Starting phenix.real_space_refine on Sun Mar 17 11:34:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qca_18326/03_2024/8qca_18326.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qca_18326/03_2024/8qca_18326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qca_18326/03_2024/8qca_18326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qca_18326/03_2024/8qca_18326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qca_18326/03_2024/8qca_18326.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qca_18326/03_2024/8qca_18326.pdb" } resolution = 2.84 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= -0.002 sd= 0.147 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 76 5.16 5 C 11172 2.51 5 N 2961 2.21 5 O 3243 1.98 5 H 117 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 391": "OD1" <-> "OD2" Residue "A PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1131": "OE1" <-> "OE2" Residue "A GLU 1217": "OE1" <-> "OE2" Residue "B GLU 785": "OE1" <-> "OE2" Residue "B ASP 914": "OD1" <-> "OD2" Residue "B GLU 1015": "OE1" <-> "OE2" Residue "B PHE 1238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1311": "OD1" <-> "OD2" Residue "B TYR 1351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1378": "OD1" <-> "OD2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 253": "OD1" <-> "OD2" Residue "D ASP 359": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17573 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6111 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 768} Chain breaks: 10 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 489 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 9, 'ASN:plan1': 10, 'HIS:plan': 3, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 210 Chain: "B" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 5575 Classifications: {'peptide': 756} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 741} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 473 Unresolved non-hydrogen angles: 575 Unresolved non-hydrogen dihedrals: 378 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 25, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 235 Chain: "C" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3000 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 5, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2646 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 348} Chain breaks: 5 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 7, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 115 Chain: "E" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 172 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 22} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "X" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Classifications: {'RNA': 4} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 9 Time building chain proxies: 9.75, per 1000 atoms: 0.55 Number of scatterers: 17573 At special positions: 0 Unit cell: (109.805, 142.15, 153.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 4 15.00 O 3243 8.00 N 2961 7.00 C 11172 6.00 H 117 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=0, symmetry=0 Time building additional restraints: 6.51 Conformation dependent library (CDL) restraints added in 3.3 seconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 19 sheets defined 47.2% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.645A pdb=" N LYS A 18 " --> pdb=" O TYR A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 4.138A pdb=" N ILE A 50 " --> pdb=" O HIS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.757A pdb=" N MET A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.692A pdb=" N LEU A 92 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 344 Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.742A pdb=" N ALA A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 removed outlier: 4.203A pdb=" N ASN A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 431 through 436 removed outlier: 5.986A pdb=" N LEU A 434 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 435 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 480 through 493 removed outlier: 3.846A pdb=" N PHE A 484 " --> pdb=" O ASN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.508A pdb=" N ASN A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 624 Processing helix chain 'A' and resid 635 through 645 removed outlier: 3.509A pdb=" N CYS A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 668 Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 678 through 689 Processing helix chain 'A' and resid 700 through 713 Processing helix chain 'A' and resid 723 through 727 removed outlier: 3.884A pdb=" N MET A 727 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 785 through 794 Processing helix chain 'A' and resid 807 through 818 Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 1088 through 1102 Processing helix chain 'A' and resid 1112 through 1118 Processing helix chain 'A' and resid 1125 through 1135 removed outlier: 3.858A pdb=" N LEU A1129 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP A1135 " --> pdb=" O GLU A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 4.353A pdb=" N SER A1140 " --> pdb=" O PHE A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1150 Processing helix chain 'A' and resid 1151 through 1154 Processing helix chain 'A' and resid 1168 through 1192 removed outlier: 3.537A pdb=" N ALA A1172 " --> pdb=" O THR A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1202 Processing helix chain 'A' and resid 1211 through 1221 Processing helix chain 'A' and resid 1223 through 1230 