Starting phenix.real_space_refine on Sun Mar 24 03:24:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5k_27913/03_2024/8e5k_27913_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5k_27913/03_2024/8e5k_27913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5k_27913/03_2024/8e5k_27913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5k_27913/03_2024/8e5k_27913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5k_27913/03_2024/8e5k_27913_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5k_27913/03_2024/8e5k_27913_neut.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 87 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 17285 2.51 5 N 4941 2.21 5 O 5571 1.98 5 H 11229 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 892": "OE1" <-> "OE2" Residue "A GLU 898": "OE1" <-> "OE2" Residue "A ASP 912": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 86": "OE1" <-> "OE2" Residue "F ASP 105": "OD1" <-> "OD2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39229 Number of models: 1 Model: "" Number of chains: 10 Chain: "5" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 913 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "6" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1031 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "7" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 464 Classifications: {'RNA': 17} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 15} Chain: "A" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "B" Number of atoms: 21000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 21000 Classifications: {'peptide': 1335} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1277} Chain breaks: 2 Chain: "C" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1677 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1276 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13860 SG CYS B 70 63.703 115.009 44.860 1.00 45.60 S ATOM 14119 SG CYS B 85 60.565 116.911 41.764 1.00 49.94 S ATOM 25701 SG CYS B 814 35.180 99.275 105.275 1.00 22.38 S ATOM 26838 SG CYS B 888 38.067 98.160 101.961 1.00 20.48 S ATOM 26929 SG CYS B 895 38.676 100.534 104.649 1.00 14.28 S ATOM 26966 SG CYS B 898 38.083 97.423 106.260 1.00 16.02 S Time building chain proxies: 18.49, per 1000 atoms: 0.47 Number of scatterers: 39229 At special positions: 0 Unit cell: (157.776, 154.662, 174.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 113 16.00 P 87 15.00 Mg 1 11.99 O 5571 8.00 N 4941 7.00 C 17285 6.00 H 11229 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 88 " distance=2.27 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: 23.17 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1502 " pdb="ZN ZN B1502 " - pdb=" SG CYS B 70 " pdb="ZN ZN B1502 " - pdb=" SG CYS B 85 " pdb=" ZN B1503 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 888 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 895 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 814 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 898 " Number of angles added : 6 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6182 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 46 sheets defined 35.5% alpha, 15.1% beta 29 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 17.64 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 48 through 56 removed outlier: 4.129A pdb=" N ALA A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.838A pdb=" N SER A 166 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 167 " --> pdb=" O THR A 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 167' Processing helix chain 'A' and resid 206 through 213 removed outlier: 4.057A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.579A pdb=" N ARG A 247 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.688A pdb=" N GLN A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 377 through 389 removed outlier: 4.130A pdb=" N PHE A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.757A pdb=" N ILE A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 480 removed outlier: 4.513A pdb=" N SER A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 609 through 614 removed outlier: 4.045A pdb=" N ASN A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 609 through 614' Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 738 through 741 removed outlier: 3.791A pdb=" N MET A 741 " --> pdb=" O GLU A 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 858 through 863 Processing helix chain 'A' and resid 942 through 979 Processing helix chain 'A' and resid 987 through 991 removed outlier: 3.828A pdb=" N ASP A 990 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A 991 " --> pdb=" O LYS A 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 991' Processing helix chain 'A' and resid 1005 through 1038 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 4.548A pdb=" N SER