Starting phenix.real_space_refine on Sun May 18 14:58:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vnv_43361/05_2025/8vnv_43361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vnv_43361/05_2025/8vnv_43361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vnv_43361/05_2025/8vnv_43361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vnv_43361/05_2025/8vnv_43361.map" model { file = "/net/cci-nas-00/data/ceres_data/8vnv_43361/05_2025/8vnv_43361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vnv_43361/05_2025/8vnv_43361.cif" } resolution = 3.1 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1328 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 95 5.16 5 C 9928 2.51 5 N 2871 2.21 5 O 2984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15927 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3340 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 7 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 9, 'ASN:plan1': 9, 'HIS:plan': 1, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 184 Chain: "L" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2874 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3080 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4278 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 753 Unresolved non-hydrogen dihedrals: 486 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 15, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 372 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 290 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'M3L:plan-1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "P" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "H" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "I" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 159 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 19} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 537 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 9.29, per 1000 atoms: 0.58 Number of scatterers: 15927 At special positions: 0 Unit cell: (160.65, 130.2, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 95 16.00 P 49 15.00 O 2984 8.00 N 2871 7.00 C 9928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 294 " distance=2.02 Simple disulfide: pdb=" SG CYS C 523 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 549 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 553 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 4.26 Conformation dependent library (CDL) restraints added in 2.1 seconds 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 23 sheets defined 25.6% alpha, 20.7% beta 20 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'A' and resid 83 through 107 Proline residue: A 93 - end of helix removed outlier: 4.095A pdb=" N ILE A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 6.182A pdb=" N THR A 116 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR A 117 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 119 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 459 through 470 Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.375A pdb=" N HIS A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 589 through 602 removed outlier: 4.011A pdb=" N ILE A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 602 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 623 removed outlier: 3.875A pdb=" N VAL A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 651 removed outlier: 4.675A pdb=" N HIS A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 Processing helix chain 'A' and resid 670 through 682 removed outlier: 3.810A pdb=" N ILE A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 267 through 279 removed outlier: 3.656A pdb=" N TYR L 278 " --> pdb=" O ILE L 274 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP L 279 " --> pdb=" O LYS L 275 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 399 removed outlier: 3.835A pdb=" N ALA L 399 " --> pdb=" O PRO L 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 28 Processing helix chain 'N' and resid 155 through 157 No H-bonds generated for 'chain 'N' and resid 155 through 157' Processing helix chain 'N' and resid 210 through 214 removed outlier: 4.262A pdb=" N GLY N 214 " --> pdb=" O PRO N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 350 No H-bonds generated for 'chain 'N' and resid 348 through 350' Processing helix chain 'N' and resid 355 through 362 Processing helix chain 'N' and resid 406 through 409 Processing helix chain 'C' and resid 18 through 62 removed outlier: 4.416A pdb=" N LEU C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.563A pdb=" N ASP C 142 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 153 removed outlier: 4.044A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 178 Processing helix chain 'C' and resid 221 through 231 Processing helix chain 'C' and resid 236 through 250 removed outlier: 3.906A pdb=" N LEU C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 278 through 284 Processing helix chain 'C' and resid 328 through 338 removed outlier: 3.624A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 448 removed outlier: 3.882A pdb=" N GLY C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR C 446 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 457 Processing helix chain 'C' and resid 462 through 474 Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.613A pdb=" N LEU C 498 " --> pdb=" O ARG C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 