Starting phenix.real_space_refine on Sun Mar 24 04:41:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6x_27930/03_2024/8e6x_27930_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6x_27930/03_2024/8e6x_27930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6x_27930/03_2024/8e6x_27930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6x_27930/03_2024/8e6x_27930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6x_27930/03_2024/8e6x_27930_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6x_27930/03_2024/8e6x_27930_neut.pdb" } resolution = 4.27 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= 0.001 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 97 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 17430 2.51 5 N 4985 2.21 5 O 5665 1.98 5 H 11239 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 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 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 105": "OD1" <-> "OD2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39532 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: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1029 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "7" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 676 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 13} Link IDs: {'rna2p': 5, 'rna3p': 21} 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: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "F" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1392 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 164} 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 14070 SG CYS B 70 126.283 83.930 111.386 1.00 45.60 S ATOM 14329 SG CYS B 85 128.233 83.378 115.737 1.00 49.94 S ATOM 25911 SG CYS B 814 84.650 32.143 94.180 1.00 22.38 S ATOM 27048 SG CYS B 888 85.476 36.602 94.165 1.00 20.48 S ATOM 27139 SG CYS B 895 86.896 34.132 91.902 1.00 14.28 S ATOM 27176 SG CYS B 898 83.386 33.979 91.378 1.00 16.02 S Time building chain proxies: 18.65, per 1000 atoms: 0.47 Number of scatterers: 39532 At special positions: 0 Unit cell: (186.006, 157.143, 160.35, 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 97 15.00 Mg 1 11.99 O 5665 8.00 N 4985 7.00 C 17430 6.00 H 11239 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 Atom "ATOM 311 O5' DA 5 100 .*. O " rejected from bonding due to valence issues. Atom "ATOM 311 O5' DA 5 100 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.82 Conformation dependent library (CDL) restraints added in 9.0 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 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6200 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 49 sheets defined 35.7% alpha, 15.2% beta 28 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 17.10 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: 3.839A pdb=" N SER A 166 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.132A 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: 4.129A 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: 3.758A pdb=" N ILE A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 480 removed outlier: 4.512A 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: 4.046A pdb=" N ASN A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.900A 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: 3.792A 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 896 through 901 Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.932A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 981 removed outlier: 4.147A pdb=" N ALA A 981 " --> pdb=" O ALA A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 998 removed outlier: 3.589A pdb=" N LEU A 998 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1038 removed outlier: 3.626A pdb=" N GLN A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) 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: 3.594A pdb=" N GLN A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.879A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.981A 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: 3.652A 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: 3.548A 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: 4.147A 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: 3.521A 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: 3.610A 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: 3.533A 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: 3.642A pdb=" N ARG B 838 " --> pdb=" O PRO B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.796A 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: 3.943A 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: 4.195A 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: 3.543A 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: 4.420A 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: 3.526A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.686A 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 74 Processing helix chain 'F' and resid 18 through 33 Processing helix chain 'F' and resid 35 through 39 removed outlier: 3.816A pdb=" N PHE F 39 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 86 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.646A 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: 4.216A pdb=" N ARG F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.570A 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: 5.617A 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: 6.321A 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: 3.580A 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: 4.966A 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: 6.632A pdb=" N ARG A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 727 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.668A 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: 6.444A pdb=" N ARG A 801 " --> pdb=" O ILE A1096 " (cutoff:3.500A) removed outlier: 7.412A 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: 6.411A pdb=" N ASP A 842 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A1046 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP A 930 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA A1055 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL A 928 " --> pdb=" O ALA A1055 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 882 through 884 removed outlier: 3.626A pdb=" N VAL A 884 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 887 through 889 Processing sheet with id=AC3, first strand: chain 'A' and resid 1244 through 1246 Processing sheet with id=AC4, first strand: chain 'A' and resid 1269 through 1270 Processing sheet with id=AC5, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id=AC6, 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: 6.654A 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: 10.938A 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=AC7, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC8, first strand: chain 'B' and resid 253 through 254 removed outlier: 4.414A pdb=" N VAL B 253 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 526 through 527 Processing sheet with id=AD1, 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=AD2, first strand: chain 'B' and resid 821 through 822 Processing sheet with id=AD3, first strand: chain 'B' and resid 849 through 850 removed outlier: 4.608A pdb=" N ASP B 855 " --> pdb=" O LYS B 850 " (cutoff:3.500A) Processing sheet with id=AD4, 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=AD5, first strand: chain 'B' and resid 965 through 967 Processing sheet with id=AD6, first strand: chain 'B' and resid 1034 through 1038 removed outlier: 3.618A 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=AD7, first strand: chain 'B' and resid 1046 through 1049 removed outlier: 4.089A 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=AD8, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD9, first strand: chain 'B' and resid 1279 through 1281 removed outlier: 7.345A pdb=" N THR B1301 " --> pdb=" O VAL B1267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.341A pdb=" N ASP C 199 " --> pdb=" O PRO C 30 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 202 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.522A pdb=" N GLY C 53 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.248A pdb=" N THR C 101 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER C 141 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE C 61 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 6.678A 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: 6.632A pdb=" N LYS C 145 " --> pdb=" O THR C 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AE5, first strand: chain 'C' and resid 108 through 111 removed outlier: 3.836A pdb=" N CYS C 131 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AE6, 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=AE7, first strand: chain 'D' and resid 53 through 61 removed outlier: 4.075A pdb=" N ALA D 55 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 7.041A 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=AE8, first strand: chain 'D' and resid 90 through 91 Processing sheet with