Starting phenix.real_space_refine on Tue Feb 20 08:57:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2024/6p19_20234.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2024/6p19_20234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2024/6p19_20234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2024/6p19_20234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2024/6p19_20234.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2024/6p19_20234.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 66 5.49 5 Mg 1 5.21 5 S 114 5.16 5 C 16968 2.51 5 N 4853 2.21 5 O 5412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C ASP 340": "OD1" <-> "OD2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 549": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ASP 596": "OD1" <-> "OD2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C ASP 728": "OD1" <-> "OD2" Residue "C ASP 739": "OD1" <-> "OD2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 930": "OD1" <-> "OD2" Residue "C GLU 940": "OE1" <-> "OE2" Residue "C ASP 959": "OD1" <-> "OD2" Residue "C GLU 1016": "OE1" <-> "OE2" Residue "C ASP 1019": "OD1" <-> "OD2" Residue "C GLU 1026": "OE1" <-> "OE2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1064": "OD1" <-> "OD2" Residue "C TYR 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1088": "OD1" <-> "OD2" Residue "C ASP 1203": "OD1" <-> "OD2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1240": "OD1" <-> "OD2" Residue "C TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1297": "OD1" <-> "OD2" Residue "C ASP 1310": "OD1" <-> "OD2" Residue "C GLU 1342": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D ASP 684": "OD1" <-> "OD2" Residue "D GLU 765": "OE1" <-> "OE2" Residue "D ASP 837": "OD1" <-> "OD2" Residue "D ASP 902": "OD1" <-> "OD2" Residue "D PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1039": "OD1" <-> "OD2" Residue "D ASP 1051": "OD1" <-> "OD2" Residue "D GLU 1052": "OE1" <-> "OE2" Residue "D ASP 1082": "OD1" <-> "OD2" Residue "D ASP 1087": "OD1" <-> "OD2" Residue "D TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1110": "OE1" <-> "OE2" Residue "D ASP 1111": "OD1" <-> "OD2" Residue "D GLU 1168": "OE1" <-> "OE2" Residue "D ASP 1181": "OD1" <-> "OD2" Residue "D TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1188": "OE1" <-> "OE2" Residue "D ASP 1208": "OD1" <-> "OD2" Residue "D ASP 1273": "OD1" <-> "OD2" Residue "D GLU 1291": "OE1" <-> "OE2" Residue "D ASP 1368": "OD1" <-> "OD2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "Q GLU 14": "OE1" <-> "OE2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ASP 61": "OD1" <-> "OD2" Residue "Q GLU 129": "OE1" <-> "OE2" Residue "Q GLU 132": "OE1" <-> "OE2" Residue "Q PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 156": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27416 Number of models: 1 Model: "" Number of chains: 10 Chain: "1" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 478 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "2" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 542 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} 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: 10437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1324, 10437 Classifications: {'peptide': 1324} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1268} Chain breaks: 1 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: "Q" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1129 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 1 Chain: "R" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 355 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 13} 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 15468 SG CYS D 70 43.245 119.165 62.351 1.00103.34 S ATOM 15482 SG CYS D 72 44.915 122.455 61.689 1.00 94.59 S ATOM 21302 SG CYS D 814 41.460 52.961 47.558 1.00 74.88 S ATOM 21867 SG CYS D 888 43.473 56.080 48.436 1.00 69.19 S ATOM 21918 SG CYS D 895 41.008 54.351 50.914 1.00 60.42 S ATOM 21939 SG CYS D 898 43.952 51.936 49.962 1.00 58.11 S Time building chain proxies: 14.17, per 1000 atoms: 0.52 Number of scatterers: 27416 At special positions: 0 Unit cell: (141.312, 137.216, 146.432, 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 114 16.00 P 66 15.00 Mg 1 11.99 O 5412 8.00 N 4853 7.00 C 16968 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: 11.69 Conformation dependent library (CDL) restraints added in 4.6 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 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 : 6 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6140 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 45 sheets defined 40.2% alpha, 15.0% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 9.28 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.262A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.450A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (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 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.534A 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 207 through 213 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: 3.719A 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 346 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.550A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.879A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.797A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.604A 