Starting phenix.real_space_refine on Fri Jan 19 23:22:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh7_22184/01_2024/6xh7_22184.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh7_22184/01_2024/6xh7_22184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh7_22184/01_2024/6xh7_22184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh7_22184/01_2024/6xh7_22184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh7_22184/01_2024/6xh7_22184.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh7_22184/01_2024/6xh7_22184.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 Cu 2 5.60 5 P 102 5.49 5 S 143 5.16 5 C 20518 2.51 5 N 5923 2.21 5 O 6630 1.98 5 H 32688 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66008 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3556 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 21153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 21153 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 21011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21011 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1261 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 8105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 8105 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 15, 'TRANS': 481} Chain breaks: 1 Chain: "G" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2038 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "H" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2038 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "1" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1713 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "2" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1530 Classifications: {'DNA': 48} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29208 SG CYS D 70 101.300 60.291 84.140 1.00156.63 S ATOM 29237 SG CYS D 72 99.329 57.832 81.734 1.00162.79 S ATOM 29467 SG CYS D 85 102.080 59.990 80.347 1.00156.69 S ATOM 41049 SG CYS D 814 117.010 122.830 110.752 1.00105.16 S ATOM 42186 SG CYS D 888 114.486 119.690 109.343 1.00100.73 S ATOM 42277 SG CYS D 895 115.936 120.005 112.517 1.00 99.93 S ATOM 42314 SG CYS D 898 114.037 122.782 112.619 1.00 99.91 S ATOM 60491 SG CYS G 112 66.618 12.516 93.942 1.00209.55 S ATOM 60579 SG CYS G 120 69.335 14.269 95.461 1.00217.51 S ATOM 62529 SG CYS H 112 79.239 17.052 46.014 1.00204.04 S ATOM 62617 SG CYS H 120 78.517 20.414 45.878 1.00207.84 S Residues with excluded nonbonded symmetry interactions: 43 residue: pdb=" P DA 1 41 " occ=0.50 ... (30 atoms not shown) pdb=" H2 DA 1 41 " occ=0.50 residue: pdb=" P DC 1 42 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 42 " occ=0.50 residue: pdb=" P DC 1 43 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 43 " occ=0.50 residue: pdb=" P DT 1 44 " occ=0.50 ... (30 atoms not shown) pdb=" H6 DT 1 44 " occ=0.50 residue: pdb=" P DT 1 45 " occ=0.50 ... (30 atoms not shown) pdb=" H6 DT 1 45 " occ=0.50 residue: pdb=" P DC 1 46 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 46 " occ=0.50 residue: pdb=" P DC 1 47 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 47 " occ=0.50 residue: pdb=" P DC 1 48 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 48 " occ=0.50 residue: pdb=" P DC 1 49 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 49 " occ=0.50 residue: pdb=" P DT 1 50 " occ=0.50 ... (30 atoms not shown) pdb=" H6 DT 1 50 " occ=0.50 residue: pdb=" P DT 1 51 " occ=0.50 ... (30 atoms not shown) pdb=" H6 DT 1 51 " occ=0.50 residue: pdb=" P DG 1 52 " occ=0.50 ... (31 atoms not shown) pdb=" H22 DG 1 52 " occ=0.50 ... (remaining 31 not shown) Time building chain proxies: 21.41, per 1000 atoms: 0.32 Number of scatterers: 66008 At special positions: 0 Unit cell: (153.08, 188.68, 201.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Cu 2 28.99 S 143 16.00 P 102 15.00 O 6630 8.00 N 5923 7.00 C 20518 6.00 H 32688 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 44.56 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " Number of angles added : 6 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7382 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 49 sheets defined 44.5% alpha, 12.3% beta 37 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 23.18 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.686A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.918A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 234 removed outlier: 3.754A pdb=" N ALA A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.638A 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 85 removed outlier: 3.886A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 229 through 232 removed outlier: 4.027A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.753A pdb=" N LYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.896A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.704A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.017A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 89 " --> pdb=" O CYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.019A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.507A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.796A pdb=" N ALA C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.899A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 422 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.632A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 493 Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.751A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.710A 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 539 through 543 Processing helix chain 'C' and resid 609 through 614 removed outlier: 3.597A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.634A pdb=" N ALA C 679 " --> pdb=" O ASP C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 