Starting phenix.real_space_refine on Thu Aug 8 03:07:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/08_2024/7jk3_22360.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/08_2024/7jk3_22360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/08_2024/7jk3_22360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/08_2024/7jk3_22360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/08_2024/7jk3_22360.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/08_2024/7jk3_22360.cif" } resolution = 3.4 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= 0.002 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: 6 Type Number sf(0) Gaussians P 78 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 13529 2.51 5 N 3818 2.21 5 O 4121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 326": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 699": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D ARG 401": "NH1" <-> "NH2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 725": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A ARG 827": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "G GLU 271": "OE1" <-> "OE2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G GLU 343": "OE1" <-> "OE2" Residue "G GLU 353": "OE1" <-> "OE2" Residue "G GLU 377": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G GLU 427": "OE1" <-> "OE2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G GLU 455": "OE1" <-> "OE2" Residue "G ARG 480": "NH1" <-> "NH2" Residue "G ARG 498": "NH1" <-> "NH2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21661 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2290 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Chain: "C" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4934 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 6 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3161 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3129 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 383} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2974 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 2 Chain: "H" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 684 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "I" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 669 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" 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} Chain: "E" 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} Chain: "A" 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} Chain: "G" 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: 12.08, per 1000 atoms: 0.56 Number of scatterers: 21661 At special positions: 0 Unit cell: (128.14, 162.54, 120.4, 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 111 16.00 P 78 15.00 Mg 4 11.99 O 4121 8.00 N 3818 7.00 C 13529 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: 8.28 Conformation dependent library (CDL) restraints added in 4.0 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 13 sheets defined 63.1% alpha, 6.9% beta 32 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 7.18 Creating SS restraints... Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.693A pdb=" N GLU B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.529A pdb=" N MET B 393 " --> pdb=" O THR B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 424 removed outlier: 3.974A pdb=" N LEU B 424 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 455 removed outlier: 3.680A pdb=" N GLN B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 475 removed outlier: 3.560A pdb=" N LEU B 473 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 474 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP B 475 " --> pdb=" O PRO B 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 470 through 475' Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 516 through 524 Processing helix chain 'B' and resid 527 through 544 Processing helix chain 'B' and resid 554 through 565 removed outlier: 3.675A pdb=" N LEU B 558 " --> pdb=" O PRO B 554 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.896A pdb=" N LEU B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 removed outlier: 3.710A pdb=" N LEU B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.848A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 47 through 88 removed outlier: 3.610A pdb=" N GLU C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 122 removed outlier: 5.721A pdb=" N SER C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE C 114 " --> pdb=" O HIS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.513A pdb=" N CYS C 137 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 159 Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.652A pdb=" N CYS C 183 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 216 through 230 Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.999A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 293 through 307 Processing helix chain 'C' and resid 310 through 327 Processing helix chain 'C' and resid 328 through 335 removed outlier: 5.686A pdb=" N ALA C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 334 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS C 335 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 346 Processing helix chain 'C' and resid 349 through 357 removed outlier: 4.247A pdb=" N MET C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU C 354 " --> pdb=" O HIS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.618A pdb=" N THR C 380 " --> pdb=" O ILE C 376 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 416 Proline residue: C 390 - end of helix removed outlier: 4.305A pdb=" N ASP C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.970A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 440 Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.713A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 453 " --> pdb=" O GLN C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 removed outlier: 3.501A pdb=" N GLU C 477 " --> pdb=" O PHE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 508 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 576 removed outlier: 3.786A pdb=" N LYS C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 581 removed outlier: 3.641A pdb=" N HIS C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 581 " --> pdb=" O VAL C 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 576 through 581' Processing helix chain 'C' and resid 590 through 593 Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.594A pdb=" N ALA C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 