33: 27067 4.33 - 4.90: 46078 Nonbonded interactions: 107049 Sorted by model distance: nonbonded pdb=" OG SER C 251 " pdb=" OD1 ASP C 253 " model vdw 2.067 2.440 nonbonded pdb=" OE2 GLU B1314 " pdb=" ND2 ASN B1321 " model vdw 2.094 2.520 nonbonded pdb=" OG SER B1157 " pdb=" OE1 GLN B1160 " model vdw 2.108 2.440 nonbonded pdb=" OD1 ASP D 253 " pdb=" OG SER D 255 " model vdw 2.172 2.440 nonbonded pdb=" OE1 GLN B 588 " pdb=" OH TYR B 608 " model vdw 2.188 2.440 ... (remaining 107044 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 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.960 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 37.960 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.005 0.056 14097 Z= 0.310 Angle : 0.856 17.416 19141 Z= 0.456 Chirality : 0.049 0.209 2162 Planarity : 0.006 0.139 2434 Dihedral : 14.594 86.633 5093 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.06 % 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: -0.33 (0.21), residues: 1761 helix: 2.76 (0.18), residues: 806 sheet: -1.96 (0.31), residues: 250 loop : -3.37 (0.18), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 936 HIS 0.013 0.002 HIS B 992 PHE 0.029 0.003 PHE D 240 TYR 0.034 0.002 TYR D 156 ARG 0.007 0.001 ARG B1553 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.446 Fit side-chains REVERT: A 192 LYS cc_start: 0.8440 (mttt) cc_final: 0.8177 (tttp) REVERT: B 1118 LYS cc_start: 0.7763 (pptt) cc_final: 0.7221 (mmtt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2237 time to fit residues: 41.9705 Evaluate side-chains 82 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 GLN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1404 GLN C 173 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14097 Z= 0.239 Angle : 0.668 13.075 19141 Z= 0.343 Chirality : 0.043 0.169 2162 Planarity : 0.005 0.077 2434 Dihedral : 5.196 24.826 1886 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 1.15 % Allowed : 9.65 % Favored : 89.20 % 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: -0.26 (0.21), residues: 1761 helix: 2.53 (0.18), residues: 826 sheet: -1.79 (0.32), residues: 268 loop : -3.18 (0.20), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 936 HIS 0.004 0.001 HIS B1187 PHE 0.021 0.002 PHE D 240 TYR 0.017 0.001 TYR B 935 ARG 0.005 0.000 ARG B1005 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.620 Fit side-chains REVERT: A 192 LYS cc_start: 0.8415 (mttt) cc_final: 0.8113 (tttt) REVERT: B 773 MET cc_start: 0.7826 (mmm) cc_final: 0.7620 (mmm) REVERT: B 1118 LYS cc_start: 0.7763 (pptt) cc_final: 0.7171 (mmtt) REVERT: B 1383 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7965 (t0) outliers start: 17 outliers final: 8 residues processed: 121 average time/residue: 0.2264 time to fit residues: 42.4813 Evaluate side-chains 100 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1383 ASP Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 154 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 942 GLN B1205 GLN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14097 Z= 0.391 Angle : 0.725 14.083 19141 Z= 0.378 Chirality : 0.046 0.181 2162 Planarity : 0.005 0.059 2434 Dihedral : 5.445 26.536 1886 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 2.90 % Allowed : 12.96 % Favored : 84.14 % 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: -0.48 (0.21), residues: 1761 helix: 2.21 (0.18), residues: 827 sheet: -1.76 (0.32), residues: 270 loop : -3.16 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 936 HIS 0.005 0.002 HIS B 709 PHE 0.026 0.003 PHE B1316 TYR 0.016 0.002 TYR B 935 ARG 0.004 0.001 ARG B1005 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 96 time to evaluate : 1.475 Fit side-chains REVERT: A 192 LYS cc_start: 0.8583 (mttt) cc_final: 0.8214 (tttt) REVERT: B 735 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.7985 (p) REVERT: B 1118 LYS cc_start: 0.7835 (pptt) cc_final: 0.7089 (mmtt) REVERT: B 1383 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8046 (t0) REVERT: B 1504 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8061 (tp) REVERT: C 275 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: D 94 GLU cc_start: 0.8074 (tp30) cc_final: 0.7654 (tp30) outliers start: 43 outliers final: 22 residues processed: 133 average time/residue: 0.2087 time to fit residues: 44.5732 Evaluate side-chains 110 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1383 ASP Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain B residue 1504 LEU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 83 optimal weight: 0.0970 