712 Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 865 removed outlier: 3.552A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 972 Processing helix chain 'C' and resid 973 through 978 removed outlier: 3.849A pdb=" N ALA C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 991 removed outlier: 3.873A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1037 removed outlier: 3.776A pdb=" N GLN C1008 " --> pdb=" O ASP C1004 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.328A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 3.846A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.986A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 removed outlier: 4.074A pdb=" N VAL C1169 " --> pdb=" O SER C1165 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.650A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1272 through 1282 removed outlier: 3.672A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 3.744A pdb=" N ARG C1301 " --> pdb=" O ASP C1297 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 4.217A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.542A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.552A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 4.211A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 4.006A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.874A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.589A pdb=" N LEU D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 284 removed outlier: 4.000A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.738A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.802A pdb=" N ALA D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.815A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.727A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.547A pdb=" N GLN D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.796A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.774A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.628A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 4.049A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 671 Processing helix chain 'D' and resid 674 through 699 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 788 removed outlier: 4.297A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 805 removed outlier: 4.376A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.517A pdb=" N VAL D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.570A pdb=" N CYS D 869 " --> pdb=" O HIS D 865 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1063 through 1067 removed outlier: 3.648A pdb=" N GLU D1066 " --> pdb=" O ASP D1063 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D1067 " --> pdb=" O SER D1064 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1063 through 1067' Processing helix chain 'D' and resid 1138 through 1147 removed outlier: 3.723A pdb=" N ALA D1142 " --> pdb=" O LEU D1138 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D1147 " --> pdb=" O ASP D1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1226 through 1243 Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 3.909A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1288 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1321 through 1325 removed outlier: 4.191A pdb=" N PHE D1325 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.649A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D1339 " --> pdb=" O ALA D1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1375 removed outlier: 3.954A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.548A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.736A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 79 Processing helix chain 'F' and resid 80 through 90 Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.583A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 134 Processing helix chain 'F' and resid 143 through 152 removed outlier: 3.601A pdb=" N GLU F 152 " --> pdb=" O TYR F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 165 removed outlier: 4.264A pdb=" N THR F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 232 removed outlier: 4.278A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 237 removed outlier: 3.578A pdb=" N LYS F 236 " --> pdb=" O ASP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 259 removed outlier: 3.602A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 292 removed outlier: 3.912A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR F 282 " --> pdb=" O ASP F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 309 removed outlier: 3.529A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 321 removed outlier: 4.082A pdb=" N ALA F 318 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.090A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 383 removed outlier: 3.633A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 383 " --> pdb=" O MET F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 395 removed outlier: 3.674A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 4.135A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.524A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.680A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 Processing helix chain 'F' and resid 490 through 502 removed outlier: 3.799A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS F 502 " --> pdb=" O LEU F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 530 through 551 removed outlier: 3.559A pdb=" N GLY F 550 " --> pdb=" O ASP F 546 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 551 " --> pdb=" O VAL F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 564 Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 584 through 600 removed outlier: 3.952A pdb=" N HIS F 600 " --> pdb=" O ARG F 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 