Starting phenix.real_space_refine on Fri Dec 15 21:11:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/12_2023/6p18_20233.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/12_2023/6p18_20233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/12_2023/6p18_20233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/12_2023/6p18_20233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/12_2023/6p18_20233.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p18_20233/12_2023/6p18_20233.pdb" } resolution = 3.5 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= 0.008 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 123 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 20120 2.51 5 N 5793 2.21 5 O 6491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 950": "OE1" <-> "OE2" Residue "C GLU 987": "OE1" <-> "OE2" Residue "C GLU 1020": "OE1" <-> "OE2" Residue "C GLU 1137": "OE1" <-> "OE2" Residue "C GLU 1342": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D GLU 765": "OE1" <-> "OE2" Residue "D PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1052": "OE1" <-> "OE2" Residue "D GLU 1110": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F GLU 369": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 32673 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1153 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "2" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1142 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10568 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10319 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1271} Chain breaks: 2 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2665 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 6, 'TRANS': 318} Chain breaks: 2 Chain: "P" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1165 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "Q" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1261 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "R" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 244 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "D" 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 16874 SG CYS D 70 58.979 119.013 85.312 1.00 46.06 S ATOM 16888 SG CYS D 72 60.321 122.141 84.051 1.00 47.41 S ATOM 16996 SG CYS D 85 58.195 120.359 81.163 1.00 51.55 S ATOM 17020 SG CYS D 88 61.752 119.701 81.629 1.00 46.73 S ATOM 22708 SG CYS D 814 58.114 52.188 74.105 1.00 40.48 S ATOM 23273 SG CYS D 888 60.903 55.573 74.913 1.00 31.50 S ATOM 23324 SG CYS D 895 58.341 53.893 77.348 1.00 27.28 S ATOM 23345 SG CYS D 898 60.983 51.584 76.680 1.00 26.31 S Time building chain proxies: 16.37, per 1000 atoms: 0.50 Number of scatterers: 32673 At special positions: 0 Unit cell: (158.834, 179.088, 172.692, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 143 16.00 P 123 15.00 Mg 1 11.99 O 6491 8.00 N 5793 7.00 C 20120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.53 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " Number of angles added : 12 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 47 sheets defined 43.7% alpha, 13.1% beta 50 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 11.02 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.531A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.222A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.657A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.044A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.884A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.799A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.192A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.887A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.737A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.552A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.629A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 549' Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.812A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.065A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 removed outlier: 4.095A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.777A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1334 removed outlier: 3.921A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.694A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.606A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.907A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 515 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.522A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.573A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.596A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.763A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.991A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.325A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.941A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.798A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.343A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1361 through 1375 removed outlier: 4.515A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 114 through 135 removed outlier: 3.690A pdb=" N ASP F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 216 through 232 Processing helix chain 'F' and resid 243 through 257 removed outlier: 3.673A pdb=" N LYS F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 294 removed outlier: 4.195A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 315 through 321 Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.681A pdb=" N LEU F 330 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 381 removed outlier: 