chunk 151 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14097 Z= 0.210 Angle : 0.618 13.991 19141 Z= 0.319 Chirality : 0.042 0.171 2162 Planarity : 0.004 0.052 2434 Dihedral : 5.069 22.838 1886 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 2.70 % Allowed : 15.18 % Favored : 82.12 % 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: -0.26 (0.21), residues: 1761 helix: 2.40 (0.18), residues: 829 sheet: -1.66 (0.32), residues: 277 loop : -3.09 (0.20), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 47 HIS 0.004 0.001 HIS C 126 PHE 0.013 0.001 PHE D 150 TYR 0.012 0.001 TYR B 935 ARG 0.003 0.000 ARG B1433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 1.756 Fit side-chains REVERT: A 192 LYS cc_start: 0.8510 (mttt) cc_final: 0.8170 (tttt) REVERT: B 773 MET cc_start: 0.8035 (mmm) cc_final: 0.7789 (mmm) REVERT: B 1118 LYS cc_start: 0.7773 (pptt) cc_final: 0.7017 (mmtt) REVERT: B 1383 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8141 (t0) REVERT: C 275 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.8013 (m-30) REVERT: D 94 GLU cc_start: 0.7808 (tp30) cc_final: 0.7559 (tp30) outliers start: 40 outliers final: 24 residues processed: 135 average time/residue: 0.2345 time to fit residues: 50.1759 Evaluate side-chains 117 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1269 ASP Chi-restraints excluded: chain B residue 1272 ILE Chi-restraints excluded: chain B residue 1383 ASP Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 0.0770 chunk 151 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN B1146 ASN B1151 HIS ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14097 Z= 0.332 Angle : 0.668 12.434 19141 Z= 0.348 Chirality : 0.044 0.172 2162 Planarity : 0.004 0.049 2434 Dihedral : 5.203 25.665 1886 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 3.64 % Allowed : 16.60 % Favored : 79.76 % 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: -0.37 (0.21), residues: 1761 helix: 2.28 (0.18), residues: 830 sheet: -1.62 (0.33), residues: 256 loop : -3.12 (0.20), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 47 HIS 0.005 0.001 HIS C 126 PHE 0.030 0.002 PHE B1316 TYR 0.013 0.002 TYR B 935 ARG 0.003 0.000 ARG B 947 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 96 time to evaluate : 2.084 Fit side-chains REVERT: A 192 LYS cc_start: 0.8601 (mttt) cc_final: 0.8224 (tttt) REVERT: B 735 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8053 (p) REVERT: B 773 MET cc_start: 0.8209 (mmm) cc_final: 0.7859 (mmm) REVERT: B 1118 LYS cc_start: 0.7724 (pptt) cc_final: 0.6979 (mmtt) REVERT: B 1383 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8029 (t0) REVERT: B 1504 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8085 (tp) REVERT: C 275 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: D 94 GLU cc_start: 0.7996 (tp30) cc_final: 0.7612 (tp30) REVERT: D 156 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7618 (t80) outliers start: 54 outliers final: 33 residues processed: 145 average time/residue: 0.2189 time to fit residues: 50.3666 Evaluate side-chains 124 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1272 ILE Chi-restraints excluded: chain B residue 1383 ASP Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain B residue 1504 LEU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 267 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14097 Z= 0.204 Angle : 0.606 11.535 19141 Z= 0.312 Chirality : 0.041 0.172 2162 Planarity : 0.004 0.050 2434 Dihedral : 4.923 23.245 1886 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 3.04 % Allowed : 18.22 % Favored : 78.74 % 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: -0.23 (0.21), residues: 1761 helix: 2.40 (0.18), residues: 831 sheet: -1.55 (0.34), residues: 257 loop : -3.07 (0.20), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 47 HIS 0.005 0.001 HIS C 126 PHE 0.014 0.001 PHE D 150 TYR 0.011 0.001 TYR C 120 ARG 0.002 0.000 ARG B 611 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 100 time to evaluate : 1.625 Fit side-chains revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8547 (mttt) cc_final: 0.8203 (tttt) REVERT: B 735 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.8053 (p) REVERT: B 773 MET cc_start: 0.8242 (mmm) cc_final: 0.7900 (mmm) REVERT: B 1383 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8041 (t0) REVERT: B 1504 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8068 (tp) REVERT: C 275 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8095 (m-30) REVERT: D 94 GLU cc_start: 0.7837 (tp30) cc_final: 0.7593 (tp30) REVERT: D 156 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7487 (t80) outliers start: 45 outliers final: 30 residues processed: 139 average time/residue: 0.2110 time to fit residues: 47.3798 Evaluate side-chains 128 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1269 ASP Chi-restraints excluded: chain B residue 1272 ILE Chi-restraints excluded: chain B residue 1383 ASP Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain B residue 1504 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 168 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14097 Z= 0.192 Angle : 0.606 14.919 19141 Z= 0.310 Chirality : 0.041 0.176 2162 Planarity : 0.004 0.050 2434 Dihedral : 4.815 23.466 1886 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 2.97 % Allowed : 19.03 % Favored : 78.00 % 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: -0.14 (0.21), residues: 1761 helix: 2.45 (0.18), residues: 831 sheet: -1.46 (0.34), residues: 255 loop : -3.01 (0.20), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 47 HIS 0.005 0.001 HIS C 126 PHE 0.032 0.001 PHE B1316 TYR 0.011 0.001 TYR C 120 ARG 0.003 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 97 time to evaluate : 1.659 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7601 (tpp80) REVERT: A 192 LYS cc_start: 0.8509 (mttt) cc_final: 0.8228 (tttt) REVERT: B 735 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.8061 (p) REVERT: B 1118 LYS cc_start: 0.7298 (pptt) cc_final: 0.6684 (mmtt) REVERT: B 1227 ASN cc_start: 0.7970 (p0) cc_final: 0.7578 (p0) REVERT: B 1383 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8005 (t0) REVERT: B 1504 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8000 (tp) REVERT: C 275 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: D 94 GLU cc_start: 0.8006 (tp30) cc_final: 0.7611 (tp30) REVERT: D 156 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7532 (t80) outliers start: 44 outliers final: 34 residues processed: 134 average time/residue: 0.2261 time to fit residues: 48.3217 Evaluate side-chains 133 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 94 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1269 ASP Chi-restraints excluded: chain B residue 1272 ILE Chi-restraints excluded: chain B residue 1383 ASP Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain B residue 1500 GLU Chi-restraints excluded: chain B residue 1504 LEU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 83 optimal weight: 0.0060 chunk 15 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14097 Z= 0.273 Angle : 0.641 14.557 19141 Z= 0.330 Chirality : 0.042 0.173 2162 Planarity : 0.004 0.051 2434 Dihedral : 4.931 24.197 1886 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 3.31 % Allowed : 19.37 % Favored : 77.33 % 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: -0.20 (0.21), residues: 1761 helix: 2.42 (0.18), residues: 831 sheet: -1.57 (0.33), residues: 254 loop : -3.03 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 47 HIS 0.006 0.001 HIS C 126 PHE 0.016 0.002 PHE D 150 TYR 0.012 0.001 TYR B1320 ARG 0.002 0.000 ARG B1553 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 91 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7682 (tpp80) REVERT: A 192 LYS cc_start: 0.8584 (mttt) cc_final: 0.8258 (tttt) REVERT: B 735 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.8068 (p) REVERT: B 1118 LYS cc_start: 0.7481 (pptt) cc_final: 0.6840 (mmtt) REVERT: B 1383 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 1504 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8081 (tp) REVERT: C 275 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: D 94 GLU cc_start: 0.7865 (tp30) cc_final: 0.7662 (tp30) REVERT: D 156 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7740 (t80) outliers start: 49 outliers final: 35 residues processed: 136 average time/residue: 0.2273 time to fit residues: 49.1990 Evaluate side-chains 128 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 88 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1272 ILE Chi-restraints excluded: chain B residue 1383 ASP Chi-restraints excluded: chain B residue 1500 GLU Chi-restraints excluded: chain B residue 1504 LEU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 TRP Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 0.0050 chunk 148 optimal weight: 0.3980 chunk 156 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14097 Z= 0.192 Angle : 0.610 14.086 19141 Z= 0.309 Chirality : 0.041 0.175 2162 Planarity : 0.004 0.050 2434 Dihedral : 4.765 22.923 1886 