Starting phenix.real_space_refine (version: dev) on Mon Feb 27 08:19:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/02_2023/8gxw_34363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/02_2023/8gxw_34363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/02_2023/8gxw_34363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/02_2023/8gxw_34363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/02_2023/8gxw_34363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/02_2023/8gxw_34363_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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 Process input model Symmetric amino acids flipped Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29530 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.09, per 1000 atoms: 0.54 Number of scatterers: 29530 At special positions: 0 Unit cell: (149.4, 151.06, 173.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 6 15.00 Mg 1 11.99 O 5568 8.00 N 5126 7.00 C 18725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 4.3 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 134 helices and 34 sheets defined 42.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 315 removed outlier: 3.609A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.808A pdb=" N ARG A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 433 through 442 Proline residue: A 437 - end of helix removed outlier: 3.571A pdb=" N ASN A 442 " --> pdb=" O TYR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 471 removed outlier: 4.013A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 539 No H-bonds generated for 'chain 'A' and resid 536 through 539' Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.597A pdb=" N ALA A 551 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.848A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.983A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.832A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.639A pdb=" N ILE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 463 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 543 through 549 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.863A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.661A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.566A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.039A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 532 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 559 through 575 removed outlier: 3.595A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.391A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.916A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.878A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 467 through 471 removed outlier: 3.765A pdb=" N TRP D 471 " --> pdb=" O GLU D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 175 through 178 Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.506A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.534A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 332 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.882A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.792A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 462 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 136 through 141 Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 229 through 249 removed outlier: 3.619A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.546A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 287 through 295 removed outlier: 3.606A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 360 through 364 removed outlier: 4.290A pdb=" N ASN F 363 " --> pdb=" O ARG F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.686A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 4.008A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'F' and resid 467 through 469 No H-bonds generated for 'chain 'F' and resid 467 through 469' Processing helix chain 'G' and resid 8 through 65 removed outlier: 3.698A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 70 No H-bonds generated for 'chain 'G' and resid 67 through 70' Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 123 through 207 removed outlier: 4.213A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 15 removed outlier: 3.527A pdb=" N GLN H 11 " --> pdb=" O PRO H 7 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 55 through 63 removed outlier: 6.787A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 3.820A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 77 through 82' Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 82 through 118 removed outlier: 3.512A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 96 Proline residue: J 95 - end of helix Processing helix chain 'J' and resid 100 through 114 Processing helix chain 'J' and resid 125 through 138 Proline residue: J 129 - end of helix removed outlier: 4.518A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.499A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 3.971A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 96 Proline residue: L 95 - end of helix Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 5.259A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 5.346A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.373A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.001A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= E, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.515A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.633A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.132A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.124A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.036A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 249 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA B 405 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TRP B 407 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.822A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 197 through 199 removed outlier: 3.527A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS B 367 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.533A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.514A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= P, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.075A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 