612 removed outlier: 3.672A pdb=" N VAL F 606 " --> pdb=" O ARG F 603 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG F 608 " --> pdb=" O GLU F 605 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N SER F 609 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 11 removed outlier: 3.838A pdb=" N VAL G 6 " --> pdb=" O ASN G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 23 Processing helix chain 'G' and resid 40 through 57 removed outlier: 4.078A pdb=" N ARG G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 72 Processing helix chain 'G' and resid 76 through 112 removed outlier: 3.536A pdb=" N ALA G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 127 Processing helix chain 'H' and resid 2 through 11 Processing helix chain 'H' and resid 13 through 23 Processing helix chain 'H' and resid 40 through 55 Processing helix chain 'H' and resid 59 through 72 removed outlier: 3.653A pdb=" N ASN H 71 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 112 Processing helix chain 'H' and resid 120 through 127 removed outlier: 3.812A pdb=" N GLU H 124 " --> pdb=" O CYS H 120 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER H 127 " --> pdb=" O ILE H 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 15 removed outlier: 3.743A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.792A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 18 removed outlier: 3.803A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 3.803A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.735A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.850A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.878A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.607A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU C 106 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N VAL C 114 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 73 through 75 removed outlier: 5.051A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 161 removed outlier: 5.409A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE C 176 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 287 removed outlier: 3.929A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 4.897A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.036A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 750 through 752 removed outlier: 4.256A pdb=" N TYR C 751 " --> pdb=" O ILE C 732 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 732 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 798 through 801 removed outlier: 7.619A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.575A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE C 934 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.520A pdb=" N LEU C 883 " --> pdb=" O LEU C 918 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD1, first strand: chain 'C' and resid 1209 through 1210 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.533A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.533A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD5, first strand: chain 'C' and resid 1338 through 1340 removed outlier: 3.686A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.251A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.038A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 365 through 366 Processing sheet with id=AE1, first strand: chain 'D' and resid 547 through 556 Processing sheet with id=AE2, first strand: chain 'D' and resid 705 through 706 removed outlier: 3.856A pdb=" N THR D 705 " --> pdb=" O GLN D 716 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN D 716 " --> pdb=" O THR D 705 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE4, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'D' and resid 901 through 902 removed outlier: 3.595A pdb=" N HIS D 907 " --> pdb=" O ASP D 902 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.813A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D1017 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU D1015 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 991 through 996 removed outlier: 3.793A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE9, first strand: chain 'D' and resid 1027 through 1029 removed outlier: 6.898A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU D1121 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1079 through 1081 Processing sheet with id=AF2, first strand: chain 'D' and resid 1161 through 1162 removed outlier: 3.515A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1278 through 1279 Processing sheet with id=AF4, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.911A pdb=" N MET H 30 " --> pdb=" O THR H 38 " (cutoff:3.500A) 1332 hydrogen bonds defined for protein. 3765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 25.39 Time building geometry restraints manager: 46.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 32659 1.03 - 1.22: 95 1.22 - 1.42: 13820 1.42 - 1.62: 19888 1.62 - 1.81: 248 Bond restraints: 66710 Sorted by residual: bond pdb=" CA GLU C 562 " pdb=" CB GLU C 562 " ideal model delta sigma weight residual 1.525 1.449 0.076 1.29e-02 6.01e+03 3.48e+01 bond pdb=" C VAL D 808 " pdb=" N VAL D 809 " ideal model delta sigma weight residual 1.334 1.274 0.060 1.24e-02 6.50e+03 2.33e+01 bond pdb=" C LEU D 807 " pdb=" N VAL D 808 " ideal model delta sigma weight residual 1.333 1.299 0.033 9.00e-03 1.23e+04 1.36e+01 bond pdb=" C ILE D1090 " pdb=" N PRO D1091 " ideal model delta sigma weight residual 1.331 1.373 -0.042 1.20e-02 6.94e+03 1.23e+01 bond pdb=" N VAL D 244 " pdb=" H VAL D 244 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.48e+00 ... (remaining 66705 not shown) Histogram of bond angle deviations from ideal: 96.85 - 104.36: 836 104.36 - 111.87: 76097 111.87 - 119.38: 18777 119.38 - 126.89: 24711 126.89 - 134.40: 548 