514 Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 571 through 576 removed outlier: 3.549A pdb=" N ALA C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 648 through 662 removed outlier: 3.883A pdb=" N VAL C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 687 removed outlier: 3.511A pdb=" N ARG C 685 " --> pdb=" O ASN C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.952A pdb=" N SER B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'P' and resid 191 through 210 removed outlier: 3.630A pdb=" N ALA P 197 " --> pdb=" O GLN P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 259 No H-bonds generated for 'chain 'P' and resid 257 through 259' Processing helix chain 'P' and resid 270 through 272 No H-bonds generated for 'chain 'P' and resid 270 through 272' Processing helix chain 'P' and resid 277 through 281 Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 232 removed outlier: 3.837A pdb=" N GLU A 314 " --> pdb=" O LYS P 231 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS P 231 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE P 227 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA P 228 " --> pdb=" O LEU P 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 211 removed outlier: 3.568A pdb=" N THR A 208 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL A 186 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS A 210 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 184 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU A 185 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE A 252 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU A 187 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU A 250 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 189 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TYR A 248 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 191 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 444 removed outlier: 4.595A pdb=" N ILE A 428 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG A 427 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 487 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE A 429 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 489 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLN A 431 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 491 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N LEU A 433 " --> pdb=" O ILE A 491 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 557 through 560 removed outlier: 3.689A pdb=" N ILE A 525 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL N 35 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL N 389 " --> pdb=" O TRP N 382 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TRP N 382 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS N 391 " --> pdb=" O PHE N 380 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE N 380 " --> pdb=" O CYS N 391 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL N 393 " --> pdb=" O SER N 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 413 through 418 removed outlier: 4.277A pdb=" N GLN L 415 " --> pdb=" O VAL L 428 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER L 433 " --> pdb=" O CYS L 429 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN L 86 " --> pdb=" O ARG L 436 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP L 438 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS L 84 " --> pdb=" O ASP L 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 96 through 101 removed outlier: 5.784A pdb=" N GLY L 98 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL L 116 " --> pdb=" O GLY L 98 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU L 111 " --> pdb=" O CYS L 126 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU L 123 " --> pdb=" O GLN L 136 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN L 136 " --> pdb=" O LEU L 123 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU L 125 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU L 134 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 151 through 154 removed outlier: 3.951A pdb=" N LYS L 184 " --> pdb=" O ILE L 174 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN L 176 " --> pdb=" O CYS L 182 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N CYS L 182 " --> pdb=" O ASN L 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 193 through 198 removed outlier: 6.351A pdb=" N VAL L 209 " --> pdb=" O ASN L 194 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU L 196 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU L 207 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE L 198 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU L 205 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER L 210 " --> pdb=" O ALA L 214 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA L 214 " --> pdb=" O SER L 210 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE L 228 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 239 through 244 removed outlier: 3.582A pdb=" N SER L 241 " --> pdb=" O CYS L 254 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET L 252 " --> pdb=" O ASP L 243 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE L 299 " --> pdb=" O LEU L 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 309 through 315 removed outlier: 3.691A pdb=" N CYS L 311 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER L 323 " --> pdb=" O ALA L 327 