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: 4.086A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.736A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 614 removed outlier: 4.310A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 609 through 614' Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.281A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.506A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (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 861 through 865 removed outlier: 3.860A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 993 through 997 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.643A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (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 1160 through 1164 removed outlier: 3.941A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 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 1311 Processing helix chain 'C' and resid 1320 through 1334 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: 3.671A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.636A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 4.483A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.538A pdb=" N ARG D 250 " --> pdb=" O PRO D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.090A 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 404 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 504 through 515 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.844A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.709A 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: 4.006A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.229A 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 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.622A 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 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.055A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1316 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: 4.457A 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 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 39 through 48 Processing helix chain 'Q' and resid 60 through 74 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 3.986A pdb=" N PHE Q 81 " --> pdb=" O ASP Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 103 Processing helix chain 'Q' and resid 123 through 151 Proline residue: Q 143 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 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: 7.510A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY A 149 " --> pdb=" O GLY A 53 " (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 111 removed outlier: 3.627A 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 removed outlier: 3.509A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.835A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.405A 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: 3.686A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.078A 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: 3.661A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.625A 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 108 through 111 removed outlier: 7.259A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.556A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.847A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.708A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C 106 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL C 114 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.234A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'C' and resid 158 through 160 removed outlier: 3.830A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AC1, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.843A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.894A 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: 3.589A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.510A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.510A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 615 through 617 Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.940A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.094A 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 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 7.675A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.668A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.987A pdb=" N LYS C 914 " --> pdb=" O THR C 888 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1269 through 1270 removed outlier: 3.591A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1341 Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.319A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.132A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 254 removed outlier: 4.238A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 350 through 357 removed outlier: 7.612A pdb=" N ALA D 446 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.555A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 958 through 961 removed outlier: 3.551A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 966 removed outlier: 4.302A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1025 through 1026 removed outlier: 3.615A pdb=" N ILE D1124 " --> pdb=" O MET D1025 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.756A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.950A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1174 