3.576A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.528A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.642A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 4.309A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 444 removed outlier: 4.644A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 467 Processing helix chain 'P' and resid 9 through 29 removed outlier: 3.801A pdb=" N SER P 29 " --> pdb=" O ALA P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 44 Processing helix chain 'P' and resid 59 through 74 removed outlier: 3.779A pdb=" N GLY P 63 " --> pdb=" O ASN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 89 Processing helix chain 'P' and resid 93 through 103 removed outlier: 3.500A pdb=" N ILE P 97 " --> pdb=" O SER P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 150 Proline residue: P 143 - end of helix Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 29 through 31 No H-bonds generated for 'chain 'Q' and resid 29 through 31' Processing helix chain 'Q' and resid 38 through 48 Processing helix chain 'Q' and resid 60 through 74 Processing helix chain 'Q' and resid 77 through 89 Processing helix chain 'Q' and resid 93 through 104 Processing helix chain 'Q' and resid 122 through 151 removed outlier: 3.536A pdb=" N CYS Q 126 " --> pdb=" O SER Q 122 " (cutoff:3.500A) Proline residue: Q 143 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 6.812A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.518A pdb=" N GLU A 60 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.560A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 16 removed outlier: 4.013A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 105 removed outlier: 6.286A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.509A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.186A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.440A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.891A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 68 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 98 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.151A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 160 removed outlier: 3.640A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AC1, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.966A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.089A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.526A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.526A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.783A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.962A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 1065 through 1066 removed outlier: 7.099A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.677A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 877 " --> pdb=" O GLY C 926 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.850A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.548A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.623A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD7, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.689A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.228A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.942A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.513A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.645A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 958 through 961 removed outlier: 3.503A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 984 " --> pdb=" O GLU D 993 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 966 removed outlier: 4.040A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1025 through 1026 removed outlier: 3.962A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.571A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D1077 " --> pdb=" O THR D1038 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AE9, first strand: chain 'D' and resid 1164 through 1165 Processing sheet with id=AF1, first strand: chain 'D' and resid 1280 through 1281 removed outlier: 4.008A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 108 through 109 1363 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 17.75 Time building geometry restraints manager: 13.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8109 1.33 - 1.45: 6360 1.45 - 1.57: 18478 1.57 - 1.69: 244 1.69 - 1.81: 249 Bond restraints: 33440 Sorted by residual: bond pdb=" N LEU F 305 " pdb=" CA LEU F 305 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.27e-02 6.20e+03 6.68e+00 bond pdb=" N GLU D1276 " pdb=" CA GLU D1276 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.16e-02 7.43e+03 6.67e+00 bond pdb=" N LEU D1275 " pdb=" CA LEU D1275 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.08e-02 8.57e+03 6.03e+00 bond pdb=" N LYS C 991 " pdb=" CA LYS C 991 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.33e-02 5.65e+03 5.75e+00 bond pdb=" N LEU C 992 " pdb=" CA LEU C 992 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.69e-02 3.50e+03 4.80e+00 ... (remaining 33435 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.85: 1263 105.85 - 112.92: 17743 112.92 - 120.00: 11980 120.00 - 127.07: 14169 127.07 - 134.15: 521 Bond angle restraints: 45676 Sorted by residual: angle pdb=" C GLY B 209 " pdb=" N THR B 210 " pdb=" CA THR B 210 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C MET F 322 " pdb=" N ASN F 323 " pdb=" CA ASN F 323 " ideal model delta sigma weight residual 121.54 131.64 -10.10 1.91e+00 2.74e-01 2.80e+01 angle pdb=" N LYS C 991 " pdb=" CA LYS C 991 " pdb=" C LYS C 991 " ideal model delta sigma weight residual 113.28 