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA L 327 " --> pdb=" O SER L 323 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE L 328 " --> pdb=" O ARG L 355 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG L 355 " --> pdb=" O ILE L 328 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS L 330 " --> pdb=" O LEU L 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 368 through 370 Processing sheet with id=AB3, first strand: chain 'N' and resid 48 through 54 removed outlier: 5.206A pdb=" N ARG N 65 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASP N 52 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE N 63 " --> pdb=" O ASP N 52 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR N 54 " --> pdb=" O PHE N 61 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE N 61 " --> pdb=" O THR N 54 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER N 83 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE N 117 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLN N 85 " --> pdb=" O ILE N 115 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE N 115 " --> pdb=" O GLN N 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 129 through 132 removed outlier: 3.654A pdb=" N ARG N 129 " --> pdb=" O LYS N 143 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG N 172 " --> pdb=" O VAL N 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 182 through 185 removed outlier: 4.001A pdb=" N SER N 184 " --> pdb=" O LEU N 194 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU N 194 " --> pdb=" O SER N 184 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 230 through 235 removed outlier: 3.810A pdb=" N ASP N 232 " --> pdb=" O VAL N 246 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL N 246 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 276 through 281 removed outlier: 3.817A pdb=" N CYS N 278 " --> pdb=" O GLY N 292 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS N 311 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASP N 302 " --> pdb=" O LYS N 309 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LYS N 309 " --> pdb=" O ASP N 302 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 320 through 325 removed outlier: 6.147A pdb=" N ASP N 346 " --> pdb=" O LEU N 366 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU N 366 " --> pdb=" O ASP N 346 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 114 through 115 removed outlier: 5.930A pdb=" N SER C 114 " --> pdb=" O GLY C 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 121 removed outlier: 6.111A pdb=" N PHE C 120 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N SER C 647 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.598A pdb=" N LYS C 291 " --> pdb=" O CYS C 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 614 through 618 removed outlier: 4.006A pdb=" N GLU C 720 " --> pdb=" O ILE C 628 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 637 through 640 removed outlier: 7.001A pdb=" N PHE C 637 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA C 712 " --> pdb=" O PHE C 637 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER C 639 " --> pdb=" O ILE C 710 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 219 through 223 removed outlier: 3.521A pdb=" N VAL P 267 " --> pdb=" O VAL P 220 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 5.75 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5091 1.34 - 1.46: 3486 1.46 - 1.58: 7609 1.58 - 1.70: 96 1.70 - 1.82: 131 Bond restraints: 16413 Sorted by residual: bond pdb=" C2 SAH C 801 " pdb=" N3 SAH C 801 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.63e+00 bond pdb=" C8 SAH C 801 " pdb=" N7 SAH C 801 " ideal model delta sigma weight residual 1.299 1.349 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C2 SAH C 801 " pdb=" N1 SAH C 801 " ideal model delta sigma weight residual 1.330 1.380 -0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" C6 SAH C 801 " pdb=" N1 SAH C 801 " ideal model delta sigma weight residual 1.338 1.379 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C3' DG D 161 " pdb=" O3' DG D 161 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.00e+00 ... (remaining 16408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 22051 2.07 - 4.15: 413 4.15 - 6.22: 54 6.22 - 8.30: 11 8.30 - 10.37: 8 Bond angle restraints: 22537 Sorted by residual: angle pdb=" C LEU L 225 " pdb=" N VAL L 226 " pdb=" CA VAL L 226 " ideal model delta sigma weight residual 122.96 118.85 4.11 9.50e-01 1.11e+00 1.87e+01 angle pdb=" CA LYS P 231 " pdb=" CB LYS P 231 " pdb=" CG LYS P 231 " ideal model delta sigma weight residual 114.10 122.51 -8.41 2.00e+00 2.50e-01 1.77e+01 angle pdb=" N TYR L 148 " pdb=" CA TYR L 148 " pdb=" C TYR L 148 " ideal model delta sigma weight residual 107.60 114.67 -7.07 1.83e+00 2.99e-01 1.49e+01 angle pdb=" CG SAH C 801 " pdb=" SD SAH C 801 " pdb=" C5' SAH C 801 " ideal model delta sigma weight residual 101.77 91.40 10.37 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N ASN N 277 " pdb=" CA ASN N 277 " pdb=" C ASN N 277 " ideal model delta sigma weight residual 107.32 113.02 -5.70 1.65e+00 3.67e-01 1.19e+01 ... (remaining 22532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 9187 35.16 - 70.33: 409 70.33 - 105.49: 18 105.49 - 140.65: 1 140.65 - 175.82: 7 Dihedral angle restraints: 9622 sinusoidal: 3813 harmonic: 5809 Sorted by residual: dihedral pdb=" CB CYS C 549 " pdb=" SG CYS C 549 " pdb=" SG CYS C 553 " pdb=" CB