id=AE9, first strand: chain 'D' and resid 108 through 111 removed outlier: 4.050A pdb=" N CYS D 131 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing sheet with id=AF1, 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=AF2, first strand: chain 'F' and resid 68 through 73 removed outlier: 7.688A pdb=" N VAL F 11 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE F 92 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN F 13 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 48 through 51 Processing sheet with id=AF4, 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: 3.792A pdb=" N VAL F 171 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 162 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 164 " --> pdb=" O ARG F 167 " (cutoff:3.500A) 1018 hydrogen bonds defined for protein. 2859 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 19.16 Time building geometry restraints manager: 35.87 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: 11195 1.03 - 1.23: 346 1.23 - 1.42: 11512 1.42 - 1.62: 16899 1.62 - 1.81: 203 Bond restraints: 40155 Sorted by residual: bond pdb=" C PHE A 828 " pdb=" N THR A 829 " ideal model delta sigma weight residual 1.331 1.535 -0.204 1.43e-02 4.89e+03 2.04e+02 bond pdb=" C PRO F 102 " pdb=" N ILE F 103 " ideal model delta sigma weight residual 1.332 1.521 -0.190 1.36e-02 5.41e+03 1.94e+02 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 1.49e+02 bond pdb=" N3 U 7 17 " pdb=" H3 U 7 17 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" N3 DT 6 24 " pdb=" H3 DT 6 24 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.11e+01 ... (remaining 40150 not shown) Histogram of bond angle deviations from ideal: 59.62 - 77.30: 2 77.30 - 94.98: 4 94.98 - 112.66: 36573 112.66 - 130.34: 28408 130.34 - 148.02: 123 Bond angle restraints: 65110 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 104.00 148.02 -44.02 1.50e+00 4.44e-01 8.61e+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 75.97 33.03 1.50e+00 4.44e-01 4.85e+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 59.62 48.38 3.00e+00 1.11e-01 2.60e+02 angle pdb=" O3' DA 6 28 " pdb=" P DT 6 29 " pdb=" O5' DT 6 29 " ideal model delta sigma weight residual 104.00 126.05 -22.05 1.50e+00 4.44e-01 2.16e+02 angle pdb=" CA PRO F 102 " pdb=" C PRO F 102 " pdb=" N ILE F 103 " ideal model delta sigma weight residual 115.12 131.74 -16.62 1.25e+00 6.40e-01 1.77e+02 ... (remaining 65105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 20111 35.99 - 71.98: 869 71.98 - 107.97: 27 107.97 - 143.96: 2 143.96 - 179.95: 8 Dihedral angle restraints: 21017 sinusoidal: 10962 harmonic: 10055 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 -126.68 -53.32 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" O4' U 7 16 " pdb=" C1' U 7 16 " pdb=" N1 U 7 16 " pdb=" C2 U 7 16 " ideal model delta sinusoidal sigma weight residual 200.00 43.73 156.27 1 1.50e+01 4.44e-03 8.17e+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 -138.09 -41.91 0 5.00e+00 4.00e-02 7.03e+01 ... (remaining 21014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 4064 0.107 - 0.214: 418 0.214 - 0.322: 26 0.322 - 0.429: 4 0.429 - 0.536: 3 Chirality restraints: 4515 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 7.18e+00 chirality pdb=" CA LYS F 121 " pdb=" N LYS F 121 " pdb=" C LYS F 121 " pdb=" CB LYS F 121 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.06e+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 4.88e+00 ... (remaining 4512 not shown) Planarity restraints: 6148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " -0.211 2.00e-02 2.50e+03 2.51e-01 9.45e+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=" CA GLU F 41 " -0.028 2.00e-02 2.50e+03 5.99e-02 3.59e+01 pdb=" C GLU F 41 " 0.103 2.00e-02 2.50e+03 pdb=" O GLU F 41 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL F 42 " -0.032 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 5.75e-02 3.31e+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 ... (remaining 6145 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.75: 106 1.75 - 2.46: 14988 2.46 - 3.18: 81549 3.18 - 3.89: 122477 3.89 - 4.60: 189407 Nonbonded interactions: 408527 Sorted by model distance: nonbonded pdb=" C5' DA 5 100 " pdb=" OG SER F 16 " model vdw 1.038 3.100 nonbonded pdb=" O PRO A 847 " pdb=" CB PRO A 889 " model vdw 1.118 3.100 nonbonded pdb=" O5' DA 5 100 " pdb=" CB SER F 16 " model vdw 1.140 3.100 nonbonded pdb=" C4' DA 5 100 " pdb=" OG SER F 16 " model vdw 1.219 3.100 nonbonded pdb=" H42 DC 6 18 " pdb=" H1 G 7 32 " model vdw 1.267 2.100 ... (remaining 408522 