164 through 166 removed outlier: 5.495A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= S, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.813A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.336A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE D 60 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY D 45 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 81 through 84 Processing sheet with id= V, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.929A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= X, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.542A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU E 77 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.601A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.806A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.440A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AC, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.916A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AE, first strand: chain 'G' and resid 91 through 96 Processing sheet with id= AF, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.534A pdb=" N TYR H 21 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 141 through 144 removed outlier: 7.055A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.509A pdb=" N ALA L 123 " --> pdb=" O GLN L 143 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL L 155 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU L 121 " --> pdb=" O ARG L 153 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG L 153 " --> pdb=" O LEU L 121 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.65 Time building geometry restraints manager: 12.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9964 1.34 - 1.46: 4874 1.46 - 1.58: 15045 1.58 - 1.69: 8 1.69 - 1.81: 194 Bond restraints: 30085 Sorted by residual: bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.450 0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.453 0.046 2.00e-02 2.50e+03 5.27e+00 bond pdb=" O2 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.452 0.046 2.00e-02 2.50e+03 5.19e+00 bond pdb=" O1 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.454 0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 30080 not shown) Histogram of bond angle deviations from ideal: 99.51 - 107.57: 1232 107.57 - 115.62: 18259 115.62 - 123.68: 20533 123.68 - 131.73: 702 131.73 - 139.78: 42 Bond angle restraints: 40768 Sorted by residual: angle pdb=" N ILE C 402 " pdb=" CA ILE C 402 " pdb=" C ILE C 402 " ideal model delta sigma weight residual 113.71 110.88 2.83 9.50e-01 1.11e+00 8.88e+00 angle pdb=" C3' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O4' ATP C 601 " ideal model delta sigma weight residual 105.22 101.58 3.64 1.30e+00 5.94e-01 7.85e+00 angle pdb=" N PRO A 420 " pdb=" CA PRO A 420 " pdb=" C PRO A 420 " ideal model delta sigma weight residual 112.10 118.97 -6.87 2.60e+00 1.48e-01 6.98e+00 angle pdb=" N ILE D 325 " pdb=" CA ILE D 325 " pdb=" C ILE D 325 " ideal model delta sigma weight residual 112.35 109.39 2.96 1.20e+00 6.94e-01 6.08e+00 angle pdb=" N VAL D 76 " pdb=" CA VAL D 76 " pdb=" C VAL D 76 " ideal model delta sigma weight residual 111.67 109.38 2.29 9.50e-01 1.11e+00 5.83e+00 ... (remaining 40763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 16604 17.85 - 35.71: 1341 35.71 - 53.56: 286 53.56 - 71.42: 51 71.42 - 89.27: 28 Dihedral angle restraints: 18310 sinusoidal: 7488 harmonic: 10822 Sorted by residual: dihedral pdb=" CA VAL A 368 " pdb=" C VAL A 368 " pdb=" N ILE A 369 " pdb=" CA ILE A 369 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA LEU D 257 " pdb=" C LEU D 257 " pdb=" N THR D 258 " pdb=" CA THR D 258 " ideal model delta harmonic sigma weight residual 180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual 180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 18307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3848 0.058 - 0.117: 653 0.117 - 0.175: 61 0.175 - 0.234: 0 0.234 - 0.292: 6 Chirality restraints: 4568 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP B 601 " pdb=" C2' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" O3' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 4565 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 323 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO D 324 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 386 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO C 387 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 387 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 387 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO F 324 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.023 5.00e-02 4.00e+02 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 117 2.45 - 3.07: 20325 3.07 - 3.68: 44631 3.68 - 4.29: 67482 4.29 - 4.90: 113480 Nonbonded interactions: 246035 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.843 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.883 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 1.952 2.440 nonbonded pdb=" O LYS E 370 " pdb=" OG1 THR E 371 " model vdw 1.955 2.440 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 1.983 2.440 ... (remaining 246030 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 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 18725 2.51 5 N 5126 2.21 5 O 5568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 16.070 Check model and map are aligned: 0.400 Process input model: 74.290 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.240 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.006 0.086 30085 Z= 0.367 Angle : 0.546 6.868 40768 Z= 0.286 Chirality : 0.044 0.292 4568 Planarity : 0.004 0.057 5332 Dihedral : 13.984 89.274 11392 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3764 helix: 1.67 (0.13), residues: 1570 sheet: -0.06 (0.22), residues: 552 loop : 0.01 (0.16), residues: 1642 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 798 time to evaluate : 3.629 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 798 average time/residue: 1.8701 time to fit residues: 1689.7791 Evaluate side-chains 427 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 3.585 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 292 optimal weight: 0.7980 chunk 113 optimal weight: 0.0870 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 338 optimal weight: 4.