CYS C 553 " ideal model delta sinusoidal sigma weight residual -86.00 3.13 -89.13 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS C 530 " pdb=" SG CYS C 530 " pdb=" SG CYS C 549 " pdb=" CB CYS C 549 " ideal model delta sinusoidal sigma weight residual 93.00 173.73 -80.73 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS C 530 " pdb=" SG CYS C 530 " pdb=" SG CYS C 553 " pdb=" CB CYS C 553 " ideal model delta sinusoidal sigma weight residual -86.00 -157.11 71.11 1 1.00e+01 1.00e-02 6.49e+01 ... (remaining 9619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2051 0.053 - 0.105: 385 0.105 - 0.158: 81 0.158 - 0.210: 1 0.210 - 0.263: 1 Chirality restraints: 2519 Sorted by residual: chirality pdb=" CB THR L 149 " pdb=" CA THR L 149 " pdb=" OG1 THR L 149 " pdb=" CG2 THR L 149 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL N 210 " pdb=" CA VAL N 210 " pdb=" CG1 VAL N 210 " pdb=" CG2 VAL N 210 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA VAL L 209 " pdb=" N VAL L 209 " pdb=" C VAL L 209 " pdb=" CB VAL L 209 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 2516 not shown) Planarity restraints: 2743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 572 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO A 573 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 573 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 573 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 148 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C TYR L 148 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR L 148 " -0.015 2.00e-02 2.50e+03 pdb=" N THR L 149 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 499 " -0.015 2.00e-02 2.50e+03 1.36e-02 4.64e+00 pdb=" CG TRP C 499 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP C 499 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 499 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 499 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 499 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 499 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 499 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 499 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 499 " 0.000 2.00e-02 2.50e+03 ... (remaining 2740 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 333 2.67 - 3.22: 15264 3.22 - 3.78: 26344 3.78 - 4.34: 34337 4.34 - 4.90: 54406 Nonbonded interactions: 130684 Sorted by model distance: nonbonded pdb=" N2 DG H 149 " pdb=" O2 DC D 166 " model vdw 2.107 2.496 nonbonded pdb=" OE1 GLN L 136 " pdb=" OH TYR L 138 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR L 308 " pdb=" O ILE C 131 " model vdw 2.142 3.040 nonbonded pdb=" NE2 GLN C 717 " pdb=" OE2 GLU C 720 " model vdw 2.195 3.120 nonbonded pdb=" OG SER N 44 " pdb=" O GLY N 69 " model vdw 2.200 3.040 ... (remaining 130679 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: 4.640 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.460 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.003 0.066 16418 Z= 0.148 Angle : 0.685 10.369 22547 Z= 0.364 Chirality : 0.043 0.263 2519 Planarity : 0.004 0.071 2743 Dihedral : 18.710 175.816 5815 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.48 % Allowed : 20.84 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1941 helix: 0.97 (0.27), residues: 396 sheet: 0.08 (0.25), residues: 412 loop : -0.69 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 499 HIS 0.005 0.001 HIS C 502 PHE 0.024 0.001 PHE P 190 TYR 0.010 0.001 TYR N 21 ARG 0.009 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.21581 ( 564) hydrogen bonds : angle 7.73986 ( 1506) SS BOND : bond 0.00345 ( 5) SS BOND : angle 2.46990 ( 10) covalent geometry : bond 0.00316 (16413) covalent geometry : angle 0.68324 (22537) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 632 MET cc_start: 0.7257 (mmt) cc_final: 0.6871 (mmt) outliers start: 7 outliers final: 2 residues processed: 163 average time/residue: 0.2580 time to fit residues: 63.9735 Evaluate side-chains 156 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 ASN N 18 ASN N 85 GLN N 305 ASN N 328 HIS ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.103366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.084415 restraints weight = 63662.989| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 4.44 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 16418 Z= 0.271 Angle : 0.730 12.856 22547 Z= 0.384 Chirality : 0.047 0.194 2519 Planarity : 0.005 0.065 2743 Dihedral : 18.594 178.049 2627 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.80 % Allowed : 19.19 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1941 helix: 0.33 (0.26), residues: 407 sheet: -0.33 (0.24), residues: 432 loop : -0.94 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 314 HIS 0.011 0.002 HIS L 406 PHE 0.020 0.003 PHE C 546 TYR 0.022 0.002 TYR N 32 ARG 0.006 0.001 ARG L 355 Details of bonding type rmsd hydrogen bonds : bond 0.05473 ( 564) hydrogen bonds : angle 6.05904 ( 1506) SS BOND : bond 0.00584 ( 5) SS BOND : angle 2.39567 ( 10) covalent geometry : bond 0.00614 (16413) covalent geometry : angle 0.72820 (22537) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 153 time to evaluate : 2.038 Fit side-chains revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8142 (mt) cc_final: 0.7837 (mt) REVERT: A 185 GLU cc_start: 0.7255 (mp0) cc_final: 0.7006 (mp0) REVERT: L 100 GLN cc_start: 0.7661 (mt0) cc_final: 0.7228 (mt0) REVERT: L 131 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: L 149 THR cc_start: 0.7326 (OUTLIER) cc_final: 0.7104 (p) REVERT: L 201 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8060 (mmt90) REVERT: L 337 GLU cc_start: 0.9114 (pm20) cc_final: 0.8875 (mp0) REVERT: C 54 GLU cc_start: 0.8621 (tp30) cc_final: 0.8409 (tp30) REVERT: C 439 MET cc_start: 0.7020 (tmm) cc_final: 0.6723 (tmm) REVERT: C 653 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7208 (mtm180) REVERT: C 701 MET cc_start: 0.7826 (tpp) cc_final: 0.7503 (mpp) outliers start: 70 outliers final: 33 residues processed: 210 average time/residue: 0.2763 time to fit residues: 87.3429 Evaluate side-chains 176 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain L residue 92 HIS Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 201 ARG Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 310 ASP Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain L residue 434 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 410 ASN Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 225 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 129 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 18 ASN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.105714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.086629 restraints weight = 62763.827| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 4.50 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16418 Z= 0.146 Angle : 0.619 12.781 22547 Z= 0.323 Chirality : 0.044 0.206 2519 Planarity : 0.004 0.055 2743 Dihedral : 18.382 175.533 2626 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.18 % Allowed : 20.42 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1941 helix: 0.58 (0.26), residues: 412 sheet: -0.52 (0.24), residues: 446 loop : -0.82 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 499 HIS 0.007 0.001 HIS C 297 PHE 0.014 0.001 PHE C 120 TYR 0.029 0.001 TYR L 308 ARG 0.006 0.000 ARG L 355 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 564) hydrogen bonds : angle 5.61197 ( 1506) SS BOND : bond 0.00133 ( 5) SS BOND : angle 2.05327 ( 10) covalent geometry : bond 0.00333 (16413) covalent geometry : angle 0.61772 (22537) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 162 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8165 (mt) cc_final: 0.7897 (mt) REVERT: A 557 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6915 (p90) REVERT: L 100 GLN cc_start: 0.7689 (mt0) cc_final: 0.6884 (mt0) REVERT: L 148 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6746 (p90) REVERT: L 189 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.6878 (t-90) REVERT: L 337 GLU cc_start: 0.9074 (pm20) cc_final: 0.8799 (mp0) REVERT: N 59 LYS cc_start: 0.9175 (ptpp) cc_final: 0.8888 (ptpp) REVERT: N 258 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7357 (ptt-90) REVERT: C 52 ARG cc_start: 0.7017 (mmp80) cc_final: 0.6810 (mmp80) REVERT: C 54 GLU cc_start: 0.8626 (tp30) cc_final: 0.8380 (tp30) REVERT: C 134 MET cc_start: 0.8311 (ppp) cc_final: 0.7956 (ppp) REVERT: C 574 TYR cc_start: 0.8849 (t80) cc_final: 0.8513 (t80) REVERT: C 701 MET cc_start: 0.7760 (tpp) cc_final: 0.7434 (mpp) outliers start: 61 outliers final: 31 residues processed: 210 average time/residue: 0.2565 time to fit residues: 83.2220 Evaluate side-chains 182 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 557 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain L residue 92 HIS Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain L residue 434 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 258 ARG Chi-restraints excluded: chain N residue 410 ASN Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 127 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 123 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 18 ASN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.106162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.087131 restraints weight = 63055.722| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 4.49 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16418 Z= 0.128 Angle : 0.603 12.705 22547 Z= 0.313 Chirality : 0.044 0.232 2519 Planarity : 0.004 0.052 2743 Dihedral : 18.262 174.352 2626 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.98 % Allowed : 20.97 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1941 helix: 0.71 (0.26), residues: 409 sheet: -0.42 (0.24), residues: 434 loop : -0.74 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP L 314 HIS 0.006 0.001 HIS C 297 PHE 0.012 0.001 PHE C 724 TYR 0.016 0.001 TYR L 308 ARG 0.006 0.000 ARG L 355 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 564) hydrogen bonds : angle 5.37996 ( 1506) SS BOND : bond 0.00298 ( 5) SS BOND : angle 2.11868 ( 10) covalent geometry : bond 0.00289 (16413) covalent geometry : angle 0.60173 (22537) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8114 (mt) cc_final: 0.7853 (mt) REVERT: A 557 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6778 (p90) REVERT: A 659 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.8231 (t70) REVERT: L 100 GLN cc_start: 0.7726 (mt0) cc_final: 0.6917 (mt0) REVERT: L 131 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: L 148 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6926 (p90) REVERT: L 189 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.6855 (t-90) REVERT: N 59 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8882 (ptpp) REVERT: N 118 