Processing helix chain 'A' and resid 1234 through 1260 removed outlier: 3.577A pdb=" N VAL A1238 " --> pdb=" O ALA A1234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A1247 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1276 removed outlier: 3.850A pdb=" N HIS A1265 " --> pdb=" O ASN A1261 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.898A pdb=" N VAL A1280 " --> pdb=" O ARG A1277 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 674 removed outlier: 3.504A pdb=" N SER B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 691 removed outlier: 3.825A pdb=" N ALA B 681 " --> pdb=" O ASN B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 700 removed outlier: 3.621A pdb=" N ARG B 699 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 715 Processing helix chain 'B' and resid 717 through 732 removed outlier: 3.794A pdb=" N SER B 721 " --> pdb=" O GLU B 717 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 722 " --> pdb=" O GLU B 718 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP B 724 " --> pdb=" O ASP B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 749 removed outlier: 3.703A pdb=" N ALA B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 766 Processing helix chain 'B' and resid 770 through 784 Processing helix chain 'B' and resid 785 through 800 Processing helix chain 'B' and resid 803 through 825 removed outlier: 3.728A pdb=" N GLN B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 848 removed outlier: 4.027A pdb=" N VAL B 831 " --> pdb=" O LEU B 827 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 832 " --> pdb=" O LEU B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 869 removed outlier: 3.665A pdb=" N TRP B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE B 866 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 867 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 876 removed outlier: 5.477A pdb=" N ASP B 874 " --> pdb=" O SER B 871 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 875 " --> pdb=" O LYS B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 885 removed outlier: 3.545A pdb=" N VAL B 882 " --> pdb=" O VAL B 878 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 901 removed outlier: 3.588A pdb=" N ASP B 900 " --> pdb=" O ILE B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 909 Processing helix chain 'B' and resid 914 through 927 removed outlier: 3.630A pdb=" N LEU B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 926 " --> pdb=" O PHE B 922 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER B 927 " --> pdb=" O LEU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 963 Processing helix chain 'B' and resid 964 through 982 removed outlier: 3.686A pdb=" N ARG B 968 " --> pdb=" O GLU B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 996 removed outlier: 3.868A pdb=" N TRP B 989 " --> pdb=" O THR B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1015 removed outlier: 3.656A pdb=" N SER B1004 " --> pdb=" O ASN B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1032 removed outlier: 3.653A pdb=" N PHE B1023 " --> pdb=" O THR B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1049 Processing helix chain 'B' and resid 1053 through 1067 Processing helix chain 'B' and resid 1069 through 1084 removed outlier: 3.637A pdb=" N ASN B1084 " --> pdb=" O PHE B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1102 removed outlier: 3.510A pdb=" N GLN B1091 " --> pdb=" O SER B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1130 removed outlier: 3.696A pdb=" N LYS B1130 " --> pdb=" O GLU B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1149 Processing helix chain 'B' and resid 1151 through 1171 removed outlier: 3.545A pdb=" N ASN B1156 " --> pdb=" O TYR B1152 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B1157 " --> pdb=" O GLU B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1197 removed outlier: 3.599A pdb=" N ILE B1184 " --> pdb=" O PHE B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1213 Processing helix chain 'B' and resid 1218 through 1239 removed outlier: 4.030A pdb=" N MET B1222 " --> pdb=" O ASP B1218 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS B1223 " --> pdb=" O GLU B1219 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR B1224 " --> pdb=" O LYS B1220 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B1239 " --> pdb=" O SER B1235 " (cutoff:3.500A) Processing helix chain 'B' and resid 1242 through 1257 Processing helix chain 'B' and resid 1259 through 1274 removed outlier: 3.636A pdb=" N GLY B1274 " --> pdb=" O LEU B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1275 through 1294 Processing helix chain 'B' and resid 1296 through 1311 Processing helix chain 'B' and resid 1312 through 1324 Processing helix chain 'B' and resid 1327 through 1333 Processing helix chain 'B' and resid 1337 through 1349 Processing helix chain 'B' and resid 1356 through 1367 removed outlier: 4.391A pdb=" N TRP B1360 " --> pdb=" O GLY B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1372 through 1378 removed outlier: 4.450A pdb=" N ARG B1376 " --> pdb=" O LYS B1372 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B1377 " --> pdb=" O VAL B1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 1378 through 1386 Processing helix chain 'B' and resid 1394 through 1404 Processing helix chain 'B' and resid 1407 through 1418 Processing helix chain 'B' and resid 1421 through 1432 removed outlier: 3.668A pdb=" N VAL B1425 " --> pdb=" O ASN B1421 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B1432 " --> pdb=" O LEU B1428 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.674A