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 2.97 % Allowed : 20.38 % Favored : 76.65 % 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: -0.12 (0.21), residues: 1761 helix: 2.50 (0.18), residues: 830 sheet: -1.57 (0.33), residues: 251 loop : -2.98 (0.20), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 47 HIS 0.005 0.001 HIS C 126 PHE 0.013 0.001 PHE D 150 TYR 0.011 0.001 TYR C 120 ARG 0.002 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 100 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7844 (tpp80) cc_final: 0.7627 (tpp80) REVERT: A 192 LYS cc_start: 0.8511 (mttt) cc_final: 0.8238 (tttt) REVERT: B 773 MET cc_start: 0.8065 (mmm) cc_final: 0.7764 (mmm) REVERT: B 800 MET cc_start: 0.5992 (tpp) cc_final: 0.5047 (mmp) REVERT: B 1118 LYS cc_start: 0.7570 (pptt) cc_final: 0.6897 (mmtt) REVERT: B 1383 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8014 (t0) REVERT: B 1504 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8004 (tp) REVERT: C 275 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: D 156 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7652 (t80) outliers start: 44 outliers final: 34 residues processed: 137 average time/residue: 0.2276 time to fit residues: 48.8785 Evaluate side-chains 134 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1269 ASP Chi-restraints excluded: chain B residue 1272 ILE Chi-restraints excluded: chain B residue 1383 ASP Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1500 GLU Chi-restraints excluded: chain B residue 1504 LEU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 TRP Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 138 optimal weight: 0.0980 chunk 14 optimal weight: 0.0770 chunk 107 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 0.0970 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14097 Z= 0.161 Angle : 0.598 14.361 19141 Z= 0.304 Chirality : 0.040 0.186 2162 Planarity : 0.004 0.050 2434 Dihedral : 4.575 22.724 1886 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.23 % Allowed : 21.19 % Favored : 76.59 % 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: -0.04 (0.21), residues: 1761 helix: 2.54 (0.18), residues: 830 sheet: -1.60 (0.33), residues: 257 loop : -2.87 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 47 HIS 0.005 0.001 HIS C 126 PHE 0.012 0.001 PHE D 150 TYR 0.012 0.001 TYR B1536 ARG 0.003 0.000 ARG A 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 773 MET cc_start: 0.8136 (mmm) cc_final: 0.7818 (mmm) REVERT: B 800 MET cc_start: 0.6078 (tpp) cc_final: 0.4998 (mmp) REVERT: B 920 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8451 (m) REVERT: B 1118 LYS cc_start: 0.7370 (pptt) cc_final: 0.6740 (mmtt) REVERT: B 1383 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7963 (t0) REVERT: C 191 MET cc_start: 0.8329 (mtp) cc_final: 0.7962 (mtm) REVERT: D 156 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7524 (t80) outliers start: 33 outliers final: 27 residues processed: 135 average time/residue: 0.2420 time to fit residues: 50.6590 Evaluate side-chains 128 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1269 ASP Chi-restraints excluded: chain B residue 1272 ILE Chi-restraints excluded: chain B residue 1286 LEU Chi-restraints excluded: chain B residue 1378 GLN Chi-restraints excluded: chain B residue 1383 ASP Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1500 GLU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 259 TRP Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 122 optimal weight: 0.5980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.110715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085774 restraints weight = 28171.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.086412 restraints weight = 21944.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.087814 restraints weight = 17729.036| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14097 Z= 0.169 Angle : 0.602 13.466 19141 Z= 0.305 Chirality : 0.041 0.189 2162 Planarity : 0.004 0.050 2434 Dihedral : 4.515 22.808 1886 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 2.29 % Allowed : 21.39 % Favored : 76.32 % 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: 0.00 (0.21), residues: 1761 helix: 2.58 (0.18), residues: 830 sheet: -1.53 (0.33), residues: 257 loop : -2.87 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 47 HIS 0.006 0.001 HIS C 126 PHE 0.013 0.001 PHE D 150 TYR 0.010 0.001 TYR B1159 ARG 0.007 0.000 ARG A 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.08 seconds wall clock time: 44 minutes 50.49 seconds (2690.49 seconds total)