through 1178 removed outlier: 6.520A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1280 through 1281 removed outlier: 3.575A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL D1267 " --> pdb=" O THR D1301 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 13.77 Time building geometry restraints manager: 12.40 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: 7017 1.33 - 1.45: 5218 1.45 - 1.57: 15411 1.57 - 1.69: 127 1.69 - 1.82: 198 Bond restraints: 27971 Sorted by residual: bond pdb=" N ILE B 211 " pdb=" CA ILE B 211 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.07e-02 8.73e+03 1.35e+01 bond pdb=" C PHE D 49 " pdb=" N LYS D 50 " ideal model delta sigma weight residual 1.333 1.253 0.080 2.74e-02 1.33e+03 8.48e+00 bond pdb=" CA MET D 644 " pdb=" CB MET D 644 " ideal model delta sigma weight residual 1.526 1.481 0.046 1.76e-02 3.23e+03 6.71e+00 bond pdb=" N LYS C 991 " pdb=" CA LYS C 991 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.80e+00 bond pdb=" CG LEU C 817 " pdb=" CD1 LEU C 817 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.69e+00 ... (remaining 27966 not shown) Histogram of bond angle deviations from ideal: 96.48 - 103.99: 601 103.99 - 111.50: 11995 111.50 - 119.01: 11034 119.01 - 126.52: 13993 126.52 - 134.03: 443 Bond angle restraints: 38066 Sorted by residual: angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" N ILE B 130 " pdb=" CA ILE B 130 " pdb=" C ILE B 130 " ideal model delta sigma weight residual 111.48 106.92 4.56 9.40e-01 1.13e+00 2.35e+01 angle pdb=" C SER D 122 " pdb=" N ARG D 123 " pdb=" CA ARG D 123 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.26e+01 angle pdb=" C ARG D 709 " pdb=" N ASP D 710 " pdb=" CA ASP D 710 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" N LYS C 991 " pdb=" CA LYS C 991 " pdb=" C LYS C 991 " ideal model delta sigma weight residual 113.18 108.53 4.65 1.21e+00 6.83e-01 1.48e+01 ... (remaining 38061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.92: 16178 29.92 - 59.84: 807 59.84 - 89.76: 88 89.76 - 119.68: 1 119.68 - 149.60: 1 Dihedral angle restraints: 17075 sinusoidal: 7530 harmonic: 9545 Sorted by residual: dihedral pdb=" O4' U R 58 " pdb=" C1' U R 58 " pdb=" N1 U R 58 " pdb=" C2 U R 58 " ideal model delta sinusoidal sigma weight residual 200.00 50.40 149.60 1 1.50e+01 4.44e-03 7.95e+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 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA VAL B 192 " pdb=" C VAL B 192 " pdb=" N GLU B 193 " pdb=" CA GLU B 193 " ideal model delta harmonic sigma weight residual 180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 17072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3246 0.060 - 0.120: 910 0.120 - 0.180: 151 0.180 - 0.240: 26 0.240 - 0.300: 4 Chirality restraints: 4337 Sorted by residual: chirality pdb=" CB ILE D1177 " pdb=" CA ILE D1177 " pdb=" CG1 ILE D1177 " pdb=" CG2 ILE D1177 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB VAL C1094 " pdb=" CA VAL C1094 " pdb=" CG1 VAL C1094 " pdb=" CG2 VAL C1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE C1060 " pdb=" CA ILE C1060 " pdb=" CG1 ILE C1060 " pdb=" CG2 ILE C1060 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 4334 not shown) Planarity restraints: 4749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 504 " -0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLN D 504 " 0.085 2.00e-02 2.50e+03 pdb=" O GLN D 504 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP D 505 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 450 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO D 451 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 451 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 451 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 209 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C GLY B 209 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY B 209 " 0.017 2.00e-02 2.50e+03 pdb=" N THR B 210 " 0.015 2.00e-02 2.50e+03 ... (remaining 4746 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 452 2.63 - 3.20: 23145 3.20 - 3.76: 44219 3.76 - 4.33: 57163 4.33 - 4.90: 93319 Nonbonded interactions: 218298 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.061 2.170 nonbonded pdb=" O3' A R 70 " pdb="MG MG D1503 " model vdw 2.075 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.108 2.170 nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1503 " model vdw 2.217 2.170 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1501 " model vdw 2.222 2.310 ... (remaining 218293 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' } 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: 0.780 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: 0.020 Extract box with map and model: 5.210 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 85.730 Find NCS groups from input model: 1.