107.33 5.95 1.22e+00 6.72e-01 2.38e+01 angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 angle pdb=" CA GLU Q 11 " pdb=" CB GLU Q 11 " pdb=" CG GLU Q 11 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.13e+01 ... (remaining 45671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17341 17.93 - 35.86: 2094 35.86 - 53.78: 634 53.78 - 71.71: 175 71.71 - 89.64: 30 Dihedral angle restraints: 20274 sinusoidal: 9257 harmonic: 11017 Sorted by residual: dihedral pdb=" CA LEU C 397 " pdb=" C LEU C 397 " pdb=" N SER C 398 " pdb=" CA SER C 398 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASP D 710 " pdb=" C ASP D 710 " pdb=" N GLY D 711 " pdb=" CA GLY D 711 " ideal model delta harmonic sigma weight residual 180.00 154.53 25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA SER C 398 " pdb=" C SER C 398 " pdb=" N ALA C 399 " pdb=" CA ALA C 399 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 20271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4493 0.073 - 0.145: 622 0.145 - 0.218: 53 0.218 - 0.291: 2 0.291 - 0.364: 5 Chirality restraints: 5175 Sorted by residual: chirality pdb=" CB ILE D 707 " pdb=" CA ILE D 707 " pdb=" CG1 ILE D 707 " pdb=" CG2 ILE D 707 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL D1280 " pdb=" CA VAL D1280 " pdb=" CG1 VAL D1280 " pdb=" CG2 VAL D1280 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 5172 not shown) Planarity restraints: 5519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 324 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO F 325 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 325 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 325 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO C 190 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO C 520 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.039 5.00e-02 4.00e+02 ... (remaining 5516 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 564 2.67 - 3.23: 27476 3.23 - 3.78: 51384 3.78 - 4.34: 67563 4.34 - 4.90: 109894 Nonbonded interactions: 256881 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.110 2.170 nonbonded pdb=" O3' A R 11 " pdb="MG MG D1503 " model vdw 2.116 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.144 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.191 2.170 nonbonded pdb=" OE2 GLU D 981 " pdb=" OG SER D 994 " model vdw 2.302 2.440 ... (remaining 256876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = (chain 'P' and resid 7 through 150) selection = (chain 'Q' and resid 7 through 150) } 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: 0.960 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: 0.030 Extract box with map and model: 5.400 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 99.670 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.140 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33440 Z= 0.218 Angle : 0.754 10.854 45676 Z= 0.427 Chirality : 0.050 0.364 5175 Planarity : 0.006 0.080 5519 Dihedral : 17.437 89.640 13180 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.28 % Allowed : 6.54 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.10), residues: 3802 helix: -2.17 (0.09), residues: 1574 sheet: -2.23 (0.23), residues: 399 loop : -2.89 (0.11), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 326 HIS 0.005 0.001 HIS D 104 PHE 0.028 0.002 PHE F 266 TYR 0.021 0.001 TYR D 679 ARG 0.007 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 582 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 588 average time/residue: 0.5289 time to fit residues: 474.7427 Evaluate side-chains 394 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 3.464 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.9725 time to fit residues: 6.5009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 7.9990 chunk 295 optimal weight: 8.9990 chunk 164 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 199 optimal weight: 0.0980 chunk 157 optimal weight: 10.0000 chunk 305 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 354 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 37 HIS B 128 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 447 HIS C 622 ASN C 673 HIS C1008 GLN D 196 GLN D 232 ASN D 300 GLN D 450 HIS D 477 GLN D 504 GLN D 777 HIS D 875 ASN D1049 GLN D1098 GLN D1108 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN D1252 HIS D1259 GLN F 128 ASN F 258 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN P 90 HIS Q 12 GLN Q 90 HIS ** Q 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33440 Z= 0.184 Angle : 0.554 10.441 45676 Z= 0.294 Chirality : 0.041 0.160 5175 Planarity : 0.004 0.060 5519 Dihedral : 16.046 88.848 5621 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.56 % Allowed : 12.93 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.12), residues: 3802 helix: -0.11 (0.12), residues: 1597 sheet: -2.08 (0.24), residues: 389 loop : -2.39 (0.12), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 326 HIS 0.006 0.001 HIS F 455 PHE 0.025 0.001 PHE F 306 TYR 0.022 0.001 TYR C 70 ARG 0.009 0.000 ARG P 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 428 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 459 average time/residue: 0.4928 time to fit residues: 353.7154 Evaluate side-chains 409 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 380 time to evaluate : 3.979 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3519 time to fit residues: 24.0100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 354 optimal weight: 2.9990 chunk 383 optimal weight: 4.9990 chunk 315 optimal weight: 5.9990 chunk 351 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 214 ASN C1108 ASN C1236 ASN C1313 HIS D 157 GLN D 196 GLN D 294 ASN D 341 ASN D 910 ASN D 962 ASN ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 GLN Q 151 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 33440 Z= 0.503 Angle : 0.694 10.794 45676 Z= 0.361 Chirality : 0.046 0.195 5175 Planarity : 0.005 0.054 5519 Dihedral : 16.217 89.195 5621 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.93 % Allowed : 16.29 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 3802 helix: 0.30 (0.13), residues: 1591 sheet: -2.04 (0.24), residues: 394 loop : -2.21 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 15 HIS 0.009 0.001 HIS D 430 PHE 0.027 0.002 PHE F 221 TYR 0.031 0.002 TYR F 148 ARG 0.009 0.001 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 395 time to evaluate : 4.