A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A1106 " --> pdb=" O GLY A1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1101 through 1106' Processing helix chain 'A' and resid 1109 through 1134 removed outlier: 3.694A pdb=" N LEU A1113 " --> pdb=" O ILE A1109 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.880A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1164 removed outlier: 4.192A pdb=" N THR A1163 " --> pdb=" O ASP A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1177 Processing helix chain 'A' and resid 1191 through 1202 removed outlier: 3.552A pdb=" N GLY A1202 " --> pdb=" O LEU A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1281 removed outlier: 3.625A pdb=" N TYR A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1292 Processing helix chain 'A' and resid 1297 through 1310 Processing helix chain 'A' and resid 1320 through 1332 removed outlier: 3.653A pdb=" N ASN A1324 " --> pdb=" O PRO A1320 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 180 through 191 removed outlier: 3.744A pdb=" N ALA B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 207 Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.777A pdb=" N ARG B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 263 through 286 removed outlier: 3.807A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 308 Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 377 through 389 removed outlier: 3.550A pdb=" N GLY B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.689A pdb=" N ALA B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.567A pdb=" N ILE B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 450 through 458 removed outlier: 3.648A pdb=" N CYS B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 504 through 514 removed outlier: 3.522A pdb=" N LEU B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.612A pdb=" N ALA B 577 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 592 Processing helix chain 'B' and resid 598 through 613 Processing helix chain 'B' and resid 614 through 636 removed outlier: 3.645A pdb=" N GLY B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 670 removed outlier: 3.532A pdb=" N SER B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 703 Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.861A pdb=" N ILE B 737 " --> pdb=" O SER B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 805 removed outlier: 3.851A pdb=" N GLY B 782 " --> pdb=" O GLY B 778 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN B 792 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 805 " --> pdb=" O VAL B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 839 removed outlier: 3.643A pdb=" N ARG B 838 " --> pdb=" O PRO B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.797A pdb=" N ASN B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.521A pdb=" N TYR B 899 " --> pdb=" O CYS B 895 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 900' Processing helix chain 'B' and resid 914 through 925 removed outlier: 4.007A pdb=" N ILE B 918 " --> pdb=" O ALA B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 928 No H-bonds generated for 'chain 'B' and resid 926 through 928' Processing helix chain 'B' and resid 1137 through 1146 Processing helix chain 'B' and resid 1216 through 1224 Processing helix chain 'B' and resid 1225 through 1244 removed outlier: 4.194A pdb=" N VAL B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1250 through 1261 Processing helix chain 'B' and resid 1282 through 1294 removed outlier: 3.544A pdb=" N ALA B1294 " --> pdb=" O ARG B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1315 Processing helix chain 'B' and resid 1327 through 1339 removed outlier: 3.828A pdb=" N VAL B1331 " --> pdb=" O GLU B1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 1346 through 1353 removed outlier: 3.807A pdb=" N ASN B1350 " --> pdb=" O GLY B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1372 removed outlier: 4.421A pdb=" N TYR B1365 " --> pdb=" O THR B1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 50 removed outlier: 3.549A pdb=" N THR C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.840A pdb=" N VAL C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'D' and resid 34 through 50 removed outlier: 4.040A pdb=" N THR D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 removed outlier: 3.560A pdb=" N GLY D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 212 through 227 Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.525A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.956A pdb=" N GLN E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 33 Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 76 through 86 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.647A pdb=" N ASP F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F 115 " --> pdb=" O ILE F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.569A