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: 4.070 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: 0.730 Extract box with map and model: 14.170 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 152.470 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 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 0.204 28916 Z= 0.641 Angle : 1.191 48.380 39466 Z= 0.687 Chirality : 0.067 0.536 4515 Planarity : 0.008 0.081 4830 Dihedral : 15.972 163.690 11437 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.65 % Favored : 90.72 % Rotamer: Outliers : 4.27 % Allowed : 4.62 % Favored : 91.12 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % 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: -4.35 (0.11), residues: 3341 helix: -2.92 (0.11), residues: 1105 sheet: -2.20 (0.24), residues: 399 loop : -3.11 (0.12), residues: 1837 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 0.038 0.003 TYR A1229 ARG 0.014 0.001 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 595 time to evaluate : 3.550 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: A 241 LEU cc_start: 0.6557 (tp) cc_final: 0.6330 (tp) REVERT: A 1279 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 114 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.5882 (tp) REVERT: B 146 VAL cc_start: 0.2958 (OUTLIER) cc_final: 0.2676 (m) REVERT: B 273 ILE cc_start: 0.8540 (mt) cc_final: 0.8056 (mt) REVERT: B 506 VAL cc_start: 0.7574 (OUTLIER) cc_final: 0.7371 (p) REVERT: B 513 MET cc_start: 0.6633 (ttp) cc_final: 0.6392 (ttt) REVERT: B 560 ASN cc_start: 0.6592 (p0) cc_final: 0.6219 (p0) REVERT: B 581 MET cc_start: 0.6809 (mtp) cc_final: 0.6423 (ttm) REVERT: B 1256 ILE cc_start: 0.7494 (mm) cc_final: 0.7286 (mm) REVERT: D 46 ILE cc_start: 0.8188 (mt) cc_final: 0.7601 (tp) REVERT: F 123 ARG cc_start: 0.0371 (OUTLIER) cc_final: -0.1877 (mtt180) outliers start: 122 outliers final: 30 residues processed: 686 average time/residue: 0.7389 time to fit residues: 750.4030 Evaluate side-chains 330 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 296 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 310 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 150 HIS A 314 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN A1268 GLN A1313 HIS ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 HIS B1279 GLN C 147 GLN D 66 HIS D 117 HIS D 227 GLN ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 28916 Z= 0.184 Angle : 0.593 7.936 39466 Z= 0.322 Chirality : 0.042 0.177 4515 Planarity : 0.005 0.070 4830 Dihedral : 16.740 172.205 4862 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.17 % Favored : 93.65 % Rotamer: Outliers : 0.07 % Allowed : 1.75 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 1.43 % 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: -2.71 (0.13), residues: 3341 helix: -0.58 (0.15), residues: 1118 sheet: -1.84 (0.24), residues: 436 loop : -2.69 (0.13), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 997 HIS 0.008 0.001 HIS B 80 PHE 0.021 0.001 PHE F 65 TYR 0.020 0.001 TYR B 46 ARG 0.008 0.000 ARG F 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 363 time to evaluate : 3.653 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: A 492 MET cc_start: 0.3529 (ttm) cc_final: 0.2600 (ttt) REVERT: A 620 ASN cc_start: 0.6937 (p0) cc_final: 0.6489 (p0) REVERT: A 1279 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7693 (mt-10) REVERT: B 485 MET cc_start: 0.5793 (tpp) cc_final: 0.5583 (tpt) REVERT: B 560 ASN cc_start: 0.6678 (p0) cc_final: 0.6256 (p0) REVERT: B 1233 ILE cc_start: 0.6964 (tt) cc_final: 0.6746 (tp) REVERT: E 19 LEU cc_start: 0.8383 (pp) cc_final: 0.7030 (tt) REVERT: E 20 VAL cc_start: 0.7984 (t) cc_final: 0.7706 (t) outliers start: 2 outliers final: 0 residues processed: 365 average time/residue: 0.6525 time to fit residues: 366.0532 Evaluate side-chains 252 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 0.0980 chunk 96 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 336 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 chunk 106 optimal weight: 0.0050 chunk 249 optimal weight: 0.