pdb=" N LYS C 121 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS C 122 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.997A pdb=" N ILE C 336 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'D' and resid 50 through 53 Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.847A pdb=" N HIS D 122 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 77 through 86 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 108 removed outlier: 3.526A pdb=" N GLY A 116 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR A 108 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 114 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 190 Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 305 removed outlier: 6.839A pdb=" N VAL A 347 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER A 475 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL A 349 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU A 439 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE A 472 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 441 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU A 474 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE A 443 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LYS A 374 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 441 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 376 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE A 443 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 378 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 379 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR A 420 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 518 through 522 removed outlier: 6.931A pdb=" N ILE A 510 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 736 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N MET A 778 " --> pdb=" O VAL A 736 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE A 738 " --> pdb=" O MET A 778 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 630 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 742 through 744 Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 12 removed outlier: 5.565A pdb=" N ALA C 7 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG C 392 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 9 " --> pdb=" O TRP C 390 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER C 387 " --> pdb=" O CYS C 383 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C 359 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.886A pdb=" N SER C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 33 " --> pdb=" O TYR C 37 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 73 removed outlier: 3.745A pdb=" N HIS C 67 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS C 82 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE C 95 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 130 removed outlier: 3.837A pdb=" N ALA C 126 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS C 139 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR C 150 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR C 178 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 152 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE C 158 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER C 170 " --> pdb=" O PHE C 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 189 through 194 removed outlier: 3.840A pdb=" N SER C 191 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 209 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN C 222 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 211 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 236 through 241 removed outlier: 6.849A pdb=" N ALA C 251 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL C 239 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 249 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE C 241 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU C 247 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE C 260 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER C 273 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 262 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 269 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 294 through 299 removed outlier: 6.670A pdb=" N ALA C 309 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU C 297 " --> pdb=" O CYS C 307 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS C 307 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE C 299 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR C 305 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 315 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR C 328 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE C 317 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 324 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 6 through 11 removed outlier: 6.437A pdb=" N ALA D 7 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG D 392 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA D 9 " --> pdb=" O TRP D 390 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER D 378 " --> pdb=" O PHE D 362 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE D 362 " --> pdb=" O SER D 378 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS D 380 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL D 360 " --> pdb=" O CYS D 380 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL D 382 " --> pdb=" O PHE D 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 removed outlier: 4.082A pdb=" N SER D 21 " --> pdb=" O CYS D 32 