pdb=" N LYS A 13 " --> pdb=" O ALA A1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.928A pdb=" N LYS A 99 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TYR A 73 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG A 97 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 75 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA A 94 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU A 126 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 96 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.322A pdb=" N SER A 147 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 158 removed outlier: 3.581A pdb=" N LEU A 184 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 231 Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA8, first strand: chain 'A' and resid 255 through 257 removed outlier: 6.575A pdb=" N ALA A 257 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 302 removed outlier: 7.194A pdb=" N TYR A 301 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 580 through 581 removed outlier: 3.687A pdb=" N GLU A 588 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 593 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 602 " --> pdb=" O LYS A 593 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 580 through 581 removed outlier: 3.687A pdb=" N GLU A 588 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.633A pdb=" N ARG A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL A 727 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 733 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 757 through 758 removed outlier: 3.995A pdb=" N THR A 757 " --> pdb=" O ILE A 765 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 768 through 769 Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.590A pdb=" N ASP A 790 " --> pdb=" O GLU A 793 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1066 through 1067 removed outlier: 4.452A pdb=" N THR A1226 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N ILE A1096 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 801 " --> pdb=" O ILE A1096 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU A1098 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA A 803 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 817 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE A 816 " --> pdb=" O SER A1077 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A1079 " --> pdb=" O ILE A 816 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 818 " --> pdb=" O ILE A1079 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1066 through 1067 Processing sheet with id=AB9, first strand: chain 'A' and resid 846 through 847 removed outlier: 3.862A pdb=" N GLY A 846 " --> pdb=" O THR A 843 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR A 843 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR A 830 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS A1057 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS A 832 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A1055 " --> pdb=" O HIS A 832 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLN A 834 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR A1053 " --> pdb=" O GLN A 834 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 836 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS A1051 " --> pdb=" O LEU A 836 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS A 838 " --> pdb=" O ILE A1049 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE A1049 " --> pdb=" O CYS A 838 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 840 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP A 930 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA A1055 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 928 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS A1057 " --> pdb=" O GLY A 926 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY A 926 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 926 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1244 through 1246 Processing sheet with id=AC2, first strand: chain 'A' and resid 1269 through 1270 Processing sheet with id=AC3, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id=AC4, first strand: chain 'B' and resid 34 through 37 removed outlier: 4.452A pdb=" N SER B 34 " --> pdb=" O MET B 102 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N HIS B 104 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 36 " --> pdb=" O HIS B 104 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU B 106 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 107 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR B 240 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N SER B 109 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N ILE B 238 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC6, first strand: chain 'B' and resid 253 through 254 