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 33 residues processed: 439 average time/residue: 0.4812 time to fit residues: 338.2719 Evaluate side-chains 389 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 356 time to evaluate : 3.352 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3106 time to fit residues: 24.1308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 356 optimal weight: 4.9990 chunk 376 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 337 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 219 GLN C1236 ASN D 196 GLN D 341 ASN ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN P 12 GLN P 135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33440 Z= 0.186 Angle : 0.544 10.043 45676 Z= 0.286 Chirality : 0.041 0.158 5175 Planarity : 0.004 0.052 5519 Dihedral : 16.014 89.957 5621 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.50 % Allowed : 17.70 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3802 helix: 0.88 (0.13), residues: 1596 sheet: -1.75 (0.25), residues: 401 loop : -1.96 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP P 15 HIS 0.003 0.001 HIS P 102 PHE 0.042 0.001 PHE F 221 TYR 0.043 0.001 TYR F 137 ARG 0.009 0.000 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 398 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 23 residues processed: 430 average time/residue: 0.4889 time to fit residues: 338.5704 Evaluate side-chains 385 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 362 time to evaluate : 3.551 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3086 time to fit residues: 19.0638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 280 optimal weight: 0.0070 chunk 155 optimal weight: 0.0470 chunk 321 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 338 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 overall best weight: 3.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 490 GLN C 686 GLN D 196 GLN D 341 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 33440 Z= 0.381 Angle : 0.625 10.467 45676 Z= 0.325 Chirality : 0.043 0.162 5175 Planarity : 0.004 0.050 5519 Dihedral : 16.086 88.419 5621 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.44 % Allowed : 19.35 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 3802 helix: 0.81 (0.13), residues: 1601 sheet: -1.75 (0.25), residues: 409 loop : -1.86 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D1193 HIS 0.007 0.001 HIS D 430 PHE 0.044 0.002 PHE F 221 TYR 0.029 0.002 TYR F 421 ARG 0.009 0.000 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 369 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 30 residues processed: 406 average time/residue: 0.4785 time to fit residues: 311.1955 Evaluate side-chains 377 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 347 time to evaluate : 3.273 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3172 time to fit residues: 22.3777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 0.9980 chunk 339 optimal weight: 30.0000 chunk 74 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 377 optimal weight: 4.9990 chunk 313 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN D 196 GLN D 341 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33440 Z= 0.189 Angle : 0.548 11.583 45676 Z= 0.286 Chirality : 0.040 0.149 5175 Planarity : 0.003 0.050 5519 Dihedral : 15.938 89.706 5621 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.92 % Allowed : 20.12 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3802 helix: 1.13 (0.13), residues: 1596 sheet: -1.50 (0.25), residues: 415 loop : -1.68 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP P 15 HIS 0.003 0.001 HIS D 430 PHE 0.043 0.001 PHE F 221 TYR 0.041 0.001 TYR F 137 ARG 0.011 0.000 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 388 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 406 average time/residue: 0.4827 time to fit residues: 312.7228 Evaluate side-chains 386 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 369 time to evaluate : 3.512 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2926 time to fit residues: 14.2889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 214 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 210 optimal weight: 0.4980 chunk 375 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 235 ASN C1108 ASN D 196 GLN D 341 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33440 Z= 0.234 Angle : 0.565 11.412 45676 Z= 0.296 Chirality : 0.041 0.199 5175 Planarity : 0.004 0.051 5519 Dihedral : 15.904 89.120 5621 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.61 % Allowed : 21.28 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3802 helix: 1.20 (0.13), residues: 1596 sheet: -1.37 (0.26), residues: 394 loop : -1.59 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP P 15 HIS 0.004 0.001 HIS D 430 