643 through 653 removed outlier: 3.527A pdb=" N VAL C 647 " --> pdb=" O PRO C 643 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 672 Processing helix chain 'C' and resid 688 through 703 Processing helix chain 'D' and resid 3 through 21 removed outlier: 3.532A pdb=" N GLU D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 95 through 107 removed outlier: 3.910A pdb=" N ALA D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 134 Processing helix chain 'D' and resid 148 through 154 removed outlier: 3.555A pdb=" N PHE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 165 Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.597A pdb=" N GLU D 188 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 211 through 222 removed outlier: 3.576A pdb=" N TYR D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 244 removed outlier: 3.564A pdb=" N LEU D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 4.209A pdb=" N ARG D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 261 removed outlier: 3.828A pdb=" N GLU D 260 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 257 through 261' Processing helix chain 'D' and resid 264 through 280 Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.929A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 removed outlier: 3.616A pdb=" N MET D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 344 through 362 Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.551A pdb=" N ILE D 371 " --> pdb=" O ASN D 367 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 380 " --> pdb=" O SER D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.942A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 403 " --> pdb=" O HIS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.765A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.551A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 15 through 26 removed outlier: 3.723A pdb=" N ILE E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 62 Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.844A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 110 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 162 through 166 removed outlier: 3.538A pdb=" N LYS E 165 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 193 Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 212 through 220 removed outlier: 3.843A pdb=" N GLU E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 238 removed outlier: 4.015A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 4.033A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 264 Processing helix chain 'E' and resid 275 through 287 Proline residue: E 282 - end of helix Processing helix chain 'E' and resid 288 through 290 No H-bonds generated for 'chain 'E' and resid 288 through 290' Processing helix chain 'E' and resid 322 through 337 Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.778A pdb=" N LEU E 346 " --> pdb=" O GLN E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 394 removed outlier: 4.650A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 412 removed outlier: 4.139A pdb=" N LEU E 404 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 449 Processing helix chain 'F' and resid 224 through 238 removed outlier: 3.585A pdb=" N ALA F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.626A pdb=" N ALA A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 571 through 589 removed outlier: 3.624A pdb=" N PHE A 575 " --> pdb=" O ARG A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 641 through 650 removed outlier: 3.880A pdb=" N VAL A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 648 " --> pdb=" O TYR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 removed outlier: 4.012A pdb=" N THR A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 689 Processing helix chain 'A' and resid 695 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.801A pdb=" N LEU A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 748 through 759 removed outlier: 3.892A pdb=" N VAL A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 777 Processing helix chain 'A' and resid 782 through 800 removed outlier: 4.096A pdb=" N ALA A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 800 " --> pdb=" O ILE A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 removed outlier: 3.680A pdb=" N VAL A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 828 Processing helix chain 'A' and resid 830 through 848 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'A' and resid 874 through 888 removed outlier: 4.242A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 918 removed outlier: 3.695A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 260 removed outlier: 4.115A pdb=" N ASN G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 287 removed outlier: 3.910A pdb=" N SER G 287 " --> pdb=" O ASN G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 310 Processing helix chain 'G' and resid 313 through 319 Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 352 through 366 removed outlier: 3.613A pdb=" N HIS G 356 " --> pdb=" O THR G 352 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS G 365 " --> pdb=" O GLN G 361 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR G 366 " --> pdb=" O ARG G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 381 Processing helix chain 'G' and resid 386 through 393 Processing helix chain 'G' and resid 394 through 398 Processing helix chain 'G' and resid 413 through 418 Processing helix chain 'G' and resid 420 through 425 removed outlier: 3.593A pdb=" N ARG G 425 " --> pdb=" O LEU G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 453 removed outlier: 3.519A pdb=" N ILE G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 476 removed outlier: 3.673A pdb=" N LEU G 465 " --> pdb=" O PRO G 461 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 498 removed outlier: 3.764A pdb=" N ALA G 482 " --> pdb=" O ASP G 478 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 542 removed outlier: 3.788A pdb=" N VAL G 534 " --> pdb=" O GLN G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 573 Processing helix chain 'G' and resid 580 through 595 removed outlier: 3.563A pdb=" N LEU G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 614 removed outlier: 4.014A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 645 removed outlier: 3.761A pdb=" N SER G 645 " --> pdb=" O HIS G 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 654 removed outlier: 3.709A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 654 " --> pdb=" O ILE G 650 