removed outlier: 4.416A pdb=" N VAL B 253 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 526 through 527 Processing sheet with id=AC8, first strand: chain 'B' and resid 706 through 708 removed outlier: 3.685A pdb=" N GLU B 714 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 821 through 822 Processing sheet with id=AD1, first strand: chain 'B' and resid 849 through 850 removed outlier: 4.609A pdb=" N ASP B 855 " --> pdb=" O LYS B 850 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 957 through 961 removed outlier: 3.803A pdb=" N THR B 980 " --> pdb=" O VAL B 997 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 965 through 967 Processing sheet with id=AD4, first strand: chain 'B' and resid 1034 through 1038 removed outlier: 3.619A pdb=" N ARG B1036 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B1079 " --> pdb=" O ARG B1036 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1046 through 1049 removed outlier: 4.087A pdb=" N GLN B1049 " --> pdb=" O SER B1058 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B1058 " --> pdb=" O GLN B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD7, first strand: chain 'B' and resid 1279 through 1281 removed outlier: 7.344A pdb=" N THR B1301 " --> pdb=" O VAL B1267 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.339A pdb=" N ASP C 199 " --> pdb=" O PRO C 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 202 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.521A pdb=" N GLY C 53 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.249A pdb=" N THR C 101 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER C 141 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE C 61 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG C 143 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C 59 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS C 145 " --> pdb=" O THR C 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AE3, first strand: chain 'C' and resid 108 through 111 removed outlier: 3.837A pdb=" N CYS C 131 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 23 through 31 removed outlier: 7.013A pdb=" N ASP D 199 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG D 182 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 53 through 61 removed outlier: 4.074A pdb=" N ALA D 55 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS D 145 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL D 59 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG D 143 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 90 through 91 Processing sheet with id=AE7, first strand: chain 'D' and resid 108 through 111 removed outlier: 4.051A pdb=" N CYS D 131 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.624A pdb=" N VAL D 153 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 39 through 43 removed outlier: 4.151A pdb=" N GLU F 41 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 72 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL F 11 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE F 92 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN F 13 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.684A pdb=" N GLU F 149 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS F 159 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL F 171 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL F 162 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F 164 " --> pdb=" O ARG F 167 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 19.65 Time building geometry restraints manager: 24.44 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: 11214 1.03 - 1.23: 304 1.23 - 1.42: 11390 1.42 - 1.62: 16720 1.62 - 1.81: 203 Bond restraints: 39831 Sorted by residual: bond pdb=" CA THR B 93 " pdb=" C THR B 93 " ideal model delta sigma weight residual 1.523 1.687 -0.164 1.34e-02 5.57e+03 1.50e+02 bond pdb=" N1 G 7 30 " pdb=" H1 G 7 30 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" CA CYS B 70 " pdb=" CB CYS B 70 " ideal model delta sigma weight residual 1.527 1.405 0.122 1.38e-02 5.25e+03 7.80e+01 bond pdb=" C8 G 7 30 " pdb=" H8 G 7 30 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" N2 G 7 30 " pdb=" H22 G 7 30 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 39826 not shown) Histogram of bond angle deviations from ideal: 59.66 - 77.34: 2 77.34 - 95.02: 4 95.02 - 112.69: 36442 112.69 - 130.37: 28058 130.37 - 148.05: 122 Bond angle restraints: 64628 Sorted by residual: angle pdb=" O3' DG 6 27 " pdb=" P DA 6 28 " pdb=" O5' DA 6 28 " ideal model delta sigma weight residual 104.00 148.05 -44.05 1.50e+00 4.44e-01 8.62e+02 angle pdb=" H2' DA 5 110 " pdb=" C2' DA 5 110 " pdb="H2'' DA 5 110 " ideal model delta sigma weight residual 109.00 76.07 32.93 1.50e+00 4.44e-01 4.82e+02 angle pdb=" O3' DG 6 27 " pdb=" P DA 6 28 " pdb=" OP1 DA 6 28 " ideal model delta sigma weight residual 