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- 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 273 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 GLN B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28916 Z= 0.155 Angle : 0.512 8.203 39466 Z= 0.277 Chirality : 0.040 0.205 4515 Planarity : 0.004 0.095 4830 Dihedral : 16.373 173.306 4862 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.44 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % 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: -1.70 (0.14), residues: 3341 helix: 0.69 (0.16), residues: 1118 sheet: -1.57 (0.24), residues: 434 loop : -2.30 (0.13), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 9 HIS 0.006 0.001 HIS B 80 PHE 0.012 0.001 PHE F 65 TYR 0.010 0.001 TYR A1229 ARG 0.007 0.000 ARG B 901 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 2.977 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: A 620 ASN cc_start: 0.7114 (p0) cc_final: 0.6908 (p0) REVERT: A 1279 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 87 LYS cc_start: 0.6624 (pttp) cc_final: 0.5869 (mttt) REVERT: B 485 MET cc_start: 0.6360 (tpp) cc_final: 0.6026 (tpt) REVERT: B 560 ASN cc_start: 0.6689 (p0) cc_final: 0.6324 (p0) REVERT: B 1256 ILE cc_start: 0.7957 (mm) cc_final: 0.7742 (mm) REVERT: E 5 THR cc_start: 0.7723 (p) cc_final: 0.7518 (p) REVERT: E 19 LEU cc_start: 0.8279 (pp) cc_final: 0.6921 (tt) REVERT: E 20 VAL cc_start: 0.7997 (t) cc_final: 0.7763 (t) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.6492 time to fit residues: 306.3935 Evaluate side-chains 236 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 0.0670 chunk 233 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 overall best weight: 1.3120 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 HIS ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28916 Z= 0.166 Angle : 0.505 7.428 39466 Z= 0.272 Chirality : 0.039 0.179 4515 Planarity : 0.004 0.081 4830 Dihedral : 16.167 173.534 4862 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 31.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.35 % Favored : 93.53 % Rotamer: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % 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: -1.12 (0.15), residues: 3341 helix: 1.28 (0.16), residues: 1113 sheet: -1.37 (0.25), residues: 431 loop : -1.98 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 9 HIS 0.005 0.001 HIS B 80 PHE 0.011 0.001 PHE A 390 TYR 0.012 0.001 TYR A1285 ARG 0.003 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 3.656 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: A 620 ASN cc_start: 0.7403 (p0) cc_final: 0.7151 (p0) REVERT: B 87 LYS cc_start: 0.6629 (pttp) cc_final: 0.5939 (ptpt) REVERT: B 560 ASN cc_start: 0.6919 (p0) cc_final: 0.6468 (p0) REVERT: E 19 LEU cc_start: 0.8250 (pp) cc_final: 0.7978 (pp) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.6434 time to fit residues: 272.4305 Evaluate side-chains 213 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 41 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 437 ASN ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN A 955 GLN ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS A1135 GLN A1136 GLN B 45 ASN B 294 ASN B 424 ASN B 488 ASN B 669 GLN B1244 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28916 Z= 0.308 Angle : 0.655 9.758 39466 Z= 0.351 Chirality : 0.042 0.165 4515 Planarity : 0.005 0.102 4830 Dihedral : 16.324 177.478 4862 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 43.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.99 % Favored : 91.89 % Rotamer: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % 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: -1.31 (0.14), residues: 3341 helix: 0.96 (0.15), residues: 1136 sheet: -1.39 (0.24), residues: 470 loop : -2.05 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 9 HIS 0.010 0.002 HIS B 450 PHE 0.024 0.002 PHE A1221 TYR 0.022 0.002 TYR A1305 ARG 0.032 0.001 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 3.481 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: A 311 CYS cc_start: 0.7417 (p) cc_final: 0.6696 (p) REVERT: A 425 ILE cc_start: 0.8716 (pt) cc_final: 0.8445 (pt) REVERT: A 1180 MET cc_start: 0.8242 (tpp) cc_final: 0.7572 (tpt) REVERT: B 560 ASN cc_start: 0.6804 (p0) cc_final: 0.6390 (p0) REVERT: E 19 LEU cc_start: 0.8165 (pp) cc_final: 0.7949 (pp) REVERT: E 62 GLN cc_start: 0.7896 (tp40) cc_final: 0.7564 (tp40) REVERT: F 133 MET cc_start: 0.7250 (tmm) cc_final: 0.6437 (ttp) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.6375 time to fit residues: 243.5954 Evaluate side-chains 197 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 330 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 153 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.7172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28916 Z= 0.212 Angle : 0.528 7.316 39466 Z= 0.287 Chirality : 0.040 0.151 4515 Planarity : 0.004 0.041 4830 Dihedral : 16.138 179.539 4862 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 39.