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 238 GLN A 316 GLN A 496 GLN B 239 GLN B 397 GLN B 442 ASN C 238 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 23 ASN E 46 GLN E 58 GLN E 338 GLN E 364 ASN E 427 GLN E 448 GLN E 458 HIS F 161 ASN F 206 GLN F 262 ASN F 364 ASN F 413 GLN F 425 GLN F 465 GLN G 175 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 30085 Z= 0.184 Angle : 0.539 12.770 40768 Z= 0.276 Chirality : 0.043 0.206 4568 Planarity : 0.005 0.051 5332 Dihedral : 4.497 62.017 4186 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.06 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.14), residues: 3764 helix: 1.71 (0.13), residues: 1584 sheet: 0.09 (0.22), residues: 566 loop : 0.31 (0.16), residues: 1614 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 435 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 30 residues processed: 496 average time/residue: 1.8873 time to fit residues: 1064.9528 Evaluate side-chains 411 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 381 time to evaluate : 3.527 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 8 average time/residue: 1.5098 time to fit residues: 18.7657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 281 optimal weight: 0.0170 chunk 230 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 339 optimal weight: 8.9990 chunk 366 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 overall best weight: 2.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 397 GLN D 166 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 413 GLN E 427 GLN E 437 GLN E 448 GLN E 465 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 413 GLN F 465 GLN G 10 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 30085 Z= 0.368 Angle : 0.659 10.670 40768 Z= 0.338 Chirality : 0.048 0.180 4568 Planarity : 0.006 0.051 5332 Dihedral : 5.179 79.003 4186 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.77 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3764 helix: 1.14 (0.13), residues: 1572 sheet: -0.05 (0.22), residues: 559 loop : 0.18 (0.16), residues: 1633 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 384 time to evaluate : 3.759 Fit side-chains revert: symmetry clash outliers start: 120 outliers final: 49 residues processed: 466 average time/residue: 1.8567 time to fit residues: 990.3634 Evaluate side-chains 408 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 359 time to evaluate : 3.402 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 34 residues processed: 15 average time/residue: 1.1912 time to fit residues: 26.0155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 chunk 176 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 340 optimal weight: 7.9990 chunk 360 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 283 HIS B 316 GLN B 397 GLN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 427 GLN E 448 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 413 GLN G 10 ASN H 30 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 30085 Z= 0.297 Angle : 0.596 12.624 40768 Z= 0.306 Chirality : 0.046 0.184 4568 Planarity : 0.005 0.052 5332 Dihedral : 5.112 83.685 4186 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer Outliers : 3.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3764 helix: 1.12 (0.13), residues: 1556 sheet: 0.03 (0.22), residues: 542 loop : 0.21 (0.16), residues: 1666 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 387 time to evaluate : 3.743 Fit side-chains outliers start: 121 outliers final: 52 residues processed: 468 average time/residue: 1.9073 time to fit residues: 1023.3900 Evaluate side-chains 410 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 358 time to evaluate : 3.717 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 38 residues processed: 14 average time/residue: 1.0739 time to fit residues: 24.0460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 0.0040 chunk 204 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 249 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 184 optimal weight: 0.0770 chunk 323 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 377 GLN E 427 GLN E 448 GLN F 206 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 30085 Z= 0.218 Angle : 0.543 11.792 40768 Z= 0.276 Chirality : 0.043 0.169 4568 Planarity : 0.005 0.052 5332 Dihedral : 4.918 84.180 4186 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3764 helix: 1.29 (0.13), residues: 1570 sheet: -0.03 (0.21), residues: 557 loop : 0.30 (0.16), residues: 1637 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 373 time to evaluate : 3.675 Fit side-chains outliers start: 107 outliers final: 56 residues processed: 450 average time/residue: 1.9318 time to fit residues: 989.2215 Evaluate side-chains 411 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 355 time to evaluate : 3.872 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 45 residues processed: 11 average time/residue: 1.0559 time to fit residues: 19.4966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 211 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 360 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 167 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 427 GLN E 428 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN F 427 GLN G 10 ASN H 84 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 30085 Z= 0.196 Angle : 0.525 11.573 40768 Z= 0.267 Chirality : 0.043 0.165 4568 Planarity : 0.005 0.052 5332 Dihedral : 4.815 84.169 4186 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.06 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3764 helix: 1.37 (0.13), residues: 1568 sheet: -0.05 (0.21), residues: 566 loop : 0.33 (0.16), residues: 1630 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 375 time to evaluate : 3.846 Fit side-chains outliers start: 107 outliers final: 59 residues processed: 453 average time/residue: 1.8598 time to fit residues: 969.5849 Evaluate side-chains 417 