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.008 0.091 27971 Z= 0.523 Angle : 0.920 10.665 38066 Z= 0.507 Chirality : 0.056 0.300 4337 Planarity : 0.007 0.073 4749 Dihedral : 16.831 149.597 10935 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.46 % Allowed : 9.93 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -3.93 (0.11), residues: 3303 helix: -2.40 (0.10), residues: 1223 sheet: -2.64 (0.24), residues: 352 loop : -2.78 (0.12), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 580 HIS 0.015 0.002 HIS D 430 PHE 0.025 0.002 PHE Q 43 TYR 0.030 0.002 TYR C1281 ARG 0.005 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 401 time to evaluate : 3.156 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: A 10 LYS cc_start: 0.8881 (mppt) cc_final: 0.8599 (mmtt) REVERT: A 58 GLU cc_start: 0.7765 (mp0) cc_final: 0.7474 (mt-10) REVERT: A 117 HIS cc_start: 0.8606 (p-80) cc_final: 0.8351 (p-80) REVERT: B 104 LYS cc_start: 0.7986 (tptp) cc_final: 0.7645 (tptp) REVERT: B 128 HIS cc_start: 0.8810 (t70) cc_final: 0.8425 (t-90) REVERT: C 409 LEU cc_start: 0.9156 (mt) cc_final: 0.8779 (tp) REVERT: C 432 LEU cc_start: 0.9002 (tp) cc_final: 0.8800 (tp) REVERT: C 1131 MET cc_start: 0.8502 (mtm) cc_final: 0.8206 (mtp) REVERT: C 1273 MET cc_start: 0.8511 (mtt) cc_final: 0.8198 (mtt) REVERT: C 1329 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7921 (mt-10) REVERT: D 196 GLN cc_start: 0.8992 (tp40) cc_final: 0.8384 (tp-100) REVERT: D 197 GLU cc_start: 0.8568 (mp0) cc_final: 0.8020 (mp0) REVERT: D 458 ASN cc_start: 0.8842 (m110) cc_final: 0.8148 (t0) REVERT: D 892 PHE cc_start: 0.7641 (m-80) cc_final: 0.6597 (t80) REVERT: D 999 TYR cc_start: 0.6809 (t80) cc_final: 0.6556 (t80) REVERT: D 1241 TYR cc_start: 0.8481 (m-80) cc_final: 0.8240 (m-80) REVERT: E 63 ILE cc_start: 0.8601 (mt) cc_final: 0.8311 (mt) outliers start: 13 outliers final: 8 residues processed: 414 average time/residue: 0.4424 time to fit residues: 277.4012 Evaluate side-chains 290 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 282 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 1176 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 0.0470 chunk 253 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 303 optimal weight: 10.0000 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 23 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 208 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 314 ASN C 343 HIS C 517 GLN C 580 GLN C 618 GLN C 659 GLN C 766 ASN C 767 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN C1256 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 200 GLN D 232 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN D 680 ASN D 875 ASN D 962 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1114 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1259 GLN E 29 GLN Q 17 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27971 Z= 0.187 Angle : 0.587 11.032 38066 Z= 0.305 Chirality : 0.042 0.159 4337 Planarity : 0.005 0.057 4749 Dihedral : 14.124 147.187 4443 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.01 % Allowed : 15.37 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -2.36 (0.13), residues: 3303 helix: -0.45 (0.14), residues: 1232 sheet: -2.05 (0.26), residues: 331 loop : -2.36 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1193 HIS 0.008 0.001 HIS Q 13 PHE 0.019 0.001 PHE C1025 TYR 0.033 0.001 TYR C 62 ARG 0.010 0.000 ARG C 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 317 time to evaluate : 3.045 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: A 117 HIS cc_start: 0.8488 (p-80) cc_final: 0.8253 (p-80) REVERT: A 185 TYR cc_start: 0.8741 (p90) cc_final: 0.8494 (p90) REVERT: B 104 LYS cc_start: 0.8314 (tptp) cc_final: 0.7982 (tptp) REVERT: B 145 LYS cc_start: 0.9095 (tptp) cc_final: 0.8801 (tptp) REVERT: C 124 MET cc_start: 0.8240 (ptp) cc_final: 0.7953 (ptp) REVERT: C 1014 LEU cc_start: 0.1444 (OUTLIER) cc_final: 0.1095 (tt) REVERT: C 1171 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7597 (ttp-170) REVERT: C 1290 MET cc_start: 0.8702 (ttm) cc_final: 0.8480 (ttm) REVERT: D 136 GLU cc_start: 0.8238 (tp30) cc_final: 0.7978 (tp30) REVERT: D 196 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8543 (tp-100) REVERT: D 458 ASN cc_start: 0.8910 (m110) cc_final: 0.8397 (t0) REVERT: D 785 ASP cc_start: 0.7406 (t0) cc_final: 0.7161 (t70) REVERT: D 892 PHE cc_start: 0.7608 (m-80) cc_final: 0.6554 (t80) REVERT: D 1040 MET cc_start: 0.3117 (ptp) cc_final: 0.2477 (pmm) REVERT: D 1241 TYR cc_start: 0.8120 (m-80) cc_final: 0.7861 (m-80) REVERT: Q 36 MET cc_start: 0.5975 (tpt) cc_final: 0.5598 (tpt) REVERT: Q 138 LEU cc_start: 0.9018 (mm) cc_final: 0.8813 (mm) outliers start: 57 outliers final: 25 residues processed: 364 average time/residue: 0.4086 time to fit residues: 237.9412 Evaluate side-chains 295 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 269 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 252 optimal weight: 0.0040 chunk 206 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 303 optimal weight: 6.9990 chunk 328 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 301 optimal weight: 0.0170 chunk 103 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 overall best weight: 2.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS C 856 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS D 875 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27971 Z= 0.253 Angle : 0.594 11.793 38066 Z= 0.307 Chirality : 0.042 0.162 4337 Planarity : 0.004 0.055 4749 Dihedral : 14.013 148.115 4442 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.37 % Allowed : 17.56 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -1.82 (0.14), residues: 3303 helix: 0.19 (0.14), residues: 1239 sheet: -1.88 (0.26), residues: 350 loop : -2.18 (0.13), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 997 HIS 0.007 0.001 HIS D 430 PHE 0.024 0.001 PHE D1145 TYR 0.016 0.001 TYR C 291 ARG 0.008 0.000 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 288 time to evaluate : 3.476 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: A 10 