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.55 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % 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: -1.07 (0.15), residues: 3341 helix: 1.19 (0.16), residues: 1147 sheet: -1.44 (0.24), residues: 458 loop : -1.89 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 997 HIS 0.005 0.001 HIS B 80 PHE 0.010 0.001 PHE A 53 TYR 0.015 0.001 TYR A1149 ARG 0.006 0.000 ARG F 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 3.602 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: A 311 CYS cc_start: 0.7258 (p) cc_final: 0.6644 (p) REVERT: B 192 MET cc_start: 0.7456 (tpp) cc_final: 0.7186 (tpp) REVERT: B 560 ASN cc_start: 0.7022 (p0) cc_final: 0.6625 (p0) REVERT: F 133 MET cc_start: 0.7202 (tmm) cc_final: 0.6648 (ttp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.6078 time to fit residues: 224.6643 Evaluate side-chains 192 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 0.0980 chunk 37 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 329 optimal weight: 0.0970 chunk 206 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.7687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28916 Z= 0.195 Angle : 0.516 6.455 39466 Z= 0.278 Chirality : 0.040 0.197 4515 Planarity : 0.004 0.038 4830 Dihedral : 16.030 179.283 4862 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 41.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.60 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % 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: -0.89 (0.15), residues: 3341 helix: 1.39 (0.16), residues: 1140 sheet: -1.26 (0.23), residues: 503 loop : -1.84 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 9 HIS 0.006 0.001 HIS B 450 PHE 0.025 0.001 PHE B1325 TYR 0.013 0.001 TYR A1305 ARG 0.006 0.000 ARG B 515 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 3.565 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: A 311 CYS cc_start: 0.7319 (p) cc_final: 0.6357 (p) REVERT: A 942 ASP cc_start: 0.7524 (p0) cc_final: 0.7320 (p0) REVERT: B 87 LYS cc_start: 0.7547 (pttp) cc_final: 0.7117 (mttt) REVERT: B 192 MET cc_start: 0.7319 (tpp) cc_final: 0.7014 (tpp) REVERT: B 513 MET cc_start: 0.6918 (ttt) cc_final: 0.6682 (ttt) REVERT: B 560 ASN cc_start: 0.6947 (p0) cc_final: 0.6547 (p0) REVERT: E 19 LEU cc_start: 0.7981 (pp) cc_final: 0.7754 (pp) REVERT: F 133 MET cc_start: 0.7236 (tmm) cc_final: 0.6792 (ttp) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.6714 time to fit residues: 234.4985 Evaluate side-chains 177 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 99 optimal weight: 0.0770 chunk 64 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 259 optimal weight: 7.9990 overall best weight: 5.8146 ------------------------------------------------------------------------------- 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 HIS A 658 GLN ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 GLN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS C 132 HIS ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.9198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 28916 Z= 0.479 Angle : 0.853 10.619 39466 Z= 0.454 Chirality : 0.047 0.226 4515 Planarity : 0.006 0.066 4830 Dihedral : 16.801 170.727 4862 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 62.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.60 % Favored : 89.11 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % 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: -2.22 (0.14), residues: 3341 helix: -0.26 (0.14), residues: 1163 sheet: -1.65 (0.24), residues: 440 loop : -2.34 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 807 HIS 0.012 0.002 HIS B 450 PHE 0.028 0.003 PHE E 17 TYR 0.035 0.003 TYR A1305 ARG 0.012 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.648 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: A 311 CYS cc_start: 0.7591 (p) cc_final: 0.7308 (p) REVERT: A 704 MET cc_start: 0.6868 (mmp) cc_final: 0.6583 (mmp) REVERT: A 1180 MET cc_start: 0.8282 (tpp) cc_final: 0.7749 (tpt) REVERT: A 1287 LEU cc_start: 0.7983 (tt) cc_final: 0.7480 (tt) REVERT: B 192 MET cc_start: 0.7126 (tpp) cc_final: 0.6840 (tpp) REVERT: B 560 ASN cc_start: 0.7299 (p0) cc_final: 0.6797 (p0) REVERT: F 133 MET cc_start: 0.7128 (tmm) cc_final: 0.6628 (ttp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.6018 time to fit residues: 169.3998 Evaluate side-chains 148 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 0.0770 chunk 315 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 133 optimal weight: 0.1980 chunk 241 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 277 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 overall best weight: 1.0544 ------------------------------------------------------------------------------- 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 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 HIS ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1244 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.9046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28916 Z= 0.152 Angle : 0.514 6.456 39466 Z= 0.279 Chirality : 0.040 0.146 4515 Planarity : 0.004 0.057 4830 Dihedral : 16.400 173.175 4862 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 42.