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 65 through 74 removed outlier: 3.755A pdb=" N HIS D 67 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N GLU D 80 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARG D 100 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N CYS D 82 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 95 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 99 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 130 removed outlier: 4.032A pdb=" N HIS D 139 " --> pdb=" O PHE D 155 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR D 150 " --> pdb=" O THR D 178 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR D 178 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE D 152 " --> pdb=" O GLN D 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 189 through 194 removed outlier: 6.669A pdb=" N VAL D 209 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN D 222 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 211 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 239 through 241 removed outlier: 3.573A pdb=" N PHE D 257 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE D 260 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D 272 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU D 264 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG D 270 " --> pdb=" O GLU D 264 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 294 through 299 removed outlier: 6.511A pdb=" N ALA D 309 " --> pdb=" O MET D 295 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU D 297 " --> pdb=" O CYS D 307 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N CYS D 307 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N PHE D 299 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N THR D 305 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 310 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP D 319 " --> pdb=" O ARG D 325 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG D 325 " --> pdb=" O ASP D 319 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2583 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: 6.90 Time building geometry restraints manager: 7.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 117 1.03 - 1.23: 8 1.23 - 1.42: 7511 1.42 - 1.62: 10178 1.62 - 1.81: 117 Bond restraints: 17931 Sorted by residual: bond pdb=" CG PRO A 505 " pdb=" CD PRO A 505 " ideal model delta sigma weight residual 1.503 1.361 0.142 3.40e-02 8.65e+02 1.74e+01 bond pdb=" CB PRO A 505 " pdb=" CG PRO A 505 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.26e+00 bond pdb=" N PRO A 505 " pdb=" CD PRO A 505 " ideal model delta sigma weight residual 1.473 1.489 -0.016 1.40e-02 5.10e+03 1.29e+00 bond pdb=" N SER C 256 " pdb=" CA SER C 256 " ideal model delta sigma weight residual 1.460 1.478 -0.018 1.95e-02 2.63e+03 8.99e-01 bond pdb=" CA ASN C 255 " pdb=" CB ASN C 255 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.56e-01 ... (remaining 17926 not shown) Histogram of bond angle deviations from ideal: 92.46 - 100.77: 17 100.77 - 109.09: 1197 109.09 - 117.41: 12070 117.41 - 125.73: 10914 125.73 - 134.05: 301 Bond angle restraints: 24499 Sorted by residual: angle pdb=" N PRO A 505 " pdb=" CD PRO A 505 " pdb=" CG PRO A 505 " ideal model delta sigma weight residual 103.20 92.46 10.74 1.50e+00 4.44e-01 5.13e+01 angle pdb=" CA PRO A 505 " pdb=" N PRO A 505 " pdb=" CD PRO A 505 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C ASP A1278 " pdb=" CA ASP A1278 " pdb=" CB ASP A1278 " ideal model delta sigma weight residual 115.89 109.72 6.17 1.32e+00 5.74e-01 2.19e+01 angle pdb=" N ASP A1278 " pdb=" CA ASP A1278 " pdb=" C ASP A1278 " ideal model delta sigma weight residual 109.02 114.41 -5.39 1.68e+00 3.54e-01 1.03e+01 angle pdb=" CA PRO A 505 " pdb=" CB PRO A 505 " pdb=" CG PRO A 505 " ideal model delta sigma weight residual 104.50 98.44 6.06 1.90e+00 2.77e-01 1.02e+01 ... (remaining 24494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 9544 17.61 - 35.22: 830 35.22 - 52.83: 155 52.83 - 70.44: 22 70.44 - 88.05: 12 Dihedral angle restraints: 10563 sinusoidal: 3776 harmonic: 6787 Sorted by residual: dihedral pdb=" CA ILE B 924 " pdb=" C ILE B 924 " pdb=" N LEU B 925 " pdb=" CA LEU B 925 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA THR A 395 " pdb=" C THR A 395 " pdb=" N PHE A 396 " pdb=" CA PHE A 396 " ideal model delta harmonic sigma weight residual -180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ARG B 751 " pdb=" C ARG B 751 " pdb=" N ILE B 752 " pdb=" CA ILE B 752 " ideal model delta harmonic sigma weight residual -180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 10560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1893 0.032 - 0.065: 691 0.065 - 0.097: 147 0.097 - 0.130: 98 0.130 - 0.162: 4 Chirality restraints: 2833 Sorted by residual: chirality pdb=" CA ASN C 255 " pdb=" N ASN C 255 " pdb=" C ASN C 255 " pdb=" CB ASN C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CB ILE D 388 " pdb=" CA ILE D 388 " pdb=" CG1 ILE D 388 " pdb=" CG2 ILE D 388 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" C1' U X 1 " pdb=" O4' U X 1 " pdb=" C2' U X 1 " pdb=" N1 U X 1 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 2830 not shown) Planarity restraints: 3094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 504 " 0.049 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO A 505 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 505 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 505 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1189 " -0.020 2.00e-02 2.50e+03 1.63e-02 4.62e+00 pdb=" CG PHE B1189 