108.00 59.66 48.34 3.00e+00 1.11e-01 2.60e+02 angle pdb=" C VAL A 920 " pdb=" N PRO A 921 " pdb=" CA PRO A 921 " ideal model delta sigma weight residual 119.84 139.45 -19.61 1.25e+00 6.40e-01 2.46e+02 angle pdb=" O3' DA 6 28 " pdb=" P DT 6 29 " pdb=" O5' DT 6 29 " ideal model delta sigma weight residual 104.00 126.00 -22.00 1.50e+00 4.44e-01 2.15e+02 ... (remaining 64623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 19938 35.99 - 71.98: 826 71.98 - 107.98: 19 107.98 - 143.97: 1 143.97 - 179.96: 7 Dihedral angle restraints: 20791 sinusoidal: 10766 harmonic: 10025 Sorted by residual: dihedral pdb=" CA VAL C 192 " pdb=" C VAL C 192 " pdb=" N GLU C 193 " pdb=" CA GLU C 193 " ideal model delta harmonic sigma weight residual -180.00 -126.71 -53.29 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" O4' U 7 24 " pdb=" C1' U 7 24 " pdb=" N1 U 7 24 " pdb=" C2 U 7 24 " ideal model delta sinusoidal sigma weight residual 200.00 43.57 156.43 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" CA GLN B1326 " pdb=" C GLN B1326 " pdb=" N GLU B1327 " pdb=" CA GLU B1327 " ideal model delta harmonic sigma weight residual -180.00 -138.11 -41.89 0 5.00e+00 4.00e-02 7.02e+01 ... (remaining 20788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 4024 0.107 - 0.215: 400 0.215 - 0.322: 25 0.322 - 0.430: 2 0.430 - 0.537: 2 Chirality restraints: 4453 Sorted by residual: chirality pdb=" CB ILE A1079 " pdb=" CA ILE A1079 " pdb=" CG1 ILE A1079 " pdb=" CG2 ILE A1079 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CA TYR B 46 " pdb=" N TYR B 46 " pdb=" C TYR B 46 " pdb=" CB TYR B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CB ILE A 765 " pdb=" CA ILE A 765 " pdb=" CG1 ILE A 765 " pdb=" CG2 ILE A 765 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 4450 not shown) Planarity restraints: 6121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " 0.210 2.00e-02 2.50e+03 2.51e-01 9.42e+02 pdb=" CG ASN B 232 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 232 " -0.203 2.00e-02 2.50e+03 pdb=" ND2 ASN B 232 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 232 " 0.385 2.00e-02 2.50e+03 pdb="HD22 ASN B 232 " -0.379 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 61 " -0.029 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" N PHE B 62 " 0.098 2.00e-02 2.50e+03 pdb=" CA PHE B 62 " -0.023 2.00e-02 2.50e+03 pdb=" H PHE B 62 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 69 " 0.024 2.00e-02 2.50e+03 4.89e-02 2.40e+01 pdb=" C GLU B 69 " -0.085 2.00e-02 2.50e+03 pdb=" O GLU B 69 " 0.032 2.00e-02 2.50e+03 pdb=" N CYS B 70 " 0.029 2.00e-02 2.50e+03 ... (remaining 6118 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 254 1.89 - 2.57: 22949 2.57 - 3.24: 82409 3.24 - 3.92: 118943 3.92 - 4.60: 180977 Nonbonded interactions: 405532 Sorted by model distance: nonbonded pdb=" O3' DA 5 103 " pdb=" NH2 ARG A 473 " model vdw 1.211 2.350 nonbonded pdb=" H42 DC 6 18 " pdb=" H1 G 7 35 " model vdw 1.266 2.100 nonbonded pdb=" HA LYS B 222 " pdb=" HD2 LYS B 222 " model vdw 1.325 2.440 nonbonded pdb=" OE2 GLU A 641 " pdb=" HZ3 LYS B 749 " model vdw 1.340 1.850 nonbonded pdb=" HG2 ARG B 202 " pdb="HH11 ARG B 202 " model vdw 1.346 2.270 ... (remaining 405527 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 7 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 169 through 232)) selection = (chain 'D' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 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: 0.770 Extract box with map and model: 13.940 Check model and map are aligned: 0.630 Set scattering table: 0.370 Process input model: 137.030 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 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 : 0.010 0.164 28602 Z= 0.635 Angle : 1.170 48.338 39002 Z= 0.668 Chirality : 0.065 0.537 4453 Planarity : 0.007 0.081 4803 Dihedral : 15.482 156.433 11233 Min Nonbonded Distance : 1.211 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.74 % Favored : 90.56 % Rotamer: Outliers : 4.21 % Allowed : 4.35 % Favored : 91.44 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.71 % Twisted General : 0.19 % 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: -4.34 (0.11), residues: 3328 helix: -2.91 (0.11), residues: 1100 sheet: -2.04 (0.24), residues: 399 loop : -3.14 (0.12), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 183 HIS 0.018 0.002 HIS B 430 PHE 0.035 0.003 PHE B 620 TYR 0.039 0.003 TYR A1229 ARG 0.013 0.001 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 491 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6365 (mt) REVERT: A 306 THR cc_start: 0.7952 (p) cc_final: 0.7550 (t) REVERT: A 414 ILE cc_start: 0.3961 (pt) cc_final: 0.2923 (pt) REVERT: A 913 VAL cc_start: 0.4465 (OUTLIER) cc_final: 0.4044 (p) REVERT: B 70 CYS cc_start: 0.5666 (OUTLIER) cc_final: 0.5273 (t) REVERT: B 119 SER cc_start: 0.4289 (OUTLIER) cc_final: 