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.12 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % 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: -1.25 (0.14), residues: 3341 helix: 0.88 (0.15), residues: 1147 sheet: -1.23 (0.24), residues: 455 loop : -1.96 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 80 HIS 0.006 0.001 HIS B 80 PHE 0.014 0.001 PHE B 620 TYR 0.012 0.001 TYR A 395 ARG 0.009 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 3.708 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: A 311 CYS cc_start: 0.6763 (p) cc_final: 0.5777 (p) REVERT: A 704 MET cc_start: 0.6524 (mmp) cc_final: 0.6321 (mmp) REVERT: A 1151 LEU cc_start: 0.7800 (tp) cc_final: 0.7595 (tt) REVERT: A 1180 MET cc_start: 0.8210 (tpp) cc_final: 0.7597 (tpt) REVERT: A 1287 LEU cc_start: 0.7488 (tt) cc_final: 0.7272 (tt) REVERT: B 560 ASN cc_start: 0.7128 (p0) cc_final: 0.6751 (p0) REVERT: B 747 MET cc_start: 0.5705 (mmm) cc_final: 0.5134 (mmm) REVERT: F 133 MET cc_start: 0.7128 (tmm) cc_final: 0.6722 (ttp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.6441 time to fit residues: 202.1702 Evaluate side-chains 159 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 chunk 198 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 340 optimal weight: 8.9990 chunk 313 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.9258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28916 Z= 0.234 Angle : 0.550 6.335 39466 Z= 0.298 Chirality : 0.040 0.169 4515 Planarity : 0.004 0.092 4830 Dihedral : 16.339 172.347 4862 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 46.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.01 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % 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: -1.19 (0.15), residues: 3341 helix: 0.85 (0.15), residues: 1167 sheet: -1.15 (0.24), residues: 458 loop : -1.92 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1276 HIS 0.006 0.001 HIS B 80 PHE 0.013 0.001 PHE A 337 TYR 0.016 0.001 TYR A1305 ARG 0.013 0.001 ARG F 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 3.557 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: A 311 CYS cc_start: 0.7180 (p) cc_final: 0.6162 (p) REVERT: A 1151 LEU cc_start: 0.7697 (tp) cc_final: 0.7356 (tt) REVERT: A 1180 MET cc_start: 0.8112 (tpp) cc_final: 0.7503 (tpt) REVERT: B 560 ASN cc_start: 0.7197 (p0) cc_final: 0.6717 (p0) REVERT: B 821 MET cc_start: 0.7541 (mmm) cc_final: 0.7222 (mmm) REVERT: F 133 MET cc_start: 0.7248 (tmm) cc_final: 0.6682 (ttp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.6216 time to fit residues: 183.8181 Evaluate side-chains 156 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 250 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 235 ASN A 238 GLN ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.057973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.040125 restraints weight = 422796.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.041559 restraints weight = 217953.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.042470 restraints weight = 143440.266| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.9276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.751 28916 Z= 0.593 Angle : 0.513 28.983 39466 Z= 0.282 Chirality : 0.040 0.365 4515 Planarity : 0.004 0.060 4830 Dihedral : 16.132 173.096 4862 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 42.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.94 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % 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: -0.72 (0.15), residues: 3341 helix: 1.37 (0.16), residues: 1161 sheet: -0.97 (0.25), residues: 448 loop : -1.71 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 409 HIS 0.004 0.001 HIS B 80 PHE 0.045 0.001 PHE F 175 TYR 0.012 0.001 TYR F 10 ARG 0.008 0.000 ARG B 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7751.02 seconds wall clock time: 141 minutes 40.42 seconds (8500.42 seconds total)