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8255 (mmtp) REVERT: A 185 TYR cc_start: 0.8767 (p90) cc_final: 0.8520 (p90) REVERT: B 104 LYS cc_start: 0.8306 (tptp) cc_final: 0.7968 (tptp) REVERT: B 145 LYS cc_start: 0.9079 (tptp) cc_final: 0.8839 (tptt) REVERT: C 41 GLN cc_start: 0.8280 (mt0) cc_final: 0.7874 (pp30) REVERT: C 124 MET cc_start: 0.8362 (ptp) cc_final: 0.7827 (ptp) REVERT: C 369 MET cc_start: 0.8242 (tmm) cc_final: 0.7984 (tmm) REVERT: C 687 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7477 (ttp-170) REVERT: C 1014 LEU cc_start: 0.1365 (OUTLIER) cc_final: 0.1000 (tt) REVERT: D 136 GLU cc_start: 0.8267 (tp30) cc_final: 0.8026 (tp30) REVERT: D 151 MET cc_start: 0.7754 (pmm) cc_final: 0.7366 (pmm) REVERT: D 196 GLN cc_start: 0.9034 (tp-100) cc_final: 0.8498 (tp-100) REVERT: D 197 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: D 458 ASN cc_start: 0.8933 (m110) cc_final: 0.8375 (t0) REVERT: D 892 PHE cc_start: 0.7692 (m-80) cc_final: 0.6599 (t80) REVERT: D 1040 MET cc_start: 0.3036 (ptp) cc_final: 0.2434 (pmm) REVERT: D 1241 TYR cc_start: 0.8213 (m-80) cc_final: 0.7946 (m-80) REVERT: Q 36 MET cc_start: 0.6074 (tpt) cc_final: 0.5648 (tpt) REVERT: Q 74 MET cc_start: 0.7530 (mmp) cc_final: 0.7068 (mpp) outliers start: 67 outliers final: 42 residues processed: 339 average time/residue: 0.3803 time to fit residues: 210.1653 Evaluate side-chains 321 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 276 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1083 GLU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 300 optimal weight: 0.0770 chunk 228 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 322 optimal weight: 20.0000 chunk 159 optimal weight: 0.9990 chunk 289 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 447 HIS C 659 GLN C 673 HIS ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN D 712 GLN D 875 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27971 Z= 0.233 Angle : 0.579 11.633 38066 Z= 0.296 Chirality : 0.042 0.254 4337 Planarity : 0.004 0.048 4749 Dihedral : 13.936 147.478 4442 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.18 % Allowed : 17.98 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -1.45 (0.14), residues: 3303 helix: 0.53 (0.15), residues: 1238 sheet: -1.60 (0.27), residues: 349 loop : -2.02 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 997 HIS 0.006 0.001 HIS D 430 PHE 0.019 0.001 PHE D 172 TYR 0.015 0.001 TYR C 172 ARG 0.008 0.000 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 284 time to evaluate : 3.128 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: A 10 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8269 (mmmm) REVERT: A 104 LYS cc_start: 0.8757 (tttt) cc_final: 0.8524 (tttm) REVERT: A 185 TYR cc_start: 0.8757 (p90) cc_final: 0.8545 (p90) REVERT: B 104 LYS cc_start: 0.8314 (tptp) cc_final: 0.8061 (tptp) REVERT: B 145 LYS cc_start: 0.9002 (tptp) cc_final: 0.8783 (tptt) REVERT: C 124 MET cc_start: 0.8404 (ptp) cc_final: 0.7948 (ptp) REVERT: C 624 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.7018 (p0) REVERT: C 687 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7446 (ttp80) REVERT: C 1014 LEU cc_start: 0.1218 (OUTLIER) cc_final: 0.0845 (tt) REVERT: C 1171 ARG cc_start: 0.7826 (ttp80) cc_final: 0.7612 (ttp-170) REVERT: C 1290 MET cc_start: 0.8788 (ttm) cc_final: 0.8536 (ttm) REVERT: D 136 GLU cc_start: 0.8268 (tp30) cc_final: 0.7982 (tp30) REVERT: D 196 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8492 (tp-100) REVERT: D 197 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: D 458 ASN cc_start: 0.8902 (m110) cc_final: 0.8339 (t0) REVERT: D 560 ASN cc_start: 0.6408 (OUTLIER) cc_final: 0.6100 (p0) REVERT: D 892 PHE cc_start: 0.7667 (m-80) cc_final: 0.6533 (t80) REVERT: D 1040 MET cc_start: 0.2975 (ptp) cc_final: 0.2079 (pmm) REVERT: D 1241 TYR cc_start: 0.8178 (m-80) cc_final: 0.7923 (m-80) REVERT: E 53 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8054 (mm-30) REVERT: Q 36 MET cc_start: 0.5974 (tpt) cc_final: 0.5495 (tpt) outliers start: 90 outliers final: 64 residues processed: 357 average time/residue: 0.3681 time to fit residues: 215.3567 Evaluate side-chains 333 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 264 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1083 GLU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 81 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 268 optimal weight: 0.2980 chunk 183 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 240 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 275 optimal weight: 0.1980 chunk 223 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 289 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27971 Z= 0.152 Angle : 0.549 11.948 38066 Z= 0.279 Chirality : 0.041 0.138 4337 Planarity : 0.004 0.046 4749 Dihedral : 13.837 146.591 4442 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.86 % Allowed : 19.64 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -1.15 (0.14), residues: 3303 helix: 0.78 (0.15), residues: 1233 sheet: -1.27 (0.28), residues: 327 loop : -1.88 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 997 HIS 0.008 0.001 HIS Q 13 PHE 0.019 0.001 PHE C1025 TYR 0.018 0.001 TYR Q 88 ARG 0.012 0.000 ARG C 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 300 time to evaluate : 3.779 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: A 10 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8202 (mmmm) REVERT: A 104 LYS cc_start: 0.8711 (tttt) cc_final: 0.8490 (tttm) REVERT: B 104 LYS cc_start: 0.8317 (tptp) cc_final: 0.8067 (tptp) REVERT: C 856 ASN cc_start: 0.6470 (OUTLIER) cc_final: 0.6044 (t0) REVERT: C 1014 LEU cc_start: 0.1187 (OUTLIER) cc_final: 0.0680 (tt) REVERT: C 1290 MET cc_start: 0.8754 (ttm) cc_final: 0.8523 (ttm) REVERT: C 1316 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6863 (tm-30) REVERT: D 196 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8493 (tp-100) REVERT: D 197 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8495 (mp0) REVERT: D 227 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8674 (m-80) REVERT: D 293 ARG cc_start: 0.8329 (ttp-110) cc_final: 0.8028 (ttm110) REVERT: D 458 ASN cc_start: 0.8848 (m110) cc_final: 0.8292 (t0) REVERT: D 560 ASN cc_start: 0.6361 (OUTLIER) cc_final: 0.6077 (p0) REVERT: D 892 PHE cc_start: 0.7585 (m-80) cc_final: 0.6471 (t80) REVERT: D 1241 TYR cc_start: 0.8044 (m-80) cc_final: 0.7791 (m-80) REVERT: Q 36 MET cc_start: 0.5850 (tpt) cc_final: 0.5422 (tpt) REVERT: Q 74 MET cc_start: 0.7318 (mtm) cc_final: 0.6603 (mpp) outliers start: 81 outliers final: 53 residues processed: 367 average time/residue: 0.3680 time to fit residues: 219.8801 Evaluate side-chains 334 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 276 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 62 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 108 optimal weight: 9.9990 chunk 290 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 323 optimal weight: 9.9990 chunk 268 optimal weight: 0.1980 chunk 149 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27971 Z= 0.153 Angle : 0.552 13.563 38066 Z= 0.280 Chirality : 0.041 0.242 4337 Planarity : 0.004 0.049 4749 Dihedral : 13.773 147.561 4442 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.07 % Allowed : 20.66 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -0.97 (0.14), residues: 3303 helix: 0.93 (0.15), residues: 1237 sheet: -1.12 (0.27), residues: 350 loop : -1.78 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 997 HIS 0.005 0.001 HIS Q 13 PHE 0.018 0.001 PHE C1025 TYR 0.024 0.001 TYR A 185 ARG 0.008 0.000 ARG C1034 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 294 time to evaluate : 3.012 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: A 10 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8164 (mmmm) REVERT: A 104 LYS cc_start: 0.8736 (tttt) cc_final: 0.8517 (tttm) REVERT: B 104 LYS cc_start: 0.8263 (tptp) cc_final: 0.8013 (tptp) REVERT: C 87 ILE cc_start: 0.8215 (mm) cc_final: 0.7885 (pt) REVERT: C 588 GLU cc_start: 0.8434 (pm20) cc_final: 0.7578 (pt0) REVERT: C 1014 LEU cc_start: 0.0786 (OUTLIER) cc_final: 0.0421 (tt) REVERT: C 1060 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8162 (mt) REVERT: C 1316 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6831 (tm-30) REVERT: D 75 TYR cc_start: 0.7932 (m-80) cc_final: 0.7670 (m-10) REVERT: D 139 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8303 (mm) REVERT: D 196 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8499 (tp-100) REVERT: D 197 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: D 227 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8603 (m-80) REVERT: D 458 ASN cc_start: 0.8829 (m110) cc_final: 0.8312 (t0) REVERT: D 560 ASN cc_start: 0.6343 (OUTLIER) cc_final: 0.6053 (p0) REVERT: D 892 PHE cc_start: 0.7574 (m-80) cc_final: 0.6462 (t80) REVERT: D 1040 MET cc_start: 0.2468 (ptp) cc_final: 0.1644 (pmm) REVERT: D 1241 TYR cc_start: 0.8022 (m-80) cc_final: 0.7763 (m-80) outliers start: 87 outliers final: 62 residues processed: 364 average time/residue: 0.3746 time to fit residues: 223.3232 Evaluate side-chains 344 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 276 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 62 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 311 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 184 optimal weight: 0.2980 chunk 235 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 chunk 180 optimal weight: 0.9980 chunk 321 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 148 optimal weight: 50.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 147 GLN B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1023 HIS ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN D 875 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27971 Z= 0.210 Angle : 0.576 13.468 38066 Z= 0.291 Chirality : 0.041 0.330 4337 Planarity : 0.004 0.049 4749 Dihedral : 13.761 148.129 4440 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.00 % Allowed : 21.23 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -0.93 (0.14), residues: 3303 helix: 0.96 (0.15), residues: 1235 sheet: -1.08 (0.27), residues: 356 loop : -1.77 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 997 HIS 0.005 0.001 HIS D 430 PHE 0.018 0.001 PHE C1025 TYR 0.019 0.001 TYR Q 28 ARG 0.011 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 283 time to evaluate : 3.096 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: A 10 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8116 (mmmm) REVERT: A 104 LYS cc_start: 0.8798 (tttt) cc_final: 0.8548 (tttm) REVERT: B 104 LYS cc_start: 0.8219 (tptp) cc_final: 0.7956 (tptp) REVERT: B 212 ASP cc_start: 0.7174 (t0) cc_final: 0.6768 (t0) REVERT: C 87 ILE cc_start: 0.8201 (mm) cc_final: 0.7888 (pt) REVERT: C 687 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7317 (ttp80) REVERT: C 805 MET cc_start: 0.8382 (ptp) cc_final: 0.7933 (ptp) REVERT: C 856 ASN cc_start: 0.6508 (OUTLIER) cc_final: 0.5982 (t0) REVERT: C 1014 LEU cc_start: 0.0511 (OUTLIER) cc_final: 0.0246 (tt) REVERT: C 1316 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6875 (tm-30) REVERT: D 75 TYR cc_start: 0.7930 (m-80) cc_final: 0.7675 (m-10) REVERT: D 139 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8301 (mm) REVERT: D 180 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7395 (tmm) REVERT: D 196 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8485 (tp-100) REVERT: D 197 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: D 227 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: D 458 ASN cc_start: 0.8842 (m110) cc_final: 0.8271 (t0) REVERT: D 560 ASN cc_start: 0.6364 (OUTLIER) cc_final: 0.6067 (p0) REVERT: D 892 PHE cc_start: 0.7631 (m-80) cc_final: 0.6492 (t80) REVERT: D 1040 MET cc_start: 0.1877 (ptp) cc_final: 0.1197 (pmm) REVERT: D 1241 TYR cc_start: 0.8112 (m-80) cc_final: 0.7856 (m-80) REVERT: E 35 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8208 (mmtt) REVERT: E 53 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7756 (mm-30) outliers start: 85 outliers final: 61 residues processed: 352 average time/residue: 0.3788 time to fit residues: 216.7261 Evaluate side-chains 347 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 278 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 62 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 199 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 253 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27971 Z= 0.249 Angle : 0.602 17.223 38066 Z= 0.303 Chirality : 0.042 0.376 4337 Planarity : 0.004 0.047 4749 Dihedral : 13.740 147.908 4438 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.07 % Allowed : 21.44 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -0.91 (0.14), residues: 3303 helix: 0.93 (0.15), residues: 1235 sheet: -1.00 (0.27), residues: 361 loop : -1.73 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 997 HIS 0.006 0.001 HIS D 430 PHE 0.017 0.001 PHE C1025 TYR 0.019 0.001 TYR Q 28 ARG 0.012 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 280 time to evaluate : 3.651 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: B 104 LYS cc_start: 0.8166 (tptp) cc_final: 0.7889 (tptp) REVERT: C 687 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7397 (ttp80) REVERT: C 1014 LEU cc_start: 0.0477 (OUTLIER) cc_final: 0.0209 (tt) REVERT: C 1316 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6864 (tm-30) REVERT: D 75 TYR cc_start: 0.7969 (m-80) cc_final: 0.7712 (m-10) REVERT: D 139 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8316 (mm) REVERT: D 180 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7406 (tmm) REVERT: D 196 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8459 (tp-100) REVERT: D 197 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: D 227 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8677 (m-80) REVERT: D 458 ASN cc_start: 0.8779 (m110) cc_final: 0.8217 (t0) REVERT: D 560 ASN cc_start: 0.6450 (OUTLIER) cc_final: 0.6147 (p0) REVERT: D 892 PHE cc_start: 0.7702 (m-80) cc_final: 0.6525 (t80) REVERT: D 982 LEU cc_start: 0.8425 (pp) cc_final: 0.8041 (pt) REVERT: D 1040 MET cc_start: 0.1796 (ptp) cc_final: 0.1102 (pmm) REVERT: D 1241 TYR cc_start: 0.8171 (m-80) cc_final: 0.7926 (m-80) REVERT: E 35 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8207 (mmtt) REVERT: E 53 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7749 (mm-30) outliers start: 87 outliers final: 70 residues processed: 349 average time/residue: 0.3800 time to fit residues: 218.0215 Evaluate side-chains 349 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 272 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1083 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain Q residue 74 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 292 optimal weight: 9.9990 chunk 308 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 299 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 271 optimal weight: 0.9990 chunk 283 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.003 0.043 27971 Z= 0.182 Angle : 0.588 15.513 38066 Z= 0.292 Chirality : 0.042 0.381 4337 Planarity : 0.004 0.052 4749 Dihedral : 13.674 147.297 4438 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.90 % Allowed : 22.15 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -0.75 (0.14), residues: 3303 helix: 1.04 (0.15), residues: 1228 sheet: -0.78 (0.28), residues: 350 loop : -1.64 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 997 HIS 0.004 0.001 HIS D 430 PHE 0.017 0.001 PHE C1025 TYR 0.018 0.001 TYR Q 28 ARG 0.009 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 287 time to evaluate : 3.060 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: A 104 LYS cc_start: 0.8832 (tttt) cc_final: 0.8554 (tttm) REVERT: B 104 LYS cc_start: 0.8134 (tptp) cc_final: 0.7856 (tptp) REVERT: B 185 TYR cc_start: 0.9265 (p90) cc_final: 0.8858 (p90) REVERT: C 87 ILE cc_start: 0.8241 (mm) cc_final: 0.7920 (pt) REVERT: C 687 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7309 (ttp80) REVERT: C 1014 LEU cc_start: 0.0538 (OUTLIER) cc_final: 0.0290 (tt) REVERT: C 1316 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6803 (tm-30) REVERT: D 75 TYR cc_start: 0.7935 (m-80) cc_final: 0.7670 (m-10) REVERT: D 139 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8223 (mm) REVERT: D 180 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7384 (tmm) REVERT: D 196 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8480 (tp-100) REVERT: D 197 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: D 227 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: D 458 ASN cc_start: 0.8875 (m110) cc_final: 0.8252 (t0) REVERT: D 560 ASN cc_start: 0.6376 (OUTLIER) cc_final: 0.6051 (p0) REVERT: D 892 PHE cc_start: 0.7639 (m-80) cc_final: 0.6487 (t80) REVERT: D 982 LEU cc_start: 0.8385 (pp) cc_final: 0.8007 (pt) REVERT: D 1040 MET cc_start: 0.2276 (ptp) cc_final: 0.1414 (pmm) REVERT: D 1241 TYR cc_start: 0.8083 (m-80) cc_final: 0.7836 (m-80) REVERT: E 35 LYS cc_start: 0.8497 (mmtm) cc_final: 0.8231 (mmtt) REVERT: E 53 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7736 (mm-30) outliers start: 82 outliers final: 66 residues processed: 352 average time/residue: 0.3747 time to fit residues: 216.4613 Evaluate side-chains 352 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 279 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1083 GLU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain Q residue 74 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 196 optimal weight: 10.0000 chunk 317 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 220 optimal weight: 5.9990 chunk 332 optimal weight: 30.0000 chunk 306 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 204 optimal weight: 0.0980 chunk 162 optimal weight: 2.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 HIS B 147 GLN B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27971 Z= 0.235 Angle : 0.616 15.334 38066 Z= 0.307 Chirality : 0.042 0.386 4337 Planarity : 0.004 0.051 4749 Dihedral : 13.667 147.992 4438 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.65 % Allowed : 22.61 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -0.80 (0.14), residues: 3303 helix: 0.92 (0.15), residues: 1241 sheet: -0.85 (0.28), residues: 362 loop : -1.61 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 115 HIS 0.006 0.001 HIS D 430 PHE 0.015 0.001 PHE C1025 TYR 0.018 0.001 TYR Q 28 ARG 0.014 0.000 ARG E 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 277 time to evaluate : 2.821 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: A 104 LYS cc_start: 0.8894 (tttt) cc_final: 0.8596 (tttm) REVERT: B 104 LYS cc_start: 0.8211 (tptp) cc_final: 0.7934 (tptp) REVERT: B 185 TYR cc_start: 0.9296 (p90) cc_final: 0.8874 (p90) REVERT: C 87 ILE cc_start: 0.8259 (mm) cc_final: 0.7931 (pt) REVERT: C 370 MET cc_start: 0.8572 (tpp) cc_final: 0.8311 (tpt) REVERT: C 687 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7434 (ttp80) REVERT: C 1014 LEU cc_start: 0.0580 (OUTLIER) cc_final: 0.0331 (tt) REVERT: C 1316 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6810 (tm-30) REVERT: D 75 TYR cc_start: 0.7984 (m-80) cc_final: 0.7724 (m-10) REVERT: D 139 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8207 (mm) REVERT: D 180 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7490 (tmm) REVERT: D 196 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8457 (tp-100) REVERT: D 197 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: D 227 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8669 (m-80) REVERT: D 308 ASP cc_start: 0.7950 (t0) cc_final: 0.7698 (t0) REVERT: D 458 ASN cc_start: 0.8793 (m110) cc_final: 0.8207 (t0) REVERT: D 560 ASN cc_start: 0.6377 (OUTLIER) cc_final: 0.6038 (p0) REVERT: D 892 PHE cc_start: 0.7709 (m-80) cc_final: 0.6530 (t80) REVERT: D 982 LEU cc_start: 0.8433 (pp) cc_final: 0.8058 (pt) REVERT: D 1040 MET cc_start: 0.2035 (ptp) cc_final: 0.1280 (pmm) REVERT: D 1241 TYR cc_start: 0.8138 (m-80) cc_final: 0.7891 (m-80) REVERT: E 35 LYS cc_start: 0.8514 (mmtm) cc_final: 0.8205 (mmtt) REVERT: E 53 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7745 (mm-30) REVERT: Q 44 MET cc_start: 0.6022 (mmp) cc_final: 0.5270 (mmm) outliers start: 75 outliers final: 65 residues processed: 339 average time/residue: 0.3736 time to fit residues: 209.2988 Evaluate side-chains 343 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 271 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1083 GLU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain Q residue 74 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 210 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 81 optimal weight: 40.0000 chunk 244 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 272 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.137604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.100530 restraints weight = 54255.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098619 restraints weight = 55673.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.099928 restraints weight = 52555.641| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 27971 Z= 0.368 Angle : 0.679 14.893 38066 Z= 0.341 Chirality : 0.044 0.377 4337 Planarity : 0.004 0.051 4749 Dihedral : 13.794 147.900 4437 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.83 % Allowed : 22.50 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % 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: -0.96 (0.14), residues: 3303 helix: 0.73 (0.15), residues: 1239 sheet: -0.89 (0.27), residues: 372 loop : -1.66 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 115 HIS 0.009 0.001 HIS D 430 PHE 0.020 0.002 PHE C 804 TYR 0.018 0.002 TYR Q 28 ARG 0.012 0.000 ARG E 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5122.02 seconds wall clock time: 95 minutes 3.99 seconds (5703.99 seconds total)