Starting phenix.real_space_refine on Fri Jan 24 22:53:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9u_40249/01_2025/8s9u_40249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9u_40249/01_2025/8s9u_40249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s9u_40249/01_2025/8s9u_40249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9u_40249/01_2025/8s9u_40249.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9u_40249/01_2025/8s9u_40249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9u_40249/01_2025/8s9u_40249.cif" } resolution = 2.77 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= 0.022 sd= 0.074 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: 5 Type Number sf(0) Gaussians P 69 5.49 5 S 51 5.16 5 C 14002 2.51 5 N 3989 2.21 5 O 4493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 22604 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5995 Classifications: {'peptide': 768} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain breaks: 1 Chain: "C" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4268 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 525} Chain breaks: 2 Chain: "D" Number of atoms: 3967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3967 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 25, 'TRANS': 492} Chain: "E" Number of atoms: 5455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5455 Classifications: {'peptide': 678} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 634} Chain breaks: 1 Chain: "F" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 790 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 18, 'rna3p': 18} Chain: "G" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 696 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 17} Link IDs: {'rna2p': 7, 'rna3p': 25} Time building chain proxies: 12.60, per 1000 atoms: 0.56 Number of scatterers: 22604 At special positions: 0 Unit cell: (106.92, 118.26, 187.92, 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 51 16.00 P 69 15.00 O 4493 8.00 N 3989 7.00 C 14002 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 - 3.00 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: 5.27 Conformation dependent library (CDL) restraints added in 2.9 seconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4934 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 37 sheets defined 36.6% alpha, 21.3% beta 22 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 8.76 Creating SS restraints... Processing helix chain 'A' and resid 40 through 60 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.638A pdb=" N GLN A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 167 through 184 Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.759A pdb=" N GLY A 195 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.945A pdb=" N ILE A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'A' and resid 562 through 573 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 624 through 649 Processing helix chain 'A' and resid 650 through 659 Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 689 through 703 removed outlier: 3.635A pdb=" N VAL A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.648A pdb=" N TRP A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 726 Processing helix chain 'A' and resid 726 through 735 removed outlier: 4.213A pdb=" N ILE A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP A 731 " --> pdb=" O GLU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.597A pdb=" N THR A 742 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 780 removed outlier: 6.007A pdb=" N ALA A 757 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU A 758 " --> pdb=" O GLU A 754 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 20 through 35 removed outlier: 3.952A pdb=" N THR C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 60 through 66 removed outlier: 4.176A pdb=" N PHE C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 Processing helix chain 'C' and resid 135 through 155 removed outlier: 4.032A pdb=" N ALA C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 212 removed outlier: 4.038A pdb=" N LYS C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 228 Processing helix chain 'C' and resid 243 through 255 removed outlier: 5.546A pdb=" N GLU C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 removed outlier: 3.521A pdb=" N ASP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 318 through 337 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.731A pdb=" N VAL C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.888A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 442 through 447 Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 459 through 472 removed outlier: 3.865A pdb=" N LEU