PHE 0.041 0.001 PHE F 221 TYR 0.041 0.001 TYR F 137 ARG 0.016 0.000 ARG F 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 376 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 387 average time/residue: 0.4812 time to fit residues: 297.0306 Evaluate side-chains 371 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 363 time to evaluate : 3.719 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3200 time to fit residues: 10.0989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 224 optimal weight: 0.9980 chunk 113 optimal weight: 0.0670 chunk 73 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 238 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 295 optimal weight: 0.0370 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C1008 GLN D 196 GLN D 341 ASN ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33440 Z= 0.142 Angle : 0.534 11.435 45676 Z= 0.279 Chirality : 0.040 0.186 5175 Planarity : 0.003 0.048 5519 Dihedral : 15.744 89.940 5621 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.46 % Allowed : 21.74 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3802 helix: 1.42 (0.13), residues: 1601 sheet: -1.13 (0.26), residues: 389 loop : -1.49 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP P 15 HIS 0.006 0.000 HIS P 13 PHE 0.031 0.001 PHE F 221 TYR 0.037 0.001 TYR F 137 ARG 0.013 0.000 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 396 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 406 average time/residue: 0.4860 time to fit residues: 315.0220 Evaluate side-chains 372 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 366 time to evaluate : 3.365 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3063 time to fit residues: 8.0824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 6.9990 chunk 360 optimal weight: 6.9990 chunk 328 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 275 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 331 optimal weight: 0.9990 chunk 349 optimal weight: 20.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C1108 ASN D 341 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33440 Z= 0.308 Angle : 0.605 13.279 45676 Z= 0.313 Chirality : 0.042 0.178 5175 Planarity : 0.004 0.057 5519 Dihedral : 15.848 88.853 5621 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.61 % Allowed : 22.01 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3802 helix: 1.19 (0.13), residues: 1606 sheet: -1.20 (0.26), residues: 387 loop : -1.45 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP P 15 HIS 0.005 0.001 HIS D 430 PHE 0.034 0.001 PHE F 221 TYR 0.035 0.001 TYR F 137 ARG 0.013 0.000 ARG D1345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 368 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 375 average time/residue: 0.5112 time to fit residues: 302.9409 Evaluate side-chains 372 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 358 time to evaluate : 3.545 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3101 time to fit residues: 12.9978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 0.9990 chunk 370 optimal weight: 0.9990 chunk 226 optimal weight: 0.0020 chunk 175 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 357 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 238 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 120 GLN C 193 ASN D 341 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33440 Z= 0.163 Angle : 0.564 14.492 45676 Z= 0.293 Chirality : 0.040 0.183 5175 Planarity : 0.003 0.056 5519 Dihedral : 15.752 89.538 5621 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.18 % Allowed : 22.16 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3802 helix: 1.40 (0.13), residues: 1600 sheet: -0.99 (0.26), residues: 389 loop : -1.37 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP P 15 HIS 0.004 0.001 HIS P 90 PHE 0.031 0.001 PHE F 221 TYR 0.052 0.001 TYR D 140 ARG 0.017 0.000 ARG F 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 369 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 371 average time/residue: 0.5369 time to fit residues: 317.1906 Evaluate side-chains 365 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 360 time to evaluate : 3.575 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3350 time to fit residues: 7.9639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 0.7980 chunk 329 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 285 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 309 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 318 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 208 ASN C 193 ASN C1108 ASN D 489 ASN ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.179733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.147975 restraints weight = 41302.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148429 restraints weight = 107713.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.149691 restraints weight = 68302.602| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33440 Z= 0.152 Angle : 0.562 15.375 45676 Z= 0.291 Chirality : 0.040 0.184 5175 Planarity : 0.003 0.056 5519 Dihedral : 15.675 89.843 5621 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.37 % Allowed : 22.53 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3802 helix: 1.50 (0.13), residues: 1602 sheet: -0.87 (0.26), residues: 401 loop : -1.32 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP P 15 HIS 0.005 0.000 HIS P 90 PHE 0.031 0.001 PHE F 221 TYR 0.061 0.001 TYR D 140 ARG 0.015 0.000 ARG F 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6796.59 seconds wall clock time: 124 minutes 26.85 seconds (7466.85 seconds total)