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B1189 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B1189 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B1189 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B1189 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B1189 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 50 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO C 51 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.018 5.00e-02 4.00e+02 ... (remaining 3091 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 35 2.28 - 2.86: 6578 2.86 - 3.44: 18433 3.44 - 4.02: 32192 4.02 - 4.60: 48440 Nonbonded interactions: 105678 Sorted by model distance: nonbonded pdb=" OE2 GLU A1273 " pdb="HH21 ARG C 316 " model vdw 1.704 1.850 nonbonded pdb=" HD2 ARG C 316 " pdb="HH11 ARG C 316 " model vdw 1.984 2.270 nonbonded pdb=" HD2 ARG C 325 " pdb="HH11 ARG C 325 " model vdw 2.107 2.270 nonbonded pdb=" HB2 LYS C 323 " pdb=" HE3 LYS C 323 " model vdw 2.118 2.440 nonbonded pdb="HG11 VAL C 276 " pdb=" HD3 ARG C 325 " model vdw 2.152 2.440 ... (remaining 105673 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' and (resid 3 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 25 or (resid 26 through 27 a \ nd (name N or name CA or name C or name O or name CB )) or resid 28 through 41 o \ r (resid 42 and (name N or name CA or name C or name O or name CB )) or resid 43 \ or (resid 44 and (name N or name CA or name C or name O or name CB )) or resid \ 45 or (resid 46 through 48 and (name N or name CA or name C or name O or name CB \ )) or resid 49 through 73 or (resid 74 through 78 and (name N or name CA or nam \ e C or name O or name CB )) or resid 79 or (resid 80 and (name N or name CA or n \ ame C or name O or name CB )) or resid 81 through 100 or (resid 101 through 106 \ and (name N or name CA or name C or name O or name CB )) or resid 107 through 11 \ 9 or (resid 120 and (name N or name CA or name C or name O or name CB )) or resi \ d 121 through 133 or (resid 134 through 135 and (name N or name CA or name C or \ name O or name CB )) or resid 136 or (resid 137 through 138 and (name N or name \ CA or name C or name O or name CB )) or resid 139 through 159 or (resid 168 and \ (name N or name CA or name C or name O or name CB )) or resid 169 through 195 or \ (resid 196 through 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 211 or (resid 212 and (name N or name CA or name C or name \ O or name CB )) or resid 213 through 214 or (resid 215 and (name N or name CA o \ r name C or name O or name CB )) or resid 216 through 219 or (resid 220 and (nam \ e N or name CA or name C or name O or name CB )) or resid 221 through 223 or (re \ sid 224 and (name N or name CA or name C or name O or name CB )) or resid 225 or \ resid 231 through 243 or (resid 244 and (name N or name CA or name C or name O \ or name CB )) or resid 245 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 263 or (resid 264 through 267 \ and (name N or name CA or name C or name O or name CB )) or resid 268 or (resid \ 269 and (name N or name CA or name C or name O or name CB )) or resid 270 throu \ gh 274 or (resid 275 and (name N or name CA or name C or name O or name CB or na \ me OG )) or (resid 276 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2)) or resid 277 through 278 or resid 287 through 301 or (res \ id 302 and (name N or name CA or name C or name O or name CB )) or resid 303 thr \ ough 315 or (resid 316 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 317 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ )) or (resid 318 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name N \ E1 or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or (resid 319 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame OD2)) or resid 320 or (resid 321 and (name N or name CA or name C or name O \ or name CB )) or resid 322 or (resid 323 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ )) or (resid 324 thro \ ugh 325 and (name N or name CA or name C or name O or name CB )) or (resid 326 a \ nd (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name CD1)) or (resid 327 through 328 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2)) or resid 329 through 335 or (resid 336 and \ (name N or name CA or name C or name O or name CB )) or resid 341 through 350 or \ (resid 351 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 2 through 368 or (resid 369 and (name N or name CA or name C or name O or name C \ B )) or resid 377 or (resid 378 and (name N or name CA or name C or name O or na \ me CB )) or resid 379 through 391 or (resid 392 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'D' and (resid 3 through 20 or (resid 21 and (name N or name CA or name C \ or name O or name CB )) or resid 22 through 46 or (resid 47 through 48 and (nam \ e N or name CA or name C or name O or name CB )) or resid 49 through 61 or (resi \ d 62 and (name N or name CA or name C or name O or name CB )) or resid 63 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 through 185 or (resid 186 and (name N or name CA or name C or name O o \ r name CB )) or resid 187 through 353 or (resid 354 and (name N or name CA or na \ me C or name O or name CB )) or resid 355 through 363 or (resid 364 through 365 \ and (name N or name CA or name C or name O or name CB )) or resid 366 through 38 \ 6 or (resid 387 and (name N or name CA or name C or name O or name CB )) or resi \ d 388 through 392)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.080 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: 0.400 Extract box with map and