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 358 time to evaluate : 3.513 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 48 residues processed: 11 average time/residue: 1.3057 time to fit residues: 22.5068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 303 optimal weight: 0.6980 chunk 201 optimal weight: 0.0870 chunk 359 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN E 458 HIS F 206 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN L 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30085 Z= 0.186 Angle : 0.525 13.867 40768 Z= 0.264 Chirality : 0.043 0.163 4568 Planarity : 0.004 0.052 5332 Dihedral : 4.755 84.112 4186 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.06 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3764 helix: 1.42 (0.13), residues: 1566 sheet: -0.01 (0.21), residues: 556 loop : 0.33 (0.16), residues: 1642 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 374 time to evaluate : 3.653 Fit side-chains outliers start: 108 outliers final: 57 residues processed: 459 average time/residue: 1.8270 time to fit residues: 961.6612 Evaluate side-chains 418 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 361 time to evaluate : 3.460 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 50 residues processed: 7 average time/residue: 1.2554 time to fit residues: 15.4995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 282 optimal weight: 0.0010 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 427 GLN E 428 GLN E 458 HIS ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 30085 Z= 0.242 Angle : 0.570 14.479 40768 Z= 0.287 Chirality : 0.044 0.172 4568 Planarity : 0.005 0.062 5332 Dihedral : 4.928 86.151 4186 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.97 % Favored : 98.01 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3764 helix: 1.33 (0.13), residues: 1560 sheet: -0.08 (0.21), residues: 566 loop : 0.31 (0.16), residues: 1638 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 371 time to evaluate : 3.643 Fit side-chains outliers start: 104 outliers final: 63 residues processed: 449 average time/residue: 1.8898 time to fit residues: 970.7366 Evaluate side-chains 422 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 359 time to evaluate : 3.593 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 53 residues processed: 10 average time/residue: 0.9148 time to fit residues: 16.8242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 0.0670 chunk 344 optimal weight: 0.0980 chunk 314 optimal weight: 3.9990 chunk 335 optimal weight: 8.9990 chunk 201 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 302 optimal weight: 6.9990 chunk 316 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN B 477 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 310 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN E 458 HIS F 206 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN G 17 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 30085 Z= 0.155 Angle : 0.511 12.643 40768 Z= 0.256 Chirality : 0.042 0.162 4568 Planarity : 0.004 0.053 5332 Dihedral : 4.632 84.854 4186 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.25 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.14), residues: 3764 helix: 1.48 (0.14), residues: 1566 sheet: 0.01 (0.22), residues: 556 loop : 0.33 (0.16), residues: 1642 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 378 time to evaluate : 4.064 Fit side-chains outliers start: 73 outliers final: 53 residues processed: 438 average time/residue: 1.8625 time to fit residues: 937.1377 Evaluate side-chains 407 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 354 time to evaluate : 3.785 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 49 residues processed: 4 average time/residue: 1.5608 time to fit residues: 12.1322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.9980 chunk 354 optimal weight: 8.9990 chunk 216 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 chunk 246 optimal weight: 2.9990 chunk 371 optimal weight: 7.9990 chunk 342 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 228 optimal weight: 0.0470 chunk 181 optimal weight: 0.0870 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN G 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 30085 Z= 0.158 Angle : 0.513 12.619 40768 Z= 0.257 Chirality : 0.042 0.158 4568 Planarity : 0.004 0.052 5332 Dihedral : 4.540 84.209 4186 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.17 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3764 helix: 1.50 (0.14), residues: 1568 sheet: -0.00 (0.21), residues: 567 loop : 0.39 (0.16), residues: 1629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 362 time to evaluate : 3.732 Fit side-chains outliers start: 63 outliers final: 49 residues processed: 415 average time/residue: 1.8590 time to fit residues: 885.7552 Evaluate side-chains 408 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 359 time to evaluate : 3.811 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 46 residues processed: 3 average time/residue: 1.4287 time to fit residues: 10.2929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.0870 chunk 315 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 296 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 304 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 0.0870 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN F 206 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN G 17 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128986 restraints weight = 35259.228| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.40 r_work: 0.3255 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 30085 Z= 0.155 Angle : 0.506 12.205 40768 Z= 0.253 Chirality : 0.042 0.157 4568 Planarity : 0.004 0.052 5332 Dihedral : 4.485 83.977 4186 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.75 % Favored : 98.22 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3764 helix: 1.58 (0.14), residues: 1565 sheet: 0.07 (0.21), residues: 557 loop : 0.39 (0.16), residues: 1642 =============================================================================== Job complete usr+sys time: 14299.58 seconds wall clock time: 254 minutes 9.33 seconds (15249.33 seconds total)