0.4033 (p) REVERT: B 154 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5736 (mp) REVERT: B 299 LEU cc_start: 0.4882 (tt) cc_final: 0.4554 (tt) REVERT: C 201 LEU cc_start: 0.7360 (tp) cc_final: 0.7155 (tt) REVERT: E 10 VAL cc_start: 0.7794 (t) cc_final: 0.7568 (p) outliers start: 120 outliers final: 31 residues processed: 587 average time/residue: 0.7117 time to fit residues: 633.5933 Evaluate side-chains 313 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 277 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.6980 chunk 257 optimal weight: 9.9990 chunk 142 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS A 437 ASN A 462 ASN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 618 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 GLN A1313 HIS B 266 ASN B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN D 66 HIS D 117 HIS ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN F 33 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 28602 Z= 0.186 Angle : 0.579 8.739 39002 Z= 0.314 Chirality : 0.041 0.158 4453 Planarity : 0.005 0.051 4803 Dihedral : 15.831 148.404 4686 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.01 % Favored : 93.78 % Rotamer: Outliers : 0.11 % Allowed : 1.44 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.13), residues: 3328 helix: -0.62 (0.14), residues: 1115 sheet: -1.86 (0.24), residues: 438 loop : -2.56 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 686 HIS 0.009 0.001 HIS B 777 PHE 0.034 0.001 PHE F 175 TYR 0.021 0.001 TYR B 631 ARG 0.010 0.001 ARG F 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 310 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 THR cc_start: 0.8104 (p) cc_final: 0.7718 (t) REVERT: B 132 LEU cc_start: 0.6564 (mm) cc_final: 0.6297 (mt) REVERT: B 1309 ILE cc_start: 0.7110 (pt) cc_final: 0.6607 (mm) outliers start: 3 outliers final: 1 residues processed: 312 average time/residue: 0.6485 time to fit residues: 313.0664 Evaluate side-chains 220 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 0.4980 chunk 95 optimal weight: 0.0040 chunk 256 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 309 optimal weight: 0.0970 chunk 334 optimal weight: 0.0070 chunk 275 optimal weight: 0.0870 chunk 306 optimal weight: 0.0060 chunk 105 optimal weight: 0.0970 chunk 248 optimal weight: 0.8980 overall best weight: 0.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS A 462 ASN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1279 GLN ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 28602 Z= 0.126 Angle : 0.489 8.160 39002 Z= 0.264 Chirality : 0.040 0.152 4453 Planarity : 0.004 0.046 4803 Dihedral : 15.504 147.723 4686 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.98 % Favored : 93.81 % Rotamer: Outliers : 0.04 % Allowed : 0.91 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.77 (0.14), residues: 3328 helix: 0.47 (0.16), residues: 1115 sheet: -1.53 (0.25), residues: 426 loop : -2.25 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 183 HIS 0.005 0.001 HIS B 777 PHE 0.013 0.001 PHE A1323 TYR 0.015 0.001 TYR B 631 ARG 0.003 0.000 ARG B1373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 THR cc_start: 0.8154 (p) cc_final: 0.7766 (t) REVERT: A 315 MET cc_start: 0.4053 (ppp) cc_final: 0.3625 (ppp) REVERT: B 581 MET cc_start: 0.6899 (mmm) cc_final: 0.6688 (tpp) REVERT: B 1040 MET cc_start: -0.0972 (ttm) cc_final: -0.1661 (ttm) REVERT: E 10 VAL cc_start: 0.8136 (t) cc_final: 0.7726 (p) REVERT: E 63 ILE cc_start: 0.8433 (mp) cc_final: 0.8095 (tp) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.6112 time to fit residues: 266.1272 Evaluate side-chains 216 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 328 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 808 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS A1220 GLN B1010 GLN B1259 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28602 Z= 0.215 Angle : 0.579 13.576 39002 Z= 0.307 Chirality : 0.041 0.155 4453 Planarity : 0.004 0.072 4803 Dihedral : 15.336 142.076 4686 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 32.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.00 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.22 (0.14), residues: 3328 helix: 0.96 (0.16), residues: 1133 sheet: -1.15 (0.25), residues: 416 loop : -1.98 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 807 HIS 0.008 0.001 HIS A 673 PHE 0.088 0.002 PHE A 972 TYR 0.017 0.002 TYR B1186 ARG 0.014 0.001 ARG F 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 THR cc_start: 0.8403 (p) cc_final: 0.6865 (p) REVERT: B 1040 MET cc_start: -0.0844 (ttm) cc_final: -0.1380 (ttm) REVERT: E 10 VAL cc_start: 0.8633 (t) cc_final: 0.8201 (p) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.6064 time to fit residues: 229.4907 Evaluate side-chains 194 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 244 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 280 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1367 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS D 37 HIS ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28602 Z= 0.249 Angle : 0.594 12.831 39002 Z= 0.318 Chirality : 0.041 0.163 4453 Planarity : 0.004 0.050 4803 Dihedral : 15.287 138.536 4686 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 36.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.82 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.06 (0.15), residues: 3328 helix: 1.03 (0.16), residues: 1137 sheet: -1.05 (0.26), residues: 407 loop : -1.86 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 9 HIS 0.006 0.001 HIS B1227 PHE 0.055 0.002 PHE A 136 TYR 0.019 0.002 TYR A 742 ARG 0.004 0.001 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1290 MET cc_start: 0.6833 (tpp) cc_final: 0.6454 (tpt) REVERT: B 1040 MET cc_start: -0.0604 (ttm) cc_final: -0.1016 (ttm) REVERT: E 10 VAL cc_start: 0.8659 (t) cc_final: 0.8220 (p) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.6382 time to fit residues: 213.3895 Evaluate side-chains 168 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 1.9990 chunk 295 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 328 optimal weight: 2.9990 chunk 273 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 ASN B1244 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.7241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28602 Z= 0.147 Angle : 0.477 6.812 39002 Z= 0.257 Chirality : 0.039 0.160 4453 Planarity : 0.004 0.058 4803 Dihedral : 15.097 133.596 4686 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 33.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.83 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.65 (0.15), residues: 3328 helix: 1.45 (0.16), residues: 1144 sheet: -0.91 (0.25), residues: 439 loop : -1.66 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 9 HIS 0.004 0.001 HIS B 777 PHE 0.023 0.001 PHE A 972 TYR 0.011 0.001 TYR B 631 ARG 0.009 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 4.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.5423 (tmm) cc_final: 0.5108 (tmm) REVERT: A 681 MET cc_start: 0.7476 (ptp) cc_final: 0.7043 (mtm) REVERT: B 1040 MET cc_start: -0.0603 (ttm) cc_final: -0.1043 (ttm) REVERT: E 10 VAL cc_start: 0.8610 (t) cc_final: 0.8178 (p) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.6224 time to fit residues: 202.1001 Evaluate side-chains 166 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 240 optimal weight: 0.0980 chunk 186 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 327 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.8008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28602 Z= 0.194 Angle : 0.519 7.458 39002 Z= 0.279 Chirality : 0.039 0.147 4453 Planarity : 0.004 0.056 4803 Dihedral : 15.014 123.792 4686 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 37.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.06 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.54 (0.15), residues: 3328 helix: 1.54 (0.16), residues: 1134 sheet: -0.83 (0.25), residues: 432 loop : -1.59 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 9 HIS 0.004 0.001 HIS A 673 PHE 0.035 0.001 PHE F 144 TYR 0.024 0.001 TYR B 899 ARG 0.007 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.5986 (ppp) cc_final: 0.5061 (ppp) REVERT: A 369 MET cc_start: 0.6028 (tmm) cc_final: 0.5660 (tmm) REVERT: A 681 MET cc_start: 0.7272 (ptp) cc_final: 0.6865 (mtm) REVERT: A 1325 VAL cc_start: 0.8263 (t) cc_final: 0.8044 (t) REVERT: B 665 GLN cc_start: 0.6338 (mm110) cc_final: 0.6045 (mm110) REVERT: B 697 MET cc_start: 0.7778 (ptm) cc_final: 0.7479 (ptp) REVERT: B 1040 MET cc_start: -0.0448 (ttm) cc_final: -0.0994 (ttm) REVERT: E 10 VAL cc_start: 0.8679 (t) cc_final: 0.8277 (p) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.6355 time to fit residues: 186.3592 Evaluate side-chains 149 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 257 optimal weight: 4.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 HIS A 658 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.9702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28602 Z= 0.298 Angle : 0.657 13.807 39002 Z= 0.348 Chirality : 0.042 0.308 4453 Planarity : 0.004 0.066 4803 Dihedral : 15.238 105.838 4686 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 47.