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 660 removed outlier: 4.383A pdb=" N CYS G 659 " --> pdb=" O ASP G 656 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 660 " --> pdb=" O THR G 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 656 through 660' Processing sheet with id=AA1, first strand: chain 'B' and resid 487 through 488 removed outlier: 6.161A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 430 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU B 463 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU B 432 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER B 465 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 434 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 381 " --> pdb=" O HIS B 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'C' and resid 127 through 131 removed outlier: 6.016A pdb=" N MET C 128 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE C 208 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS C 130 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU C 205 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 239 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 207 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA C 99 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 292 removed outlier: 7.610A pdb=" N HIS C 291 " --> pdb=" O PHE C 596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 658 through 660 Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.852A pdb=" N LEU D 84 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE D 145 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL D 86 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLU D 147 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU D 88 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL D 142 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE D 144 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL D 180 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 146 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN D 50 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY D 179 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU D 52 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR D 181 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU D 54 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 406 through 408 Processing sheet with id=AA8, first strand: chain 'E' and resid 64 through 70 removed outlier: 3.527A pdb=" N ASP E 126 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE E 37 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER E 159 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU E 39 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 416 through 420 removed outlier: 5.514A pdb=" N PHE E 418 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN E 433 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER E 420 " --> pdb=" O ARG E 431 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 431 " --> pdb=" O SER E 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 627 through 633 removed outlier: 6.488A pdb=" N GLU A 628 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU A 682 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 630 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP A 684 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 632 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY A 592 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR A 715 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N MET A 594 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA A 717 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 596 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 852 through 853 Processing sheet with id=AB3, first strand: chain 'G' and resid 320 through 326 removed outlier: 6.432A pdb=" N GLN G 321 " --> pdb=" O LEU G 372 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL G 374 " --> pdb=" O GLN G 321 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL G 323 " --> pdb=" O VAL G 374 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ASP G 376 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE G 325 " --> pdb=" O ASP G 376 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY G 291 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N GLY G 407 " --> pdb=" O GLY G 291 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU G 293 " --> pdb=" O GLY G 407 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA G 409 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL G 295 " --> pdb=" O ALA G 409 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG G 431 " --> pdb=" O SER G 292 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 618 through 621 991 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 8.21 Time building geometry restraints manager: 9.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5825 1.34 - 1.46: 4252 1.46 - 1.58: 11782 1.58 - 1.70: 150 1.70 - 1.82: 163 Bond restraints: 22172 Sorted by residual: bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.52e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C5 ATP G 901 " pdb=" C6 ATP G 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.67e+01 ... (remaining 22167 not shown) Histogram of bond angle deviations from ideal: 97.46 - 105.20: 614 105.20 - 112.93: 12047 112.93 - 120.66: 10413 120.66 - 128.40: 6991 128.40 - 136.13: 193 Bond angle restraints: 30258 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 120.08 19.79 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 120.96 18.91 1.00e+00 1.00e+00 3.57e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 120.99 18.88 1.00e+00 1.00e+00 3.56e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 122.02 17.85 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 119.72 17.11 1.00e+00 1.00e+00 2.93e+02 ... (remaining 30253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11510 17.95 - 35.91: 1282 35.91 - 53.86: 458 53.86 - 71.82: 113 71.82 - 89.77: 27 Dihedral angle restraints: 13390 sinusoidal: 5977 harmonic: 7413 Sorted by residual: dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ASN G 260 " pdb=" CA ASN G 260 " ideal model delta harmonic sigma weight residual 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA MET E 134 " pdb=" C MET E 134 " pdb=" N ASP E 135 " pdb=" CA ASP E 135 " ideal model delta harmonic sigma weight residual -180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASP E 135 " pdb=" C ASP E 135 " pdb=" N ALA E 136 " pdb=" CA ALA E 136 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 13387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2487 