Bond angle restraints: 120969 Sorted by residual: angle pdb=" N ILE D1210 " pdb=" CA ILE D1210 " pdb=" C ILE D1210 " ideal model delta sigma weight residual 111.62 106.41 5.21 7.90e-01 1.60e+00 4.35e+01 angle pdb=" N VAL B 19 " pdb=" CA VAL B 19 " pdb=" C VAL B 19 " ideal model delta sigma weight residual 111.62 107.51 4.11 7.90e-01 1.60e+00 2.71e+01 angle pdb=" N GLN F 472 " pdb=" CA GLN F 472 " pdb=" C GLN F 472 " ideal model delta sigma weight residual 110.97 105.57 5.40 1.09e+00 8.42e-01 2.45e+01 angle pdb=" N PHE F 401 " pdb=" CA PHE F 401 " pdb=" C PHE F 401 " ideal model delta sigma weight residual 111.03 116.52 -5.49 1.11e+00 8.12e-01 2.44e+01 angle pdb=" N ILE C1079 " pdb=" CA ILE C1079 " pdb=" C ILE C1079 " ideal model delta sigma weight residual 109.46 102.85 6.61 1.38e+00 5.25e-01 2.30e+01 ... (remaining 120964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 29154 34.14 - 68.27: 785 68.27 - 102.41: 32 102.41 - 136.55: 0 136.55 - 170.68: 1 Dihedral angle restraints: 29972 sinusoidal: 17294 harmonic: 12678 Sorted by residual: dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 -116.77 -63.23 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" CA ARG F 599 " pdb=" C ARG F 599 " pdb=" N HIS F 600 " pdb=" CA HIS F 600 " ideal model delta harmonic sigma weight residual 180.00 141.81 38.19 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA VAL D1298 " pdb=" C VAL D1298 " pdb=" N GLY D1299 " pdb=" CA GLY D1299 " ideal model delta harmonic sigma weight residual 180.00 -142.61 -37.39 0 5.00e+00 4.00e-02 5.59e+01 ... (remaining 29969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3607 0.053 - 0.105: 1298 0.105 - 0.158: 338 0.158 - 0.211: 28 0.211 - 0.264: 3 Chirality restraints: 5274 Sorted by residual: chirality pdb=" CB VAL D 421 " pdb=" CA VAL D 421 " pdb=" CG1 VAL D 421 " pdb=" CG2 VAL D 421 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL D 769 " pdb=" CA VAL D 769 " pdb=" CG1 VAL D 769 " pdb=" CG2 VAL D 769 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA VAL D 244 " pdb=" N VAL D 244 " pdb=" C VAL D 244 " pdb=" CB VAL D 244 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5271 not shown) Planarity restraints: 9606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 274 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C ASN D 274 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN D 274 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG D 275 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 120 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO D 121 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 51 " -0.045 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO B 52 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.038 5.00e-02 4.00e+02 ... (remaining 9603 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 5598 2.21 - 2.81: 143958 2.81 - 3.40: 173978 3.40 - 4.00: 228613 4.00 - 4.60: 351509 Nonbonded interactions: 903656 Sorted by model distance: nonbonded pdb=" HZ2 LYS C1303 " pdb=" OE1 GLU C1316 " model vdw 1.609 1.850 nonbonded pdb=" OE1 GLN C 798 " pdb=" HE ARG C 827 " model vdw 1.611 1.850 nonbonded pdb=" O THR B 57 " pdb=" H VAL B 173 " model vdw 1.619 1.850 nonbonded pdb=" O MET G 30 " pdb=" H THR G 38 " model vdw 1.628 1.850 nonbonded pdb=" O CYS D 85 " pdb=" H GLY D 89 " model vdw 1.638 1.850 ... (remaining 903651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.740 Extract box with map and model: 13.530 Check model and map are aligned: 0.710 Set scattering table: 0.460 Process input model: 197.370 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.200 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:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 219.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.099 34022 Z= 0.655 Angle : 1.024 10.787 46368 Z= 0.589 Chirality : 0.056 0.264 5274 Planarity : 0.006 0.069 5721 Dihedral : 14.394 170.683 13318 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.45 % Favored : 88.50 % Rotamer: Outliers : 0.12 % Allowed : 5.26 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.11), residues: 3949 helix: -2.55 (0.10), residues: 1582 sheet: -3.96 (0.20), residues: 347 loop : -3.42 (0.12), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP F 433 HIS 0.014 0.003 HIS C 832 PHE 0.031 0.003 PHE C 629 TYR 0.026 0.003 TYR C 756 ARG 0.018 0.002 ARG D1284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 475 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8334 (mp-120) cc_final: 0.8114 (mp10) REVERT: B 57 THR cc_start: 0.5304 (m) cc_final: 0.5094 (m) REVERT: C 820 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7109 (tm-30) REVERT: C 1018 TYR cc_start: 0.7992 (m-80) cc_final: 0.7671 (m-80) REVERT: C 1064 ASP cc_start: 0.8640 (t0) cc_final: 0.8438 (t0) REVERT: C 1279 GLU cc_start: 0.8405 (pm20) cc_final: 0.8085 (pm20) REVERT: D 201 LEU cc_start: 0.8424 (mt) cc_final: 0.8106 (mp) REVERT: D 289 ASP cc_start: 0.6975 (m-30) cc_final: 0.6652 (t70) REVERT: D 654 ILE cc_start: 0.8436 (mt) cc_final: 0.8201 (mm) REVERT: D 684 ASP cc_start: 0.8493 (m-30) cc_final: 0.8025 (t0) REVERT: D 1095 MET cc_start: 0.2847 (ttm) cc_final: 0.2267 (ttm) REVERT: F 297 MET cc_start: 0.4425 (mtt) cc_final: 0.3627 (ttt) REVERT: G 54 ARG cc_start: 0.7565 (tpm170) cc_final: 0.6482 (tmt-80) REVERT: H 41 GLN cc_start: 0.8127 (mp10) cc_final: 0.7610 (pm20) outliers start: 4 outliers final: 1 residues processed: 476 average time/residue: 1.1404 time to fit residues: 794.1714 Evaluate side-chains 294 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 3.