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: C 54 GLU cc_start: 0.8558 (tp30) cc_final: 0.8304 (tp30) REVERT: C 134 MET cc_start: 0.8284 (ppp) cc_final: 0.7863 (ppp) REVERT: C 574 TYR cc_start: 0.8768 (t80) cc_final: 0.8434 (t80) REVERT: C 597 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.6017 (tptp) REVERT: C 701 MET cc_start: 0.7746 (tpp) cc_final: 0.7498 (tpp) outliers start: 58 outliers final: 27 residues processed: 205 average time/residue: 0.2586 time to fit residues: 81.1895 Evaluate side-chains 183 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 557 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain L residue 434 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 597 LYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 0.8980 chunk 190 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 121 optimal weight: 0.2980 chunk 159 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 18 ASN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.105993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.087013 restraints weight = 64099.459| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 4.47 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16418 Z= 0.147 Angle : 0.613 12.853 22547 Z= 0.317 Chirality : 0.044 0.249 2519 Planarity : 0.004 0.050 2743 Dihedral : 18.215 174.331 2626 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.73 % Allowed : 21.25 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.19), residues: 1941 helix: 0.74 (0.26), residues: 409 sheet: -0.30 (0.24), residues: 421 loop : -0.80 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 499 HIS 0.006 0.001 HIS C 297 PHE 0.012 0.001 PHE C 120 TYR 0.013 0.001 TYR L 308 ARG 0.006 0.000 ARG L 355 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 564) hydrogen bonds : angle 5.29554 ( 1506) SS BOND : bond 0.00308 ( 5) SS BOND : angle 2.19599 ( 10) covalent geometry : bond 0.00341 (16413) covalent geometry : angle 0.61164 (22537) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 156 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8195 (mt) cc_final: 0.7930 (mt) REVERT: A 557 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6827 (p90) REVERT: A 659 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.8244 (t70) REVERT: L 92 HIS cc_start: 0.5031 (OUTLIER) cc_final: 0.4782 (p-80) REVERT: L 100 GLN cc_start: 0.7722 (mt0) cc_final: 0.7319 (mt0) REVERT: L 131 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: L 189 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.6827 (t-90) REVERT: N 59 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.9030 (ptpp) REVERT: N 118 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: N 258 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6998 (ptt-90) REVERT: C 52 ARG cc_start: 0.7062 (mmp80) cc_final: 0.6854 (mmp80) REVERT: C 54 GLU cc_start: 0.8568 (tp30) cc_final: 0.8300 (tp30) REVERT: C 134 MET cc_start: 0.8378 (ppp) cc_final: 0.7932 (ppp) REVERT: C 439 MET cc_start: 0.6759 (tmm) cc_final: 0.6326 (tmm) REVERT: C 574 TYR cc_start: 0.8759 (t80) cc_final: 0.8489 (t80) REVERT: C 597 LYS cc_start: 0.6348 (OUTLIER) cc_final: 0.6038 (tptp) REVERT: C 701 MET cc_start: 0.7768 (tpp) cc_final: 0.7525 (tpp) REVERT: P 259 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7475 (mmm160) outliers start: 69 outliers final: 39 residues processed: 212 average time/residue: 0.2536 time to fit residues: 81.7104 Evaluate side-chains 195 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 557 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain L residue 92 HIS Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 258 ARG Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 597 LYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 259 ARG Chi-restraints excluded: chain I residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4638 > 50: distance: 77 - 79: 35.160 distance: 79 - 80: 41.098 distance: 79 - 142: 4.559 distance: 80 - 81: 39.318 distance: 81 - 82: 9.707 distance: 82 - 139: 50.453 distance: 83 - 84: 56.465 distance: 86 - 89: 56.858 distance: 87 - 88: 40.785 distance: 89 - 91: 40.589 distance: 92 - 125: 3.421 distance: 93 - 96: 40.995 distance: 94 - 95: 39.618 distance: 94 - 97: 39.962 distance: 97 - 98: 40.191 distance: 98 - 101: 40.475 distance: 99 - 100: 40.005 distance: 99 - 105: 41.067 distance: 102 - 103: 40.315 distance: 102 - 104: 39.811 distance: 105 - 106: 47.391 distance: 106 - 107: 49.978 distance: 106 - 109: 27.320 distance: 107 - 108: 26.893 distance: 107 - 113: 12.393 distance: 109 - 110: 41.014 distance: 110 - 111: 41.417 distance: 110 - 112: 51.907 distance: 113 - 114: 43.922 distance: 114 - 115: 19.459 distance: 114 - 117: 44.851 distance: 115 - 116: 41.110 distance: 115 - 122: 39.458 distance: 119 - 120: 40.201 distance: 119 - 121: 36.451 distance: 122 - 123: 40.985 distance: 124 - 125: 40.356 distance: 128 - 129: 10.129 distance: 129 - 130: 49.151 distance: 131 - 193: 33.792 distance: 132 - 133: 39.304 distance: 132 - 135: 40.144 distance: 133 - 134: 51.608 distance: 133 - 139: 57.719 distance: 134 - 190: 31.291 distance: 135 - 136: 35.789 distance: 136 - 138: 39.025 distance: 139 - 140: 39.177 distance: 141 - 142: 39.086 distance: 141 - 147: 10.132 distance: 143 - 144: 7.718 distance: 144 - 145: 34.083 distance: 145 - 146: 39.459 distance: 147 - 148: 29.671 distance: 149 - 155: 35.132 distance: 151 - 152: 43.319 distance: 151 - 153: 40.814 distance: 152 - 154: 21.185