C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 494 removed outlier: 4.024A pdb=" N TYR C 494 " --> pdb=" O ARG C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 506 Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.735A pdb=" N PHE C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 545 through 547 No H-bonds generated for 'chain 'C' and resid 545 through 547' Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.702A pdb=" N ILE D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 161 Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'D' and resid 206 through 214 removed outlier: 3.737A pdb=" N LEU D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 284 Processing helix chain 'D' and resid 291 through 297 removed outlier: 3.712A pdb=" N ARG D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 339 through 348 removed outlier: 3.562A pdb=" N LYS D 344 " --> pdb=" O PRO D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing helix chain 'D' and resid 369 through 375 Processing helix chain 'D' and resid 416 through 424 Processing helix chain 'D' and resid 427 through 429 No H-bonds generated for 'chain 'D' and resid 427 through 429' Processing helix chain 'D' and resid 430 through 447 removed outlier: 4.575A pdb=" N ALA D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 483 Processing helix chain 'D' and resid 495 through 512 removed outlier: 3.626A pdb=" N ASP D 512 " --> pdb=" O GLU D 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 removed outlier: 3.979A pdb=" N LEU E 133 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.532A pdb=" N GLU E 171 " --> pdb=" O ALA E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 210 Processing helix chain 'E' and resid 228 through 233 Processing helix chain 'E' and resid 260 through 264 removed outlier: 4.059A pdb=" N ASN E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 394 removed outlier: 4.058A pdb=" N HIS E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 400 Processing helix chain 'E' and resid 414 through 419 removed outlier: 3.555A pdb=" N ILE E 418 " --> pdb=" O SER E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 466 Processing helix chain 'E' and resid 475 through 479 removed outlier: 4.029A pdb=" N LEU E 479 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 486 Processing helix chain 'E' and resid 536 through 540 Processing helix chain 'E' and resid 555 through 559 Processing helix chain 'E' and resid 590 through 594 removed outlier: 4.149A pdb=" N GLN E 593 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 599 Processing helix chain 'E' and resid 641 through 652 Processing helix chain 'E' and resid 665 through 669 Processing helix chain 'E' and resid 687 through 694 Processing helix chain 'E' and resid 704 through 707 Processing helix chain 'E' and resid 708 through 724 Processing helix chain 'E' and resid 732 through 744 Processing helix chain 'E' and resid 766 through 776 removed outlier: 4.059A pdb=" N PHE E 770 " --> pdb=" O ALA E 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 787 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.810A pdb=" N ILE A 4 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 130 removed outlier: 6.009A pdb=" N PHE A 141 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 removed outlier: 6.823A pdb=" N THR A 412 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA6, first strand: chain 'A' and resid 261 through 265 removed outlier: 6.658A pdb=" N GLU A 270 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR A 264 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A 269 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ILE A 407 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N CYS A 271 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 removed outlier: 3.507A pdb=" N TYR A 360 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.641A pdb=" N LYS A 510 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.641A pdb=" N LYS A 510 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 529 Processing sheet with id=AB3, first strand: chain 'A' and resid 532 through 533 removed outlier: 3.654A pdb=" N LEU A 538 " --> pdb=" O GLN A 533 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 661 through 663 Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.799A pdb=" N ASN B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY B 92 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 123 removed outlier: 3.605A pdb=" N THR B 116 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 189 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU B 168 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU B 187 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR B 170 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU B 185 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA B 172 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE B 183 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AB8, first strand: chain 'C' and resid 82 through 88 removed outlier: 6.156A pdb=" N ILE C 93 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA C 87 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 180 through 183 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.619A pdb=" N THR C 311 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU C 305 " --> pdb=" O ASP C 309 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASP C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER C 354 " --> pdb=" O ASN C 242 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA C 355 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ASP C 406 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA C 357 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 431 through 432 Processing sheet with id=AC3, first strand: chain 'D' and resid 45 through 46 removed outlier: 6.418A pdb=" N VAL D 93 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS D 135 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 45 through 46 removed outlier: 6.418A pdb=" N VAL D 93 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS D 135 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG D 8 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER D 185 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS D 10 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU D 183 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR D 12 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU D 181 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU D 183 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 103 through 110 removed outlier: 10.989A pdb=" N GLU D 103 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N SER D 124 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N ARG D 105 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N LYS D 122 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N GLY D 107 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N GLY D 120 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLY D 109 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 171 through 172 removed outlier: 4.767A pdb=" N GLN D 412 " --> pdb=" O ASN D 330 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN D 467 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN D 229 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL D 465 " --> pdb=" O ASN D 229 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 251 through 253 removed outlier: 4.202A pdb=" N PHE D 260 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU D 336 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N ILE D 262 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N SER D 334 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 311 through 313 Processing sheet with id=AC9, first strand: chain 'D' and resid 378 through 383 Processing sheet with id=AD1, first strand: chain 'E' and resid 750 through 751 removed outlier: 3.821A pdb=" N SER E 750 " --> pdb=" O ASN E 113 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 119 through 121 Processing sheet with id=AD3, first strand: chain 'E' and resid 501 through 508 removed outlier: 5.777A pdb=" N LEU E 501 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR E 638 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE E 503 " --> pdb=" O ASP E 636 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP E 636 " --> pdb=" O ILE E 503 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER E 505 " --> pdb=" O GLU E 634 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU E 634 " --> pdb=" O SER E 505 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TYR E 149 " --> pdb=" O ASN E 639 " (cutoff:3.500A) removed outlier: 10.964A pdb=" N SER E 150 " --> pdb=" O THR E 682 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N THR E 682 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N ARG E 152 " --> pdb=" O ASP E 680 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ASP E 680 " --> pdb=" O ARG E 152 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA E 154 " --> pdb=" O ASP E 678 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 172 through 174 removed outlier: 4.531A pdb=" N ARG E 619 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 224 through 226 Processing sheet with id=AD6, first strand: chain 'E' and resid 371 through 374 removed outlier: 3.686A pdb=" N ASN E 447 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS E 437 " --> pdb=" O ILE E 445 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ILE E 445 " --> pdb=" O LYS E 