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.96 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.06 (0.14), residues: 3328 helix: 0.92 (0.15), residues: 1129 sheet: -0.99 (0.25), residues: 435 loop : -1.78 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1193 HIS 0.010 0.002 HIS D 23 PHE 0.025 0.002 PHE B 176 TYR 0.019 0.002 TYR A 291 ARG 0.010 0.001 ARG F 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 681 MET cc_start: 0.7143 (ptp) cc_final: 0.6757 (mtm) REVERT: B 1040 MET cc_start: -0.0405 (ttm) cc_final: -0.0866 (ttm) REVERT: E 10 VAL cc_start: 0.8834 (t) cc_final: 0.8515 (p) REVERT: F 32 LEU cc_start: 0.8156 (tt) cc_final: 0.6169 (tt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.6642 time to fit residues: 179.1827 Evaluate side-chains 134 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 0.8980 chunk 313 optimal weight: 0.6980 chunk 286 optimal weight: 0.0970 chunk 305 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 304 optimal weight: 9.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.9781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 28602 Z= 0.137 Angle : 0.481 5.728 39002 Z= 0.260 Chirality : 0.040 0.158 4453 Planarity : 0.003 0.079 4803 Dihedral : 14.984 97.088 4686 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 37.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.98 % Favored : 93.93 % Rotamer: Outliers : 0.04 % Allowed : 0.14 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3328 helix: 1.55 (0.16), residues: 1130 sheet: -0.79 (0.25), residues: 442 loop : -1.51 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1193 HIS 0.004 0.001 HIS B 777 PHE 0.015 0.001 PHE B 620 TYR 0.010 0.001 TYR B1099 ARG 0.007 0.000 ARG B1194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7219 (ppp) cc_final: 0.6706 (ppp) REVERT: A 369 MET cc_start: 0.6929 (tmm) cc_final: 0.6682 (tmm) REVERT: A 681 MET cc_start: 0.7118 (ptp) cc_final: 0.6582 (mtm) REVERT: B 1040 MET cc_start: -0.0297 (ttm) cc_final: -0.0840 (ttm) REVERT: E 10 VAL cc_start: 0.8846 (t) cc_final: 0.8489 (p) REVERT: E 69 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8227 (tpm170) REVERT: F 32 LEU cc_start: 0.7493 (tt) cc_final: 0.6345 (tt) REVERT: F 43 MET cc_start: 0.6455 (tpp) cc_final: 0.5607 (tpp) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.6379 time to fit residues: 165.1770 Evaluate side-chains 132 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 6.9990 chunk 322 optimal weight: 0.4980 chunk 197 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 338 optimal weight: 20.0000 chunk 311 optimal weight: 0.7980 chunk 269 optimal weight: 9.9990 chunk 28 optimal weight: 0.3980 chunk 208 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 1.0067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 28602 Z= 0.161 Angle : 0.487 5.793 39002 Z= 0.262 Chirality : 0.039 0.155 4453 Planarity : 0.003 0.058 4803 Dihedral : 14.880 91.763 4686 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 39.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.85 % Rotamer: Outliers : 0.04 % Allowed : 0.07 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -0.35 (0.15), residues: 3328 helix: 1.69 (0.16), residues: 1132 sheet: -0.70 (0.25), residues: 432 loop : -1.46 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1193 HIS 0.004 0.001 HIS D 23 PHE 0.014 0.001 PHE B 620 TYR 0.016 0.001 TYR B1363 ARG 0.024 0.000 ARG F 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 MET cc_start: 0.6642 (mmp) cc_final: 0.6363 (mmm) REVERT: A 459 MET cc_start: 0.6988 (mmp) cc_final: 0.6637 (mmp) REVERT: A 681 MET cc_start: 0.7145 (ptp) cc_final: 0.6603 (mtm) REVERT: A 704 MET cc_start: 0.7247 (mmm) cc_final: 0.6961 (mmm) REVERT: B 1040 MET cc_start: -0.0233 (ttm) cc_final: -0.0807 (ttm) REVERT: E 10 VAL cc_start: 0.8858 (t) cc_final: 0.8426 (p) REVERT: E 69 ARG cc_start: 0.8577 (mmm160) cc_final: 0.8190 (mmm160) REVERT: F 32 LEU cc_start: 0.7653 (tt) cc_final: 0.6287 (tt) REVERT: F 43 MET cc_start: 0.6504 (tpp) cc_final: 0.5688 (tpp) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.6244 time to fit residues: 155.3265 Evaluate side-chains 133 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 270 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.043534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.030139 restraints weight = 529495.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.031336 restraints weight = 274535.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032109 restraints weight = 180541.786| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 1.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28602 Z= 0.187 Angle : 0.502 7.439 39002 Z= 0.270 Chirality : 0.039 0.179 4453 Planarity : 0.004 0.060 4803 Dihedral : 14.834 92.298 4686 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 40.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.85 % Favored : 93.06 % Rotamer: Outliers : 0.04 % Allowed : 0.07 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3328 helix: 1.60 (0.16), residues: 1139 sheet: -0.72 (0.25), residues: 439 loop : -1.42 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1193 HIS 0.004 0.001 HIS D 23 PHE 0.013 0.001 PHE B 620 TYR 0.018 0.001 TYR A 367 ARG 0.016 0.000 ARG A 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7560.58 seconds wall clock time: 136 minutes 7.11 seconds (8167.11 seconds total)