model: 9.930 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 48.260 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 : 0.003 0.142 17814 Z= 0.148 Angle : 0.461 10.744 24235 Z= 0.254 Chirality : 0.039 0.162 2833 Planarity : 0.003 0.071 3084 Dihedral : 13.838 88.049 6107 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.77 (0.18), residues: 2276 helix: 1.91 (0.17), residues: 986 sheet: 0.46 (0.26), residues: 417 loop : -1.13 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 153 HIS 0.003 0.001 HIS A 696 PHE 0.037 0.001 PHE B1189 TYR 0.013 0.001 TYR B 947 ARG 0.004 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.948 Fit side-chains REVERT: A 196 ILE cc_start: 0.8202 (mt) cc_final: 0.7608 (mm) REVERT: A 535 LYS cc_start: 0.6696 (tppt) cc_final: 0.6490 (tppt) REVERT: B 687 ARG cc_start: 0.7720 (ptp-110) cc_final: 0.7075 (ppt170) REVERT: B 1376 ARG cc_start: 0.7503 (mmm160) cc_final: 0.7224 (mmp-170) REVERT: D 180 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6768 (mm-30) REVERT: D 331 MET cc_start: 0.6149 (mtp) cc_final: 0.5945 (mtm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 1.2060 time to fit residues: 256.7438 Evaluate side-chains 152 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 117 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 730 ASN B1391 ASN D 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17814 Z= 0.397 Angle : 0.597 6.973 24235 Z= 0.320 Chirality : 0.045 0.170 2833 Planarity : 0.004 0.043 3084 Dihedral : 5.195 57.774 2500 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.71 % Allowed : 9.07 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.28 (0.17), residues: 2276 helix: 1.35 (0.16), residues: 1010 sheet: 0.45 (0.25), residues: 409 loop : -1.38 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 318 HIS 0.009 0.002 HIS D 252 PHE 0.022 0.002 PHE D 241 TYR 0.018 0.002 TYR B1289 ARG 0.010 0.001 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 1.934 Fit side-chains REVERT: A 422 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6514 (pt0) REVERT: B 687 ARG cc_start: 0.7560 (ptp-110) cc_final: 0.6980 (ppt170) REVERT: B 1052 ASP cc_start: 0.6779 (t70) cc_final: 0.6551 (m-30) REVERT: C 264 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7798 (pp20) REVERT: D 180 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6651 (mm-30) REVERT: D 388 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7550 (tt) outliers start: 29 outliers final: 15 residues processed: 172 average time/residue: 1.2862 time to fit residues: 248.6500 Evaluate side-chains 168 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain B residue 1015 GLU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 388 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 226 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 167 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN C 222 ASN D 205 ASN D 252 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17814 Z= 0.181 Angle : 0.427 5.980 24235 Z= 0.232 Chirality : 0.039 0.138 2833 Planarity : 0.003 0.036 3084 Dihedral : 4.687 57.815 2500 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.12 % Allowed : 11.19 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.18), residues: 2276 helix: 1.91 (0.17), residues: 1012 sheet: 0.48 (0.26), residues: 413 loop : -1.29 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 129 HIS 0.005 0.001 HIS D 252 PHE 0.011 0.001 PHE C 223 TYR 0.013 0.001 TYR B 774 ARG 0.003 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 1.717 Fit side-chains REVERT: B 687 ARG cc_start: 0.7519 (ptp-110) cc_final: 0.6878 (ppt170) REVERT: B 1052 ASP cc_start: 0.6658 (t70) cc_final: 0.6429 (m-30) REVERT: B 1343 ILE cc_start: 0.6483 (mt) cc_final: 0.6167 (mt) REVERT: C 222 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8311 (t0) REVERT: C 264 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7688 (pp20) REVERT: D 180 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6592 (mm-30) REVERT: D 388 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7550 (tt) outliers start: 36 outliers final: 20 residues processed: 183 average time/residue: 1.1841 time to fit residues: 245.6482 Evaluate side-chains 180 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 1311 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 222 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 0.0060 chunk 157 optimal weight: 0.0030 chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 199 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.1410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17814 Z= 0.160 Angle : 0.404 6.025 24235 Z= 0.219 Chirality : 0.038 0.131 2833 Planarity : 0.002 0.032 3084 Dihedral : 4.520 57.797 2500 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.12 % Allowed : 12.37 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.98 (0.18), residues: 2276 helix: 2.17 (0.17), residues: 1013 sheet: 0.52 (0.26), residues: 419 loop : -1.23 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 129 HIS 0.004 0.001 HIS A1265 PHE 0.011 0.001 PHE B 973 TYR 0.016 0.001 TYR C 221 ARG 0.003 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: B 687 ARG cc_start: 0.7499 (ptp-110) cc_final: 0.6865 (ppt170) REVERT: B 1052 ASP cc_start: 0.6642 (t70) cc_final: 0.6407 (m-30) REVERT: B 1343 ILE cc_start: 0.6503 (mt) cc_final: 0.6194 (mt) REVERT: C 264 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7654 (pp20) REVERT: D 18 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5760 (p0) REVERT: D 92 ASP cc_start: 0.7599 (m-30) cc_final: 0.7084 (m-30) REVERT: D 180 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6592 (mm-30) REVERT: D 388 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7528 (tt) outliers start: 36 outliers final: 25 residues processed: 187 average time/residue: 1.2337 time to fit residues: 260.0397 Evaluate side-chains 188 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 1311 ASP Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 388 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 165 optimal weight: 0.0040 chunk 91 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17814 Z= 0.230 Angle : 0.457 5.872 24235 Z= 0.246 Chirality : 0.040 0.137 2833 Planarity : 0.003 0.036 3084 Dihedral : 4.736 57.801 2500 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.47 % Allowed : 13.07 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.83 (0.18), residues: 2276 helix: 2.02 (0.17), residues: 1013 sheet: 0.47 (0.26), residues: 413 loop : -1.27 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 129 HIS 0.004 0.001 HIS A1265 PHE 0.014 0.001 PHE C 223 TYR 0.015 0.001 TYR B1289 ARG 0.005 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 2.082 Fit side-chains revert: symmetry clash REVERT: B 687 ARG cc_start: 0.7527 (ptp-110) cc_final: 0.6912 (ppt170) REVERT: B 1052 ASP cc_start: 0.6742 (t70) cc_final: 0.6463 (m-30) REVERT: B 1343 ILE cc_start: 0.6472 (mt) cc_final: 0.6150 (mt) REVERT: C 264 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7609 (pp20) REVERT: D 18 ASP cc_start: 0.6008 (OUTLIER) cc_final: 0.5611 (p0) REVERT: D 92 ASP cc_start: 0.7583 (m-30) cc_final: 0.7061 (m-30) REVERT: D 109 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5658 (m-80) REVERT: D 180 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6599 (mm-30) REVERT: D 388 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7578 (tt) outliers start: 42 outliers final: 31 residues processed: 188 average time/residue: 1.2384 time to fit residues: 263.7610 Evaluate side-chains 191 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 1311 ASP Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 388 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17814 Z= 0.319 Angle : 0.525 6.430 24235 Z= 0.281 Chirality : 0.042 0.156 2833 Planarity : 0.003 0.038 3084 Dihedral : 5.019 57.758 2500 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.00 % Allowed : 13.60 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2276 helix: 1.70 (0.16), residues: 1013 sheet: 0.42 (0.25), residues: 413 loop : -1.42 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 129 HIS 0.007 0.001 HIS A 340 PHE 0.016 0.002 PHE C 223 TYR 0.016 0.002 TYR B1289 ARG 0.006 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 1.938 Fit side-chains REVERT: A 422 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6345 (pt0) REVERT: B 687 ARG cc_start: 0.7478 (ptp-110) cc_final: 0.6878 (ppt170) REVERT: B 1052 ASP cc_start: 0.6824 (t70) cc_final: 0.6524 (m-30) REVERT: B 1343 ILE cc_start: 0.6509 (mt) cc_final: 0.6178 (mt) REVERT: C 264 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7643 (pp20) REVERT: D 18 ASP cc_start: 0.6099 (OUTLIER) cc_final: 0.5676 (p0) REVERT: D 92 ASP cc_start: 0.7562 (m-30) cc_final: 0.7064 (m-30) REVERT: D 109 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5610 (m-80) REVERT: D 180 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6621 (mm-30) REVERT: D 388 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7625 (tt) outliers start: 51 outliers final: 34 residues processed: 189 average time/residue: 1.2283 time to fit residues: 262.1084 Evaluate side-chains 194 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 1311 ASP Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 388 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 138 optimal weight: 0.0170 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17814 Z= 0.252 Angle : 0.472 5.865 24235 Z= 0.254 Chirality : 0.041 0.144 2833 Planarity : 0.003 0.038 3084 Dihedral : 4.873 57.798 2500 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.65 % Allowed : 15.19 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.58 (0.18), residues: 2276 helix: 1.82 (0.16), residues: 1013 sheet: 0.38 (0.26), residues: 411 loop : -1.41 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 129 HIS 0.005 0.001 HIS A 340 PHE 0.014 0.001 PHE C 223 TYR 0.015 0.001 TYR B1289 ARG 0.004 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 158 time to evaluate : 2.084 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7790 (mm110) REVERT: A 422 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6345 (pt0) REVERT: B 687 ARG cc_start: 0.7505 (ptp-110) cc_final: 0.6901 (ppt170) REVERT: B 1052 ASP cc_start: 0.6811 (t70) cc_final: 0.6529 (m-30) REVERT: B 1343 ILE cc_start: 0.6471 (mt) cc_final: 0.6157 (mt) REVERT: C 264 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7600 (pp20) REVERT: D 18 ASP cc_start: 0.6019 (OUTLIER) cc_final: 0.5623 (p0) REVERT: D 92 ASP cc_start: 0.7537 (m-30) cc_final: 0.7058 (m-30) REVERT: D 109 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5526 (m-80) REVERT: D 180 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6576 (mm-30) outliers start: 45 outliers final: 33 residues processed: 186 average time/residue: 1.2701 time to fit residues: 265.7338 Evaluate side-chains 195 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 1311 ASP Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 350 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17814 Z= 0.341 Angle : 0.539 6.762 24235 Z= 0.289 Chirality : 0.043 0.163 2833 Planarity : 0.003 0.041 3084 Dihedral : 5.112 57.757 2500 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.89 % Allowed : 15.49 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.30 (0.17), residues: 2276 helix: 1.51 (0.16), residues: 1015 sheet: 0.35 (0.26), residues: 408 loop : -1.52 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 129 HIS 0.006 0.001 HIS A 340 PHE 0.016 0.002 PHE D 358 TYR 0.017 0.002 TYR A 497 ARG 0.006 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 155 time to evaluate : 1.926 Fit side-chains revert: symmetry clash REVERT: A 422 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6425 (pt0) REVERT: B 687 ARG cc_start: 0.7477 (ptp-110) cc_final: 0.6881 (ppt170) REVERT: B 1052 ASP cc_start: 0.6890 (t70) cc_final: 0.6588 (m-30) REVERT: B 1343 ILE cc_start: 0.6498 (mt) cc_final: 0.6166 (mt) REVERT: C 264 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7653 (pp20) REVERT: D 92 ASP cc_start: 0.7510 (m-30) cc_final: 0.7055 (m-30) REVERT: D 109 PHE cc_start: 0.6100 (OUTLIER) cc_final: 0.5515 (m-80) REVERT: D 180 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6621 (mm-30) outliers start: 49 outliers final: 36 residues processed: 188 average time/residue: 1.2754 time to fit residues: 270.2141 Evaluate side-chains 192 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 1110 ARG Chi-restraints excluded: chain B residue 1311 ASP Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain B residue 1426 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 350 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 chunk 193 optimal weight: 0.2980 chunk 206 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17814 Z= 0.122 Angle : 0.382 6.174 24235 Z= 0.208 Chirality : 0.038 0.129 2833 Planarity : 0.002 0.033 3084 Dihedral : 4.479 57.817 2500 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.83 % Allowed : 16.73 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.04 (0.18), residues: 2276 helix: 2.32 (0.17), residues: 1011 sheet: 0.42 (0.26), residues: 420 loop : -1.26 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 129 HIS 0.004 0.001 HIS A 340 PHE 0.009 0.001 PHE D 358 TYR 0.011 0.001 TYR B1289 ARG 0.001 0.000 ARG B 706 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 2.129 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7786 (mm110) REVERT: A 302 TRP cc_start: 0.5785 (OUTLIER) cc_final: 0.5188 (t-100) REVERT: B 687 ARG cc_start: 0.7472 (ptp-110) cc_final: 0.6879 (ppt170) REVERT: B 1343 ILE cc_start: 0.6482 (mt) cc_final: 0.6171 (mt) REVERT: B 1400 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7734 (tttm) REVERT: C 221 TYR cc_start: 0.7751 (m-80) cc_final: 0.7373 (m-10) REVERT: D 92 ASP cc_start: 0.7585 (m-30) cc_final: 0.7085 (m-30) REVERT: D 109 PHE cc_start: 0.6140 (OUTLIER) cc_final: 0.5540 (m-80) REVERT: D 180 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6574 (mm-30) outliers start: 31 outliers final: 19 residues processed: 189 average time/residue: 1.2675 time to fit residues: 270.0640 Evaluate side-chains 182 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 1311 ASP Chi-restraints excluded: chain B residue 1400 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17814 Z= 0.365 Angle : 0.554 6.999 24235 Z= 0.296 Chirality : 0.044 0.164 2833 Planarity : 0.004 0.038 3084 Dihedral : 5.083 57.742 2500 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.00 % Allowed : 16.67 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.42 (0.17), residues: 2276 helix: 1.64 (0.16), residues: 1019 sheet: 0.40 (0.26), residues: 408 loop : -1.51 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 129 HIS 0.006 0.001 HIS A1265 PHE 0.018 0.002 PHE D 358 TYR 0.016 0.002 TYR B1289 ARG 0.007 0.001 ARG C 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 2.468 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7791 (mm110) REVERT: A 490 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.7048 (ttp-170) REVERT: B 687 ARG cc_start: 0.7463 (ptp-110) cc_final: 0.6870 (ppt170) REVERT: B 1343 ILE cc_start: 0.6527 (mt) cc_final: 0.6210 (mt) REVERT: C 264 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7748 (pp20) REVERT: D 18 ASP cc_start: 0.5896 (OUTLIER) cc_final: 0.5441 (p0) REVERT: D 92 ASP cc_start: 0.7507 (m-30) cc_final: 0.7041 (m-30) REVERT: D 109 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5536 (m-80) REVERT: D 180 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6619 (mm-30) outliers start: 34 outliers final: 24 residues processed: 175 average time/residue: 1.3703 time to fit residues: 268.4214 Evaluate side-chains 178 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 1311 ASP Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 26 optimal weight: 0.0040 chunk 50 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 overall best weight: 0.9752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131760 restraints weight = 23966.336| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.61 r_work: 0.3402 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17814 Z= 0.142 Angle : 0.398 6.077 24235 Z= 0.216 Chirality : 0.038 0.130 2833 Planarity : 0.003 0.033 3084 Dihedral : 4.562 57.817 2500 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.77 % Allowed : 16.96 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.94 (0.18), residues: 2276 helix: 2.20 (0.17), residues: 1018 sheet: 0.38 (0.26), residues: 426 loop : -1.30 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 129 HIS 0.004 0.001 HIS A 340 PHE 0.010 0.001 PHE D 358 TYR 0.012 0.001 TYR B1289 ARG 0.002 0.000 ARG D 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5450.35 seconds wall clock time: 97 minutes 22.32 seconds (5842.32 seconds total)