437 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU E 439 " --> pdb=" O TYR E 443 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 268 through 272 removed outlier: 7.430A pdb=" N ALA E 268 " --> pdb=" O TRP E 310 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL E 312 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TRP E 270 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLN E 314 " --> pdb=" O TRP E 270 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N ALA E 316 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP E 298 " --> pdb=" O ARG E 313 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE E 315 " --> pdb=" O ARG E 296 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG E 296 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG E 317 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N HIS E 294 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL E 340 " --> pdb=" O ARG E 301 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N THR E 303 " --> pdb=" O THR E 338 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR E 338 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 362 " --> pdb=" O TYR E 349 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 487 through 489 Processing sheet with id=AD9, first strand: chain 'E' and resid 514 through 516 removed outlier: 3.547A pdb=" N TRP E 624 " --> pdb=" O ASP E 515 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 541 through 542 907 hydrogen bonds defined for protein. 2487 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 9.95 Time building geometry restraints manager: 6.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4376 1.32 - 1.44: 5887 1.44 - 1.57: 12735 1.57 - 1.69: 136 1.69 - 1.81: 74 Bond restraints: 23208 Sorted by residual: bond pdb=" CB ARG A 192 " pdb=" CG ARG A 192 " ideal model delta sigma weight residual 1.520 1.429 0.091 3.00e-02 1.11e+03 9.26e+00 bond pdb=" CB TRP D 388 " pdb=" CG TRP D 388 " ideal model delta sigma weight residual 1.498 1.412 0.086 3.10e-02 1.04e+03 7.66e+00 bond pdb=" CB VAL A 147 " pdb=" CG1 VAL A 147 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.74e+00 bond pdb=" C LYS D 231 " pdb=" N ASP D 232 " ideal model delta sigma weight residual 1.339 1.223 0.117 5.57e-02 3.22e+02 4.40e+00 bond pdb=" CG1 ILE D 110 " pdb=" CD1 ILE D 110 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.31e+00 ... (remaining 23203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 30689 2.28 - 4.55: 947 4.55 - 6.83: 100 6.83 - 9.11: 15 9.11 - 11.38: 6 Bond angle restraints: 31757 Sorted by residual: angle pdb=" C GLY A 17 " pdb=" N THR A 18 " pdb=" CA THR A 18 " ideal model delta sigma weight residual 122.37 112.84 9.53 1.72e+00 3.38e-01 3.07e+01 angle pdb=" N GLY A 17 " pdb=" CA GLY A 17 " pdb=" C GLY A 17 " ideal model delta sigma weight residual 115.40 122.52 -7.12 1.32e+00 5.74e-01 2.91e+01 angle pdb=" N GLY A 586 " pdb=" CA GLY A 586 " pdb=" C GLY A 586 " ideal model delta sigma weight residual 113.18 101.94 11.24 2.37e+00 1.78e-01 2.25e+01 angle pdb=" N GLY A 195 " pdb=" CA GLY A 195 " pdb=" C GLY A 195 " ideal model delta sigma weight residual 113.18 123.92 -10.74 2.37e+00 1.78e-01 2.05e+01 angle pdb=" O5' U F 32 " pdb=" C5' U F 32 " pdb=" C4' U F 32 " ideal model delta sigma weight residual 111.50 117.48 -5.98 1.50e+00 4.44e-01 1.59e+01 ... (remaining 31752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 13626 35.80 - 71.61: 355 71.61 - 107.41: 59 107.41 - 143.22: 4 143.22 - 179.02: 3 Dihedral angle restraints: 14047 sinusoidal: 6350 harmonic: 7697 Sorted by residual: dihedral pdb=" O4' C F 2 " pdb=" C1' C F 2 " pdb=" N1 C F 2 " pdb=" C2 C F 2 " ideal model delta sinusoidal sigma weight residual -128.00 49.28 -177.28 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U F 14 " pdb=" C1' U F 14 " pdb=" N1 U F 14 " pdb=" C2 U F 14 " ideal model delta sinusoidal sigma weight residual -128.00 43.89 -171.89 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" CA VAL A 16 " pdb=" C VAL A 16 " pdb=" N GLY A 17 " pdb=" CA GLY A 17 " ideal model delta harmonic sigma weight residual 180.00 144.63 35.37 0 5.00e+00 4.00e-02 5.00e+01 ... (remaining 14044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2563 0.062 - 0.124: 829 0.124 - 0.186: 129 0.186 - 0.247: 20 0.247 - 0.309: 3 Chirality restraints: 3544 Sorted by residual: chirality pdb=" C3' G G 24 " pdb=" C4' G G 24 " pdb=" O3' G G 24 " pdb=" C2' G G 24 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ARG C 436 " pdb=" N ARG C 436 " pdb=" C ARG C 436 " pdb=" CB ARG C 436 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C4' G G 24 " pdb=" C5' G G 24 " pdb=" O4' G G 24 " pdb=" C3' G G 24 " both_signs ideal model delta sigma weight residual False -2.50 -2.24 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 3541 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C F 19 " 0.059 2.00e-02 2.50e+03 3.67e-02 3.03e+01 pdb=" N1 C F 19 " -0.090 2.00e-02 2.50e+03 pdb=" C2 C F 19 " 0.017 2.00e-02 2.50e+03 pdb=" O2 C F 19 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C F 19 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C F 19 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C F 19 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C F 19 " 0.006 2.00e-02 2.50e+03 pdb=" C6 C F 19 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 126 " 0.109 9.50e-02 1.11e+02 6.21e-02 2.00e+01 pdb=" NE ARG E 126 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG E 126 " 0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG E 126 " -0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG E 126 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 419 " 0.113 9.50e-02 1.11e+02 6.20e-02 1.77e+01 pdb=" NE ARG D 419 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG D 419 " 0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG D 419 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG D 419 " -0.019 2.00e-02 2.50e+03 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 487 2.66 - 3.22: 21807 3.22 - 3.78: 37289 3.78 - 4.34: 54830 4.34 - 4.90: 87719 Nonbonded interactions: 202132 Sorted by model distance: nonbonded pdb=" OE2 GLU B 99 " pdb=" OH TYR B 170 " model vdw 2.099 3.040 nonbonded pdb=" O ASP A 140 " pdb=" O2' C G 44 " model vdw 2.135 3.040 nonbonded pdb=" NH2 ARG A 489 " pdb=" OE1 GLN B 112 " model vdw 2.155 3.120 nonbonded pdb=" OD2 ASP D 162 " pdb=" OH TYR D 216 " model vdw 2.182 3.040 nonbonded pdb=" OE1 GLN E 287 " pdb=" NH2 ARG E 317 " model vdw 2.197 3.120 ... (remaining 202127 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=0.00 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: 3.740 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: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 56.530 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.110 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:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.117 23208 Z= 0.651 Angle : 0.928 11.382 31757 Z= 0.519 Chirality : 0.060 0.309 3544 Planarity : 0.007 0.064 3898 Dihedral : 16.422 179.022 9113 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.68 % Favored : 96.02 % Rotamer: Outliers : 1.33 % Allowed : 5.66 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 2664 helix: -1.55 (0.15), residues: 834 sheet: -0.05 (0.23), residues: 474 loop : -0.61 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP D 388 HIS 0.012 0.003 HIS E 177 PHE 0.029 0.003 PHE E 633 TYR 0.032 0.005 TYR A 279 ARG 0.075 0.009 ARG E 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 425 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 THR cc_start: 0.8709 (m) cc_final: 0.8437 (p) REVERT: A 694 THR cc_start: 0.8309 (m) cc_final: 0.8001 (p) REVERT: C 81 ASP cc_start: 0.6659 (p0) cc_final: 0.6230 (t0) REVERT: C 309 ASP cc_start: 0.7225 (t0) cc_final: 0.6365 (m-30) REVERT: C 351 ASP cc_start: 0.7651 (p0) cc_final: 0.7425 (m-30) REVERT: C 362 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.5877 (pt) REVERT: C 374 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5939 (tt) REVERT: C 420 ARG cc_start: 0.6689 (mpt180) cc_final: 0.5411 (mtm180) REVERT: C 478 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.6079 (mmmt) REVERT: C 509 GLN cc_start: 0.7651 (mm110) cc_final: 0.7152 (pm20) REVERT: C 515 LYS cc_start: 0.8654 (mttt) cc_final: 0.8335 (mttp) REVERT: D 235 MET cc_start: 0.9114 (ptm) cc_final: 0.8907 (ppp) REVERT: D 241 ASP cc_start: 0.6820 (m-30) cc_final: 0.6554 (m-30) REVERT: E 245 ILE cc_start: 0.8279 (pp) cc_final: 0.7977 (mt) REVERT: E 266 MET cc_start: 0.8443 (mmt) cc_final: 0.8188 (mmm) REVERT: E 548 ILE cc_start: 0.8615 (mm) cc_final: 0.8306 (mm) outliers start: 30 outliers final: 7 residues processed: 452 average time/residue: 1.6424 time to fit residues: 831.4250 Evaluate side-chains 237 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 227 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain E residue 355 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 0.9990 chunk 205 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 0.0980 chunk 212 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 246 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 84 GLN A 493 ASN A 745 GLN A 750 GLN B 120 GLN C 435 ASN D 61 GLN D 362 GLN D 414 HIS E 174 ASN E 287 GLN E 320 GLN E 354 ASN E 425 ASN E 617 GLN E 731 GLN E 788 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089828 restraints weight = 34725.035| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.15 r_work: 0.3030 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23208 Z= 0.203 Angle : 0.654 10.389 31757 Z= 0.349 Chirality : 0.045 0.304 3544 Planarity : 0.005 0.052 3898 Dihedral : 15.265 179.776 3986 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.25 % Favored : 97.60 % Rotamer: Outliers : 3.05 % Allowed : 11.72 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.07 (0.16), residues: 2664 helix: 0.34 (0.17), residues: 844 sheet: 0.01 (0.24), residues: 460 loop : 0.02 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 14 HIS 0.008 0.001 HIS C 458 PHE 0.017 0.002 PHE D 134 TYR 0.015 0.002 TYR B 170 ARG 0.008 0.001 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 272 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.6238 (mmt) REVERT: A 24 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.4807 (mm-30) REVERT: A 469 THR cc_start: 0.8755 (m) cc_final: 0.8480 (p) REVERT: A 488 ASP cc_start: 0.8039 (p0) cc_final: 0.7582 (p0) REVERT: A 694 THR cc_start: 0.7921 (m) cc_final: 0.7566 (p) REVERT: B 78 LEU cc_start: 0.8931 (mm) cc_final: 0.8587 (tp) REVERT: B 98 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8380 (m) REVERT: B 116 THR cc_start: 0.8914 (t) cc_final: 0.8682 (p) REVERT: B 171 ILE cc_start: 0.8633 (mt) cc_final: 0.8407 (mp) REVERT: C 81 ASP cc_start: 0.7042 (p0) cc_final: 0.6175 (t0) REVERT: C 211 ARG cc_start: 0.7927 (tmm160) cc_final: 0.7451 (ttp80) REVERT: C 309 ASP cc_start: 0.6967 (t0) cc_final: 0.5895 (m-30) REVERT: C 351 ASP cc_start: 0.7668 (p0) cc_final: 0.7030 (m-30) REVERT: C 362 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6172 (pt) REVERT: C 420 ARG cc_start: 0.5902 (mpt180) cc_final: 0.4627 (mtm180) REVERT: C 426 ARG cc_start: 0.7357 (ttm110) cc_final: 0.7077 (mtp85) REVERT: C 478 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5693 (mmmt) REVERT: C 509 GLN cc_start: 0.7632 (mm110) cc_final: 0.6851 (pm20) REVERT: C 515 LYS cc_start: 0.8427 (mttt) cc_final: 0.8117 (mttp) REVERT: C 530 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: D 101 ASP cc_start: 0.7942 (t0) cc_final: 0.7704 (t70) REVERT: D 297 ARG cc_start: 0.8604 (ptp-110) cc_final: 0.8378 (mtm110) REVERT: D 480 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: E 136 CYS cc_start: 0.8939 (t) cc_final: 0.8527 (m) REVERT: E 245 ILE cc_start: 0.8283 (pp) cc_final: 0.8031 (mt) REVERT: E 266 MET cc_start: 0.8939 (mmp) cc_final: 0.8659 (mmm) REVERT: E 314 GLN cc_start: 0.8650 (tt0) cc_final: 0.8435 (tt0) REVERT: E 330 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7599 (ptm160) REVERT: E 354 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7991 (m110) REVERT: E 452 MET cc_start: 0.9029 (mtp) cc_final: 0.8755 (mtt) REVERT: E 467 ASP cc_start: 0.8194 (t70) cc_final: 0.7985 (m-30) REVERT: E 630 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: E 763 ASP cc_start: 0.7928 (m-30) cc_final: 0.7461 (m-30) outliers start: 69 outliers final: 17 residues processed: 319 average time/residue: 1.6225 time to fit residues: 582.6602 Evaluate side-chains 244 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 630 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 72.3376 > 50: distance: 35 - 37: 35.857 distance: 38 - 39: 55.457 distance: 38 - 41: 55.435 distance: 39 - 40: 69.387 distance: 39 - 45: 40.867 distance: 42 - 44: 69.275 distance: 45 - 46: 39.924 distance: 46 - 47: 56.603 distance: 47 - 48: 68.127 distance: 47 - 49: 57.099 distance: 49 - 50: 40.559 distance: 50 - 51: 70.710 distance: 50 - 53: 55.329 distance: 51 - 52: 55.408 distance: 51 - 57: 60.425 distance: 53 - 54: 57.138 distance: 54 - 55: 39.884 distance: 57 - 58: 22.272 distance: 58 - 61: 60.654 distance: 59 - 60: 39.897 distance: 59 - 62: 42.546 distance: 62 - 63: 27.886 distance: 63 - 64: 40.756 distance: 63 - 66: 39.782 distance: 64 - 65: 39.506 distance: 64 - 70: 42.593 distance: 66 - 67: 39.217 distance: 66 - 68: 40.017 distance: 67 - 69: 40.748 distance: 70 - 71: 47.761 distance: 71 - 72: 56.597 distance: 71 - 74: 40.486 distance: 72 - 73: 56.728 distance: 72 - 78: 55.472 distance: 74 - 75: 38.831 distance: 75 - 76: 39.245 distance: 75 - 77: 40.273 distance: 78 - 79: 57.917 distance: 79 - 80: 68.522 distance: 79 - 82: 40.445 distance: 80 - 81: 40.383 distance: 82 - 84: 58.540 distance: 83 - 85: 38.723 distance: 86 - 87: 56.984 distance: 87 - 88: 56.466 distance: 87 - 90: 40.157 distance: 90 - 91: 40.522 distance: 94 - 95: 40.665 distance: 94 - 100: 31.672 distance: 95 - 96: 57.835 distance: 95 - 98: 56.535 distance: 96 - 97: 39.802 distance: 96 - 101: 39.284 distance: 98 - 99: 57.474 distance: 99 - 100: 48.987 distance: 101 - 102: 38.864 distance: 102 - 103: 56.517 distance: 103 - 104: 40.408 distance: 103 - 109: 34.779 distance: 105 - 106: 39.829 distance: 106 - 107: 54.390 distance: 106 - 108: 55.321