0.044 - 0.089: 774 0.089 - 0.133: 188 0.133 - 0.178: 36 0.178 - 0.222: 7 Chirality restraints: 3492 Sorted by residual: chirality pdb=" CA ASP C 714 " pdb=" N ASP C 714 " pdb=" C ASP C 714 " pdb=" CB ASP C 714 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB THR A 679 " pdb=" CA THR A 679 " pdb=" OG1 THR A 679 " pdb=" CG2 THR A 679 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLU E 260 " pdb=" N GLU E 260 " pdb=" C GLU E 260 " pdb=" CB GLU E 260 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3489 not shown) Planarity restraints: 3603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 712 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" C LYS C 712 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS C 712 " -0.020 2.00e-02 2.50e+03 pdb=" N THR C 713 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP G 395 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO G 396 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 74 " 0.049 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO D 75 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.042 5.00e-02 4.00e+02 ... (remaining 3600 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 23 2.35 - 2.99: 9278 2.99 - 3.62: 31585 3.62 - 4.26: 48614 4.26 - 4.90: 81904 Nonbonded interactions: 171404 Sorted by model distance: nonbonded pdb=" NH1 ARG C 711 " pdb=" O3' DA I 43 " model vdw 1.709 3.120 nonbonded pdb=" OG1 THR G 304 " pdb="MG MG G 902 " model vdw 2.106 2.170 nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.117 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 2.122 2.170 nonbonded pdb=" OG1 THR E 48 " pdb="MG MG E 902 " model vdw 2.128 2.170 ... (remaining 171399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.750 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: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.490 Set scattering table: 0.000 Process input model: 61.940 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.005 0.081 22172 Z= 0.280 Angle : 0.866 19.789 30258 Z= 0.553 Chirality : 0.046 0.222 3492 Planarity : 0.007 0.076 3603 Dihedral : 17.808 89.771 8550 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.18 % Allowed : 5.82 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.13), residues: 2478 helix: -2.55 (0.09), residues: 1448 sheet: -1.77 (0.30), residues: 228 loop : -2.42 (0.17), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 57 HIS 0.011 0.001 HIS G 629 PHE 0.019 0.002 PHE D 256 TYR 0.015 0.001 TYR E 258 ARG 0.007 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 2.382 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: B 562 CYS cc_start: 0.9246 (m) cc_final: 0.8941 (p) REVERT: C 52 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8212 (mm-30) REVERT: C 353 MET cc_start: 0.9122 (mmt) cc_final: 0.8864 (mmm) REVERT: C 383 ASP cc_start: 0.9088 (m-30) cc_final: 0.8859 (p0) REVERT: C 454 LEU cc_start: 0.7557 (tp) cc_final: 0.6884 (tt) REVERT: C 699 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7537 (mt-10) REVERT: D 426 MET cc_start: 0.8449 (mmm) cc_final: 0.8221 (mmp) REVERT: F 224 ASP cc_start: 0.9297 (t0) cc_final: 0.8988 (t70) REVERT: F 226 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9253 (mp0) REVERT: A 622 ASN cc_start: 0.9018 (t0) cc_final: 0.8797 (t0) REVERT: A 631 GLU cc_start: 0.8033 (pp20) cc_final: 0.7828 (pm20) REVERT: A 788 ASP cc_start: 0.8471 (m-30) cc_final: 0.8229 (m-30) REVERT: A 817 MET cc_start: 0.8916 (mmm) cc_final: 0.8200 (mmm) REVERT: G 491 GLU cc_start: 0.8308 (tt0) cc_final: 0.7859 (pt0) REVERT: G 563 MET cc_start: 0.8404 (tmm) cc_final: 0.7867 (tmm) REVERT: G 592 CYS cc_start: 0.9046 (m) cc_final: 0.8460 (m) outliers start: 4 outliers final: 0 residues processed: 212 average time/residue: 0.3683 time to fit residues: 117.7619 Evaluate side-chains 134 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 149 optimal weight: 0.3980 chunk 232 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 ASN B 348 ASN B 374 HIS B 498 ASN B 577 GLN C 368 GLN C 578 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 HIS D 455 GLN E 150 ASN E 414 ASN E 433 GLN A 621 GLN A 718 ASN A 747 HIS A 749 GLN A 809 HIS A 838 GLN A 902 GLN G 265 GLN G 284 HIS G 386 GLN G 585 HIS G 634 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22172 Z= 0.159 Angle : 0.531 10.965 30258 Z= 0.279 Chirality : 0.037 0.167 3492 Planarity : 0.004 0.055 3603 Dihedral : 17.342 89.023 3578 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.68 % Allowed : 9.78 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.38 (0.16), residues: 2478 helix: -0.34 (0.13), residues: 1469 sheet: -1.39 (0.32), residues: 227 loop : -1.64 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 276 HIS 0.006 0.001 HIS A 747 PHE 0.009 0.001 PHE D 121 TYR 0.014 0.001 TYR A 629 ARG 0.009 0.000 ARG C 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9355 (m-40) cc_final: 0.8987 (m110) REVERT: B 420 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8788 (tp30) REVERT: B 562 CYS cc_start: 0.9231 (m) cc_final: 0.8907 (m) REVERT: C 324 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8228 (tm-30) REVERT: C 383 ASP cc_start: 0.9171 (m-30) cc_final: 0.8850 (p0) REVERT: C 699 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7712 (mt-10) REVERT: D 347 GLU cc_start: 0.8533 (mp0) cc_final: 0.8090 (mp0) REVERT: D 440 MET cc_start: 0.8680 (mmp) cc_final: 0.8362 (mmm) REVERT: E 101 MET cc_start: 0.8180 (mmm) cc_final: 0.7973 (mmm) REVERT: E 249 LEU cc_start: 0.9288 (mt) cc_final: 0.8927 (tt) REVERT: E 254 CYS cc_start: 0.7905 (m) cc_final: 0.7658 (t) REVERT: F 231 ARG cc_start: 0.9527 (mtp-110) cc_final: 0.9296 (ttp-110) REVERT: F 232 MET cc_start: 0.8994 (mmm) cc_final: 0.8748 (mmm) REVERT: A 622 ASN cc_start: 0.9104 (t0) cc_final: 0.8841 (t0) REVERT: A 631 GLU cc_start: 0.8015 (pp20) cc_final: 0.7780 (pm20) REVERT: A 817 MET cc_start: 0.8988 (mmm) cc_final: 0.7886 (mmm) REVERT: G 491 GLU cc_start: 0.8348 (tt0) cc_final: 0.7861 (pt0) REVERT: G 575 ARG cc_start: 0.7346 (tpt90) cc_final: 0.6971 (tpt90) REVERT: G 592 CYS cc_start: 0.8984 (m) cc_final: 0.8464 (m) outliers start: 15 outliers final: 12 residues processed: 156 average time/residue: 0.3945 time to fit residues: 96.4252 Evaluate side-chains 142 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 230 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 186 optimal weight: 8.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN C 652 HIS D 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1984 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: