Starting phenix.real_space_refine on Tue Dec 12 15:15:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/12_2023/7jgr_22329_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/12_2023/7jgr_22329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/12_2023/7jgr_22329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/12_2023/7jgr_22329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/12_2023/7jgr_22329_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/12_2023/7jgr_22329_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 80 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 13572 2.51 5 N 3813 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B GLU 613": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C GLU 354": "OE1" <-> "OE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 699": "OE1" <-> "OE2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E ARG 431": "NH1" <-> "NH2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 725": "NH1" <-> "NH2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "G GLU 279": "OE1" <-> "OE2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G GLU 343": "OE1" <-> "OE2" Residue "G GLU 358": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G GLU 455": "OE1" <-> "OE2" Residue "G ARG 498": "NH1" <-> "NH2" Residue "G GLU 574": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 21717 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2321 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 3 Chain: "C" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4918 Classifications: {'peptide': 612} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 588} Chain breaks: 7 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: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} 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: 11.66, per 1000 atoms: 0.54 Number of scatterers: 21717 At special positions: 0 Unit cell: (122.98, 159.1, 123.84, 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 80 15.00 Mg 4 11.99 O 4137 8.00 N 3813 7.00 C 13572 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: 8.92 Conformation dependent library (CDL) restraints added in 3.8 seconds 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 13 sheets defined 55.9% alpha, 6.8% beta 28 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 10.52 Creating SS restraints... Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 411 through 423 Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 471 through 473 No H-bonds generated for 'chain 'B' and resid 471 through 473' Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 528 through 544 Processing helix chain 'B' and resid 555 through 564 Processing helix chain 'B' and resid 571 through 583 Processing helix chain 'B' and resid 605 through 614 Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 48 through 88 removed outlier: 5.136A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.571A pdb=" N LEU C 111 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 112 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 122 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 140 through 158 Processing helix chain 'C' and resid 185 through 198 removed outlier: 3.995A pdb=" N ASP C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER C 198 " --> pdb=" O ASN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 217 through 229 Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 255 through 260 removed outlier: 4.118A pdb=" N LYS C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 281 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 311 through 328 removed outlier: 4.563A pdb=" N GLY C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 360 through 367 Proline residue: C 364 - end of helix Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'C' and resid 383 through 415 Proline residue: C 390 - end of helix removed outlier: 4.666A pdb=" N GLU C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 413 " --> pdb=" O PHE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 456 through 476 Processing helix chain 'C' and resid 485 through 507 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 564 through 575 Processing helix chain 'C' and resid 584 through 586 No H-bonds generated for 'chain 'C' and resid 584 through 586' Processing helix chain 'C' and resid 591 through 593 No H-bonds generated for 'chain 'C' and resid 591 through 593' Processing helix chain 'C' and resid 599 through 606 Processing helix chain 'C' and resid 610 through 619 Processing helix chain 'C' and resid 621 through 625 removed outlier: 4.093A pdb=" N MET C 625 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.522A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 688 through 702 Processing helix chain 'D' and resid 4 through 20 removed outlier: 3.742A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 9 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 Processing helix chain 'D' and resid 63 through 76 Proline residue: D 75 - end of helix Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 121 through 133 Processing helix chain 'D' and resid 149 through 154 removed outlier: 3.772A pdb=" N ALA D 154 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 5.984A pdb=" N LEU D 160 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE D 165 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL D 167 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.532A pdb=" N LEU D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 243 Processing helix chain 'D' and resid 251 through 254 Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 298 through 311 removed outlier: 4.071A pdb=" N HIS D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 332 Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 345 through 361 Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.723A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 433 through 442 removed outlier: 3.569A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.819A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 101 through 111 removed outlier: 3.722A pdb=" N GLN E 111 " --> pdb=" O GLN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.754A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.536A pdb=" N ARG E 144 " --> pdb=" O PRO E 140 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 185 through 204 removed outlier: 4.302A pdb=" N ASP E 195 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 218 Processing helix chain 'E' and resid 223 through 237 removed outlier: 4.106A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 4.300A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 No H-bonds generated for 'chain 'E' and resid 260 through 263' Processing helix chain 'E' and resid 276 through 289 Proline residue: E 282 - end of helix removed outlier: 3.584A pdb=" N SER E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN E 289 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 337 Processing helix chain 'E' and resid 343 through 347 Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'F' and resid 225 through 237 Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.525A pdb=" N ALA A 643 " --> pdb=" O PRO A 640 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 647 " --> pdb=" O TYR A 644 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A 648 " --> pdb=" O VAL A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 669 Processing helix chain 'A' and resid 686 through 689 Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 722 through 725 No H-bonds generated for 'chain 'A' and resid 722 through 725' Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.861A pdb=" N GLN A 751 " --> pdb=" O HIS A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 777 Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.618A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 831 through 847 removed outlier: 3.652A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 875 through 887 removed outlier: 3.823A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.734A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 259 Processing helix chain 'G' and resid 272 through 286 Processing helix chain 'G' and resid 303 through 310 Processing helix chain 'G' and resid 314 through 319 Processing helix chain 'G' and resid 333 through 344 removed outlier: 3.850A pdb=" N VAL G 336 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR G 337 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 365 Processing helix chain 'G' and resid 378 through 381 Processing helix chain 'G' and resid 387 through 393 Processing helix chain 'G' and resid 414 through 418 Processing helix chain 'G' and resid 420 through 424 removed outlier: 3.631A pdb=" N ALA G 424 " --> pdb=" O ARG G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 453 removed outlier: 3.616A pdb=" N ALA G 452 " --> pdb=" O LYS G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 462 through 475 removed outlier: 3.670A pdb=" N ALA G 470 " --> pdb=" O GLN G 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 497 removed outlier: 3.797A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 541 Processing helix chain 'G' and resid 558 through 573 Processing helix chain 'G' and resid 581 through 594 removed outlier: 3.795A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 602 through 615 removed outlier: 4.033A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG G 615 " --> pdb=" O LEU G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 626 through 628 No H-bonds generated for 'chain 'G' and resid 626 through 628' Processing helix chain 'G' and resid 637 through 644 removed outlier: 3.767A pdb=" N ALA G 642 " --> pdb=" O GLU G 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 647 through 654 removed outlier: 3.647A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 657 through 659 No H-bonds generated for 'chain 'G' and resid 657 through 659' Processing sheet with id= A, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.265A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 430 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU B 463 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 432 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N SER B 465 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL B 434 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 381 " --> pdb=" O HIS B 435 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 588 through 591 Processing sheet with id= C, first strand: chain 'C' and resid 261 through 267 removed outlier: 7.321A pdb=" N LEU C 96 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ARG C 264 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR C 98 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE C 266 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 100 " --> pdb=" O PHE C 266 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 127 through 131 removed outlier: 6.072A pdb=" N GLN C 204 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N CYS C 130 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL C 206 " --> pdb=" O CYS C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 658 through 660 Processing sheet with id= F, first strand: chain 'D' and resid 50 through 55 Processing sheet with id= G, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.255A pdb=" N SER D 141 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL D 86 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE D 143 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU D 88 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE D 145 " --> pdb=" O LEU D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 406 through 408 Processing sheet with id= I, first strand: chain 'E' and resid 176 through 180 removed outlier: 8.009A pdb=" N ILE E 37 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL E 155 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU E 39 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU E 157 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY E 41 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER E 159 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG E 65 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA E 124 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA E 67 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP E 126 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 69 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 739 through 742 removed outlier: 8.963A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 851 through 853 removed outlier: 3.531A pdb=" N THR A 852 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 431 through 435 removed outlier: 6.031A pdb=" N LEU G 371 " --> pdb=" O LEU G 404 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL G 406 " --> pdb=" O LEU G 371 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU G 373 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE G 408 " --> pdb=" O LEU G 373 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU G 375 " --> pdb=" O ILE G 408 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 618 through 621 895 hydrogen bonds defined for protein. 2544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 7.96 Time building geometry restraints manager: 9.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5636 1.33 - 1.46: 4757 1.46 - 1.58: 11524 1.58 - 1.70: 153 1.70 - 1.82: 163 Bond restraints: 22233 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.20e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.73e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.51e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 ... (remaining 22228 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.68: 717 105.68 - 113.21: 12256 113.21 - 120.75: 10651 120.75 - 128.28: 6515 128.28 - 135.81: 210 Bond angle restraints: 30349 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 139.87 118.67 21.20 1.00e+00 1.00e+00 4.49e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 121.08 18.79 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 119.69 17.14 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 122.91 16.96 1.00e+00 1.00e+00 2.88e+02 ... (remaining 30344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11566 17.93 - 35.86: 1278 35.86 - 53.79: 492 53.79 - 71.72: 116 71.72 - 89.64: 26 Dihedral angle restraints: 13478 sinusoidal: 6058 harmonic: 7420 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 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN C 347 " pdb=" C GLN C 347 " pdb=" N LEU C 348 " pdb=" CA LEU C 348 " ideal model delta harmonic sigma weight residual -180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA SER G 349 " pdb=" C SER G 349 " pdb=" N GLY G 350 " pdb=" CA GLY G 350 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 13475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2834 0.063 - 0.126: 566 0.126 - 0.189: 97 0.189 - 0.252: 4 0.252 - 0.315: 2 Chirality restraints: 3503 Sorted by residual: chirality pdb=" CG LEU C 275 " pdb=" CB LEU C 275 " pdb=" CD1 LEU C 275 " pdb=" CD2 LEU C 275 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C4' DA I 42 " pdb=" C5' DA I 42 " pdb=" O4' DA I 42 " pdb=" C3' DA I 42 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL E 221 " pdb=" CA VAL E 221 " pdb=" CG1 VAL E 221 " pdb=" CG2 VAL E 221 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 3500 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 873 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 150 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" CG ASN E 150 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN E 150 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN E 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 281 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO E 282 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 282 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 282 " -0.032 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 53 2.42 - 3.04: 11046 3.04 - 3.66: 33618 3.66 - 4.28: 50376 4.28 - 4.90: 82648 Nonbonded interactions: 177741 Sorted by model distance: nonbonded pdb=" O2 DC H 18 " pdb=" N2 DG I 51 " model vdw 1.799 2.496 nonbonded pdb=" N3 DC H 18 " pdb=" N1 DG I 51 " model vdw 2.066 2.560 nonbonded pdb=" OG1 THR G 304 " pdb="MG MG G 902 " model vdw 2.089 2.170 nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.114 2.170 nonbonded pdb=" O2B ATP G 901 " pdb="MG MG G 902 " model vdw 2.128 2.170 ... (remaining 177736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.820 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 65.800 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 0.097 22233 Z= 0.370 Angle : 0.952 21.197 30349 Z= 0.589 Chirality : 0.053 0.315 3503 Planarity : 0.006 0.087 3607 Dihedral : 17.946 89.644 8634 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.36 % Allowed : 5.00 % Favored : 94.64 % 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: -2.88 (0.14), residues: 2481 helix: -2.59 (0.08), residues: 1479 sheet: -2.73 (0.28), residues: 233 loop : 0.54 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 191 HIS 0.006 0.001 HIS E 278 PHE 0.026 0.003 PHE C 215 TYR 0.028 0.002 TYR E 258 ARG 0.009 0.001 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 587 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 593 average time/residue: 0.4009 time to fit residues: 346.4151 Evaluate side-chains 241 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 108 optimal weight: 0.0170 chunk 66 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 233 optimal weight: 0.7980 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 ASN B 436 ASN B 498 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN C 194 ASN C 250 HIS C 391 GLN C 435 ASN C 605 ASN D 35 ASN D 202 GLN D 421 GLN E 70 ASN E 127 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 GLN E 451 ASN A 749 GLN A 828 ASN A 838 GLN G 284 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 22233 Z= 0.245 Angle : 0.662 10.846 30349 Z= 0.342 Chirality : 0.041 0.188 3503 Planarity : 0.005 0.108 3607 Dihedral : 17.788 83.031 3661 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.67 % Allowed : 13.87 % Favored : 84.46 % 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: -0.67 (0.16), residues: 2481 helix: -0.22 (0.12), residues: 1477 sheet: -2.34 (0.29), residues: 224 loop : 0.14 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 276 HIS 0.007 0.001 HIS G 641 PHE 0.027 0.002 PHE C 662 TYR 0.025 0.001 TYR A 648 ARG 0.009 0.001 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 239 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 266 average time/residue: 0.3375 time to fit residues: 142.6471 Evaluate side-chains 211 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 2.394 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2081 time to fit residues: 9.7611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 9.9990 chunk 72 optimal weight: 0.0060 chunk 194 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 208 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 609 GLN C 368 GLN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22233 Z= 0.179 Angle : 0.607 11.533 30349 Z= 0.307 Chirality : 0.039 0.302 3503 Planarity : 0.004 0.079 3607 Dihedral : 17.580 78.958 3661 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.17 % Allowed : 14.95 % Favored : 83.87 % 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: 0.05 (0.17), residues: 2481 helix: 0.54 (0.13), residues: 1485 sheet: -2.03 (0.30), residues: 234 loop : 0.03 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 276 HIS 0.004 0.001 HIS B 285 PHE 0.018 0.001 PHE C 594 TYR 0.015 0.001 TYR G 324 ARG 0.006 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 236 average time/residue: 0.3188 time to fit residues: 121.6107 Evaluate side-chains 188 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 2.634 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2320 time to fit residues: 8.2544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 HIS ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22233 Z= 0.207 Angle : 0.582 12.372 30349 Z= 0.297 Chirality : 0.039 0.283 3503 Planarity : 0.004 0.052 3607 Dihedral : 17.392 80.388 3661 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.31 % Allowed : 15.81 % Favored : 82.88 % 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: 0.52 (0.17), residues: 2481 helix: 0.94 (0.14), residues: 1503 sheet: -1.74 (0.31), residues: 240 loop : 0.12 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 276 HIS 0.005 0.001 HIS G 434 PHE 0.021 0.001 PHE C 318 TYR 0.021 0.001 TYR A 648 ARG 0.006 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 209 average time/residue: 0.3138 time to fit residues: 107.4170 Evaluate side-chains 171 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 2.412 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1962 time to fit residues: 6.9331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 0.6980 chunk 222 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN C 113 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22233 Z= 0.153 Angle : 0.562 12.276 30349 Z= 0.283 Chirality : 0.038 0.297 3503 Planarity : 0.003 0.050 3607 Dihedral : 17.234 77.991 3661 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.17 % Allowed : 16.53 % Favored : 82.30 % 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: 0.74 (0.17), residues: 2481 helix: 1.12 (0.14), residues: 1491 sheet: -1.47 (0.31), residues: 240 loop : 0.12 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 276 HIS 0.004 0.001 HIS C 230 PHE 0.018 0.001 PHE C 318 TYR 0.022 0.001 TYR A 648 ARG 0.006 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 208 average time/residue: 0.3246 time to fit residues: 109.3669 Evaluate side-chains 170 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 2.511 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1918 time to fit residues: 6.2624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 0.2980 chunk 223 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 115 optimal weight: 0.0470 chunk 20 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 overall best weight: 0.4880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22233 Z= 0.144 Angle : 0.548 13.173 30349 Z= 0.277 Chirality : 0.038 0.240 3503 Planarity : 0.003 0.044 3607 Dihedral : 17.100 85.322 3661 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.90 % Allowed : 17.30 % Favored : 81.80 % 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: 0.86 (0.17), residues: 2481 helix: 1.25 (0.14), residues: 1484 sheet: -1.30 (0.31), residues: 251 loop : 0.09 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 276 HIS 0.006 0.001 HIS E 337 PHE 0.018 0.001 PHE C 318 TYR 0.034 0.001 TYR C 72 ARG 0.007 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 204 average time/residue: 0.3263 time to fit residues: 107.0762 Evaluate side-chains 173 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 2.513 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1991 time to fit residues: 6.3298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.8448 > 50: distance: 46 - 67: 15.040 distance: 52 - 76: 27.619 distance: 65 - 67: 12.837 distance: 67 - 68: 23.386 distance: 68 - 69: 11.100 distance: 68 - 71: 18.758 distance: 69 - 70: 14.213 distance: 69 - 76: 10.527 distance: 71 - 72: 3.566 distance: 72 - 73: 6.782 distance: 73 - 74: 20.428 distance: 74 - 75: 36.907 distance: 76 - 77: 21.101 distance: 77 - 78: 27.908 distance: 77 - 80: 30.826 distance: 78 - 79: 3.992 distance: 78 - 87: 7.165 distance: 80 - 81: 17.138 distance: 81 - 82: 13.978 distance: 82 - 83: 16.407 distance: 83 - 84: 7.110 distance: 84 - 85: 5.286 distance: 84 - 86: 4.238 distance: 87 - 88: 3.742 distance: 88 - 89: 8.445 distance: 88 - 91: 24.642 distance: 89 - 90: 10.137 distance: 89 - 96: 30.061 distance: 91 - 92: 41.160 distance: 92 - 93: 42.502 distance: 93 - 94: 9.767 distance: 93 - 95: 34.490 distance: 96 - 97: 22.400 distance: 97 - 100: 19.684 distance: 98 - 104: 47.664 distance: 100 - 101: 12.650 distance: 101 - 102: 9.565 distance: 101 - 103: 28.937 distance: 104 - 105: 19.471 distance: 105 - 106: 15.676 distance: 105 - 108: 29.230 distance: 106 - 107: 7.753 distance: 108 - 109: 26.600 distance: 108 - 110: 52.047 distance: 111 - 112: 5.684 distance: 112 - 113: 16.468 distance: 112 - 115: 32.618 distance: 113 - 114: 15.272 distance: 113 - 122: 46.896 distance: 115 - 116: 11.744 distance: 116 - 117: 22.393 distance: 117 - 118: 14.697 distance: 118 - 119: 6.444 distance: 119 - 120: 12.217 distance: 119 - 121: 4.691 distance: 122 - 123: 5.433 distance: 123 - 124: 15.579 distance: 123 - 126: 7.254 distance: 124 - 125: 7.758 distance: 124 - 129: 7.220 distance: 126 - 127: 13.008 distance: 126 - 128: 13.079 distance: 129 - 130: 15.185 distance: 130 - 131: 18.245 distance: 130 - 133: 14.304 distance: 131 - 132: 13.623 distance: 131 - 134: 18.296 distance: 134 - 135: 26.810 distance: 135 - 136: 29.538 distance: 135 - 138: 17.066 distance: 136 - 137: 38.227 distance: 136 - 144: 16.404 distance: 138 - 139: 20.994 distance: 139 - 140: 30.113 distance: 139 - 141: 30.618 distance: 140 - 142: 26.597 distance: 141 - 143: 19.678 distance: 142 - 143: 22.718 distance: 144 - 145: 30.188 distance: 145 - 146: 12.191 distance: 145 - 148: 37.579 distance: 146 - 152: 34.905 distance: 148 - 149: 19.491 distance: 149 - 150: 57.775 distance: 149 - 151: 25.790