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 435 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 340 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 315 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 235 optimal weight: 0.7980 chunk 365 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 66 HIS B 75 GLN B 186 ASN ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 824 GLN C1070 HIS C1236 ASN ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 712 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN D 929 GLN D 954 ASN D1350 ASN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN G 110 ASN H 42 GLN H 125 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34022 Z= 0.188 Angle : 0.642 7.104 46368 Z= 0.351 Chirality : 0.042 0.161 5274 Planarity : 0.005 0.060 5721 Dihedral : 15.392 165.884 5449 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.14 % Favored : 92.81 % Rotamer: Outliers : 0.88 % Allowed : 8.70 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.12), residues: 3949 helix: -1.19 (0.12), residues: 1619 sheet: -3.22 (0.21), residues: 375 loop : -2.93 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 433 HIS 0.004 0.001 HIS F 545 PHE 0.020 0.002 PHE B 8 TYR 0.015 0.001 TYR D 537 ARG 0.009 0.001 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 336 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8623 (tt) REVERT: A 103 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.8041 (m-40) REVERT: A 181 GLU cc_start: 0.7638 (tt0) cc_final: 0.7357 (tt0) REVERT: C 81 ASP cc_start: 0.7320 (p0) cc_final: 0.6524 (p0) REVERT: C 1156 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7111 (pmt170) REVERT: C 1290 MET cc_start: 0.7986 (ttm) cc_final: 0.7740 (ttm) REVERT: D 289 ASP cc_start: 0.7004 (m-30) cc_final: 0.6692 (t70) REVERT: D 684 ASP cc_start: 0.8568 (m-30) cc_final: 0.8000 (t0) REVERT: D 747 MET cc_start: 0.6148 (mmt) cc_final: 0.5922 (mmt) REVERT: D 1095 MET cc_start: 0.3250 (ttm) cc_final: 0.2663 (ttm) REVERT: D 1326 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6562 (mp10) REVERT: F 102 MET cc_start: 0.8144 (mtm) cc_final: 0.7944 (mtt) REVERT: F 273 MET cc_start: 0.6177 (mmm) cc_final: 0.5760 (mmm) REVERT: F 297 MET cc_start: 0.4040 (mtt) cc_final: 0.3493 (ttt) REVERT: H 41 GLN cc_start: 0.8121 (mp10) cc_final: 0.7503 (pm20) outliers start: 30 outliers final: 17 residues processed: 356 average time/residue: 0.9722 time to fit residues: 536.5377 Evaluate side-chains 306 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 285 time to evaluate : 3.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 1156 ARG Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 68 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 203 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 304 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 396 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 363 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN B 186 ASN C 462 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS F 383 ASN ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 34022 Z= 0.378 Angle : 0.717 7.229 46368 Z= 0.398 Chirality : 0.044 0.164 5274 Planarity : 0.006 0.063 5721 Dihedral : 15.318 165.239 5449 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.43 % Favored : 89.49 % Rotamer: Outliers : 1.32 % Allowed : 9.81 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -3.13 (0.12), residues: 3949 helix: -1.01 (0.12), residues: 1630 sheet: -2.91 (0.21), residues: 399 loop : -2.87 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 433 HIS 0.008 0.002 HIS B 132 PHE 0.021 0.002 PHE C 405 TYR 0.020 0.002 TYR C 92 ARG 0.006 0.001 ARG F 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 271 time to evaluate : 3.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7860 (tt0) cc_final: 0.7625 (tt0) REVERT: C 937 ASP cc_start: 0.7525 (p0) cc_final: 0.7309 (p0) REVERT: C 965 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8293 (tm-30) REVERT: D 289 ASP cc_start: 0.7687 (m-30) cc_final: 0.7263 (t70) REVERT: D 684 ASP cc_start: 0.8644 (m-30) cc_final: 0.8110 (t0) REVERT: D 1095 MET cc_start: 0.3290 (ttm) cc_final: 0.2720 (ttm) REVERT: D 1293 GLU cc_start: 0.8125 (mp0) cc_final: 0.7924 (mp0) REVERT: F 100 MET cc_start: 0.8579 (mtt) cc_final: 0.8357 (mtt) REVERT: F 297 MET cc_start: 0.4238 (mtt) cc_final: 0.3795 (ttp) REVERT: F 376 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8711 (pttt) REVERT: H 41 GLN cc_start: 0.8144 (mp10) cc_final: 0.7613 (pm20) outliers start: 45 outliers final: 29 residues processed: 304 average time/residue: 0.9242 time to fit residues: 441.6966 Evaluate side-chains 265 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 235 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1156 ARG Chi-restraints excluded: chain C residue 1200 LYS Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 434 TRP Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 572 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 362 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 190 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 246 optimal weight: 8.9990 chunk 367 optimal weight: 2.9990 chunk 389 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 348 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 477 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34022 Z= 0.250 Angle : 0.613 6.728 46368 Z= 0.339 Chirality : 0.042 0.172 5274 Planarity : 0.005 0.059 5721 Dihedral : 15.115 166.826 5449 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.10 % Favored : 91.85 % Rotamer: Outliers : 1.18 % Allowed : 10.81 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -2.54 (0.12), residues: 3949 helix: -0.46 (0.12), residues: 1632 sheet: -2.55 (0.22), residues: 381 loop : -2.64 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 433 HIS 0.006 0.001 HIS D 450 PHE 0.029 0.002 PHE F 259 TYR 0.016 0.001 TYR B 68 ARG 0.006 0.000 ARG F 441 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 255 time to evaluate : 3.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7885 (tt0) cc_final: 0.7684 (tt0) REVERT: C 937 ASP cc_start: 0.7480 (p0) cc_final: 0.7222 (p0) REVERT: C 965 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8307 (tm-30) REVERT: C 1156 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7241 (pmt170) REVERT: C 1200 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9143 (ttpt) REVERT: D 684 ASP cc_start: 0.8577 (m-30) cc_final: 0.8077 (t0) REVERT: D 895 CYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8167 (p) REVERT: D 1095 MET cc_start: 0.3311 (ttm) cc_final: 0.2778 (ttm) REVERT: D 1326 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: F 297 MET cc_start: 0.4189 (mtt) cc_final: 0.3768 (ttp) REVERT: H 41 GLN cc_start: 0.8148 (mp10) cc_final: 0.7594 (pm20) REVERT: H 101 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7853 (tpp) outliers start: 40 outliers final: 27 residues processed: 280 average time/residue: 0.8863 time to fit residues: 396.6476 Evaluate side-chains 265 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1156 ARG Chi-restraints excluded: chain C residue 1200 LYS Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 101 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 324 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 290 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 332 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 349 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN B 186 ASN C 447 HIS ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS E 31 GLN F 579 GLN F 600 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34022 Z= 0.253 Angle : 0.599 6.703 46368 Z= 0.330 Chirality : 0.041 0.152 5274 Planarity : 0.004 0.063 5721 Dihedral : 15.005 166.246 5449 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.34 % Favored : 90.61 % Rotamer: Outliers : 1.53 % Allowed : 11.55 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -2.22 (0.13), residues: 3949 helix: -0.14 (0.12), residues: 1634 sheet: -2.36 (0.22), residues: 392 loop : -2.53 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 686 HIS 0.007 0.001 HIS B 66 PHE 0.020 0.002 PHE F 259 TYR 0.015 0.001 TYR C 92 ARG 0.005 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 244 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 937 ASP cc_start: 0.7503 (p0) cc_final: 0.7237 (p0) REVERT: C 965 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8256 (tm-30) REVERT: C 1098 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8617 (pp) REVERT: D 684 ASP cc_start: 0.8527 (m-30) cc_final: 0.8064 (t0) REVERT: D 895 CYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8122 (p) REVERT: D 1095 MET cc_start: 0.3435 (ttm) cc_final: 0.2873 (ttm) REVERT: F 297 MET cc_start: 0.4073 (mtt) cc_final: 0.3719 (ttp) REVERT: H 41 GLN cc_start: 0.8186 (mp10) cc_final: 0.7613 (pm20) outliers start: 52 outliers final: 42 residues processed: 283 average time/residue: 0.8565 time to fit residues: 395.8823 Evaluate side-chains 271 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 227 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1200 LYS Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 101 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 131 optimal weight: 5.9990 chunk 350 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 389 optimal weight: 9.9990 chunk 323 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34022 Z= 0.267 Angle : 0.601 7.020 46368 Z= 0.331 Chirality : 0.042 0.150 5274 Planarity : 0.004 0.063 5721 Dihedral : 14.950 166.926 5449 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.56 % Favored : 91.39 % Rotamer: Outliers : 1.53 % Allowed : 12.46 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 3949 helix: -0.01 (0.13), residues: 1641 sheet: -2.27 (0.23), residues: 410 loop : -2.44 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 433 HIS 0.005 0.001 HIS B 66 PHE 0.025 0.002 PHE F 259 TYR 0.016 0.001 TYR C 92 ARG 0.004 0.000 ARG C 637 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 245 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 ASP cc_start: 0.5931 (t70) cc_final: 0.5724 (t0) REVERT: C 937 ASP cc_start: 0.7520 (p0) cc_final: 0.7240 (p0) REVERT: C 965 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 1098 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8652 (pp) REVERT: D 289 ASP cc_start: 0.7932 (m-30) cc_final: 0.7433 (t0) REVERT: D 298 MET cc_start: 0.8833 (mtp) cc_final: 0.8622 (mtm) REVERT: D 684 ASP cc_start: 0.8515 (m-30) cc_final: 0.8089 (t0) REVERT: D 895 CYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8170 (p) REVERT: D 1095 MET cc_start: 0.3411 (ttm) cc_final: 0.2895 (ttm) REVERT: F 297 MET cc_start: 0.4023 (mtt) cc_final: 0.3506 (ttt) REVERT: H 41 GLN cc_start: 0.8164 (mp10) cc_final: 0.7602 (pm20) REVERT: H 101 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7778 (tpp) outliers start: 52 outliers final: 42 residues processed: 284 average time/residue: 0.8249 time to fit residues: 381.6942 Evaluate side-chains 276 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 101 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 375 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 328 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 34022 Z= 0.253 Angle : 0.591 7.010 46368 Z= 0.325 Chirality : 0.041 0.148 5274 Planarity : 0.004 0.064 5721 Dihedral : 14.892 167.122 5447 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.94 % Favored : 91.01 % Rotamer: Outliers : 1.67 % Allowed : 12.87 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.88 (0.13), residues: 3949 helix: 0.14 (0.13), residues: 1637 sheet: -2.06 (0.23), residues: 419 loop : -2.35 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 686 HIS 0.006 0.001 HIS B 66 PHE 0.035 0.001 PHE F 259 TYR 0.016 0.001 TYR C 92 ARG 0.004 0.000 ARG C 637 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 241 time to evaluate : 3.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 515 MET cc_start: 0.8346 (ttm) cc_final: 0.8133 (ttt) REVERT: C 937 ASP cc_start: 0.7529 (p0) cc_final: 0.7279 (p0) REVERT: C 965 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8271 (tm-30) REVERT: C 1098 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8654 (pp) REVERT: D 419 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.7575 (t-90) REVERT: D 684 ASP cc_start: 0.8463 (m-30) cc_final: 0.8061 (t0) REVERT: D 895 CYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8167 (p) REVERT: D 1095 MET cc_start: 0.3421 (ttm) cc_final: 0.2897 (ttm) REVERT: D 1326 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6686 (mp10) REVERT: F 297 MET cc_start: 0.4006 (mtt) cc_final: 0.3569 (ttp) REVERT: G 101 MET cc_start: 0.9036 (mtt) cc_final: 0.8639 (ttm) REVERT: H 31 ARG cc_start: 0.7236 (mmt180) cc_final: 0.7020 (mmt180) REVERT: H 41 GLN cc_start: 0.8079 (mp10) cc_final: 0.7540 (pm20) REVERT: H 101 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7786 (tpp) outliers start: 57 outliers final: 44 residues processed: 281 average time/residue: 0.8224 time to fit residues: 377.9363 Evaluate side-chains 280 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 231 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 101 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 240 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 231 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 75 optimal weight: 0.0870 chunk 246 optimal weight: 8.9990 chunk 264 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 305 optimal weight: 9.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 737 ASN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** F 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34022 Z= 0.220 Angle : 0.572 7.599 46368 Z= 0.313 Chirality : 0.041 0.144 5274 Planarity : 0.004 0.061 5721 Dihedral : 14.808 167.201 5447 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.80 % Favored : 92.15 % Rotamer: Outliers : 1.65 % Allowed : 13.22 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.64 (0.13), residues: 3949 helix: 0.34 (0.13), residues: 1638 sheet: -1.98 (0.24), residues: 431 loop : -2.21 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 433 HIS 0.005 0.001 HIS B 66 PHE 0.020 0.001 PHE F 259 TYR 0.021 0.001 TYR D 144 ARG 0.012 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 246 time to evaluate : 3.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 937 ASP cc_start: 0.7534 (p0) cc_final: 0.7238 (p0) REVERT: C 965 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8261 (tm-30) REVERT: C 1098 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8719 (pp) REVERT: D 419 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7599 (t-90) REVERT: D 684 ASP cc_start: 0.8430 (m-30) cc_final: 0.8086 (t0) REVERT: D 895 CYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8149 (p) REVERT: D 1095 MET cc_start: 0.3336 (ttm) cc_final: 0.2833 (ttm) REVERT: D 1326 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6661 (mp10) REVERT: F 297 MET cc_start: 0.3968 (mtt) cc_final: 0.3483 (ttt) REVERT: H 31 ARG cc_start: 0.7286 (mmt180) cc_final: 0.7061 (mmt180) REVERT: H 41 GLN cc_start: 0.8100 (mp10) cc_final: 0.7531 (pm20) REVERT: H 101 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7841 (tpp) outliers start: 56 outliers final: 41 residues processed: 284 average time/residue: 0.8405 time to fit residues: 387.0720 Evaluate side-chains 283 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 101 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 353 optimal weight: 4.9990 chunk 372 optimal weight: 7.9990 chunk 339 optimal weight: 10.0000 chunk 361 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 327 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 360 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 34022 Z= 0.303 Angle : 0.620 7.794 46368 Z= 0.342 Chirality : 0.042 0.152 5274 Planarity : 0.005 0.095 5721 Dihedral : 14.870 167.315 5447 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.83 % Favored : 90.12 % Rotamer: Outliers : 1.50 % Allowed : 13.37 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3949 helix: 0.18 (0.13), residues: 1630 sheet: -1.84 (0.24), residues: 422 loop : -2.31 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 686 HIS 0.006 0.001 HIS B 66 PHE 0.018 0.002 PHE F 266 TYR 0.017 0.001 TYR D 165 ARG 0.017 0.001 ARG D 738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 3.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7834 (t) REVERT: C 127 ILE cc_start: 0.9321 (mm) cc_final: 0.8988 (pt) REVERT: C 965 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8212 (tm-30) REVERT: C 1098 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8723 (pp) REVERT: D 419 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.7657 (t-90) REVERT: D 684 ASP cc_start: 0.8435 (m-30) cc_final: 0.8061 (t0) REVERT: D 895 CYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8173 (p) REVERT: D 1095 MET cc_start: 0.3348 (ttm) cc_final: 0.2860 (ttm) REVERT: F 278 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6598 (t0) REVERT: F 297 MET cc_start: 0.4099 (mtt) cc_final: 0.3658 (ttp) REVERT: F 456 MET cc_start: 0.8376 (mpp) cc_final: 0.8075 (tpp) REVERT: F 561 MET cc_start: 0.7814 (ppp) cc_final: 0.7558 (ppp) REVERT: H 31 ARG cc_start: 0.7164 (mmt180) cc_final: 0.6959 (mmt180) REVERT: H 41 GLN cc_start: 0.8091 (mp10) cc_final: 0.7515 (pm20) REVERT: H 101 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7812 (tpp) outliers start: 51 outliers final: 42 residues processed: 285 average time/residue: 0.8307 time to fit residues: 383.4754 Evaluate side-chains 281 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 233 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 101 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 237 optimal weight: 0.1980 chunk 382 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 401 optimal weight: 8.9990 chunk 369 optimal weight: 10.0000 chunk 319 optimal weight: 8.9990 chunk 33 optimal weight: 0.0980 chunk 246 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34022 Z= 0.167 Angle : 0.562 8.961 46368 Z= 0.305 Chirality : 0.040 0.141 5274 Planarity : 0.004 0.056 5721 Dihedral : 14.722 167.898 5447 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.63 % Favored : 93.31 % Rotamer: Outliers : 1.12 % Allowed : 14.11 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.37 (0.13), residues: 3949 helix: 0.56 (0.13), residues: 1624 sheet: -1.69 (0.25), residues: 423 loop : -2.08 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 433 HIS 0.004 0.001 HIS B 66 PHE 0.016 0.001 PHE F 259 TYR 0.021 0.001 TYR D 165 ARG 0.006 0.000 ARG D 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7898 Ramachandran restraints generated. 3949 Oldfield, 0 Emsley, 3949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 245 time to evaluate : 3.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7698 (t) REVERT: C 127 ILE cc_start: 0.9338 (mm) cc_final: 0.8979 (pt) REVERT: C 158 ASP cc_start: 0.8443 (t70) cc_final: 0.8229 (t70) REVERT: C 732 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9020 (pp) REVERT: C 965 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 1098 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8725 (pp) REVERT: C 1265 PHE cc_start: 0.5726 (t80) cc_final: 0.5485 (t80) REVERT: D 419 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.7563 (t-90) REVERT: D 684 ASP cc_start: 0.8374 (m-30) cc_final: 0.8038 (t0) REVERT: D 895 CYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8034 (p) REVERT: D 1095 MET cc_start: 0.3186 (ttm) cc_final: 0.2708 (ttm) REVERT: F 297 MET cc_start: 0.3955 (mtt) cc_final: 0.3637 (ttp) REVERT: F 533 ASP cc_start: 0.8210 (m-30) cc_final: 0.8006 (m-30) REVERT: H 31 ARG cc_start: 0.7221 (mmt180) cc_final: 0.7002 (mmt180) REVERT: H 41 GLN cc_start: 0.8106 (mp10) cc_final: 0.7469 (pm20) REVERT: H 101 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7807 (tpp) outliers start: 38 outliers final: 30 residues processed: 271 average time/residue: 0.8350 time to fit residues: 370.2410 Evaluate side-chains 275 residues out of total 3403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 239 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 101 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.6926 > 50: distance: 215 - 264: 3.448 distance: 239 - 298: 4.088 distance: 253 - 254: 3.035 distance: 254 - 255: 3.417 distance: 254 - 257: 4.048 distance: 255 - 256: 7.074 distance: 255 - 264: 5.385 distance: 256 - 312: 8.767 distance: 257 - 261: 5.308 distance: 257 - 262: 7.028 distance: 258 - 263: 5.432 distance: 264 - 265: 6.960 distance: 264 - 273: 6.733 distance: 265 - 266: 4.830 distance: 265 - 274: 5.906 distance: 267 - 329: 9.215 distance: 268 - 275: 7.786 distance: 268 - 276: 9.505 distance: 269 - 277: 10.743 distance: 269 - 278: 13.145 distance: 270 - 271: 5.222 distance: 270 - 272: 3.379 distance: 279 - 280: 3.831 distance: 279 - 287: 4.283 distance: 280 - 281: 4.373 distance: 280 - 283: 5.488 distance: 280 - 288: 6.031 distance: 281 - 282: 3.766 distance: 281 - 298: 4.120 distance: 282 - 351: 4.366 distance: 283 - 284: 3.344 distance: 283 - 285: 6.092 distance: 283 - 289: 4.528 distance: 284 - 286: 5.910 distance: 284 - 290: 3.272 distance: 284 - 291: 7.299 distance: 285 - 294: 4.305 distance: 286 - 295: 3.841 distance: 286 - 296: 3.294 distance: 286 - 297: 4.592 distance: 298 - 299: 9.056 distance: 299 - 300: 11.432 distance: 299 - 302: 10.614 distance: 299 - 306: 3.800 distance: 300 - 301: 12.474 distance: 300 - 312: 25.679 distance: 302 - 303: 16.761 distance: 302 - 304: 22.385 distance: 302 - 307: 17.867 distance: 303 - 308: 26.645 distance: 304 - 309: 12.061 distance: 304 - 310: 8.379 distance: 304 - 311: 14.021 distance: 312 - 313: 8.501 distance: 312 - 322: 20.898 distance: 313 - 314: 9.430 distance: 313 - 316: 5.246 distance: 313 - 323: 7.794 distance: 314 - 315: 4.814 distance: 314 - 329: 6.471 distance: 316 - 317: 7.498 distance: 316 - 324: 5.959 distance: 316 - 325: 3.728 distance: 317 - 318: 6.426 distance: 317 - 319: 14.858 distance: 318 - 320: 10.744 distance: 319 - 321: 6.960 distance: 320 - 321: 9.162 distance: 320 - 327: 3.204 distance: 321 - 328: 8.127 distance: 331 - 332: 3.579 distance: 333 - 340: 5.136 distance: 334 - 335: 6.926 distance: 334 - 343: 3.677 distance: 336 - 347: 3.109 distance: 352 - 353: 3.083 distance: 352 - 355: 3.791 distance: 352 - 363: 4.064 distance: 355 - 356: 4.596 distance: 355 - 365: 3.284 distance: 356 - 357: 3.430 distance: 357 - 358: 3.829 distance: 357 - 368: 3.132 distance: 358 - 359: 4.511 distance: 359 - 360: 6.787 distance: 359 - 361: 4.248 distance: 361 - 373: 3.675 distance: 375 - 376: 3.112 distance: 376 - 377: 3.811 distance: 376 - 387: 5.912 distance: 377 - 378: 7.471 distance: 377 - 399: 8.128 distance: 379 - 380: 5.056 distance: 380 - 381: 4.733 distance: 382 - 383: 3.447 distance: 382 - 394: 3.190 distance: 399 - 400: 4.951 distance: 399 - 407: 4.944 distance: 400 - 401: 5.971 distance: 400 - 403: 6.636 distance: 400 - 408: 3.914 distance: 403 - 404: 7.690 distance: 403 - 405: 7.639 distance: 404 - 406: 5.639 distance: 404 - 410: 9.423 distance: 404 - 411: 6.521 distance: 405 - 412: 3.909 distance: 405 - 414: 4.424 distance: 406 - 416: 4.729 distance: 406 - 417: 5.462 distance: 418 - 419: 3.810 distance: 418 - 424: 6.132 distance: 419 - 420: 3.682 distance: 419 - 422: 6.914 distance: 419 - 425: 9.696 distance: 420 - 421: 3.067 distance: 420 - 429: 3.926 distance: 422 - 426: 8.431 distance: 422 - 427: 5.040 distance: 423 - 428: 9.538