Starting phenix.real_space_refine on Sun Oct 13 03:35:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/10_2024/7qd8_13910.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/10_2024/7qd8_13910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/10_2024/7qd8_13910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/10_2024/7qd8_13910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/10_2024/7qd8_13910.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/10_2024/7qd8_13910.cif" } resolution = 3.6 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= 0.003 sd= 0.152 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8996 2.51 5 N 2458 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 14086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 7043 Classifications: {'peptide': 865} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 839} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 7043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 7043 Classifications: {'peptide': 865} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 839} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 8.16, per 1000 atoms: 0.58 Number of scatterers: 14086 At special positions: 0 Unit cell: (164.852, 113.636, 113.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2590 8.00 N 2458 7.00 C 8996 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: 2.60 Conformation dependent library (CDL) restraints added in 1.8 seconds 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 5 sheets defined 73.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.896A pdb=" N GLU A 23 " --> pdb=" O ARG A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.660A pdb=" N HIS A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.511A pdb=" N GLU A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 69 " --> pdb=" O LEU A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.952A pdb=" N PHE A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 112 Processing helix chain 'A' and resid 118 through 136 removed outlier: 4.145A pdb=" N GLN A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP A 135 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.510A pdb=" N MET A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 184 removed outlier: 3.840A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.543A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.707A pdb=" N ASP A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.069A pdb=" N ARG A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 269 through 319 removed outlier: 3.952A pdb=" N SER A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.624A pdb=" N LYS A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.632A pdb=" N VAL A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.799A pdb=" N ASN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.790A pdb=" N VAL A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 398 removed outlier: 3.547A pdb=" N LEU A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.925A pdb=" N GLU A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.676A pdb=" N LEU A 459 " --> pdb=" O HIS A 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.853A pdb=" N TYR A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 489' Processing helix chain 'A' and resid 491 through 499 removed outlier: 5.233A pdb=" N GLU A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 530 removed outlier: 3.868A pdb=" N TYR A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 4.200A pdb=" N ALA A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 586 Processing helix chain 'A' and resid 587 through 592 removed outlier: 3.504A pdb=" N GLN A 591 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 618 removed outlier: 3.690A pdb=" N ASN A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 641 removed outlier: 3.968A pdb=" N MET A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 664 Processing helix chain 'A' and resid 665 through 670 removed outlier: 4.020A pdb=" N SER A 668 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 737 removed outlier: 4.544A pdb=" N LEU A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS A 731 " --> pdb=" O ARG A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 766 removed outlier: 4.288A pdb=" N THR A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 808 removed outlier: 3.526A pdb=" N ILE A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 812 removed outlier: 3.788A pdb=" N GLU A 812 " --> pdb=" O GLU A 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 812' Processing helix chain 'A' and resid 813 through 824 Processing helix chain 'A' and resid 827 through 838 Processing helix chain 'A' and resid 841 through 866 removed outlier: 3.661A pdb=" N MET A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A 854 " --> pdb=" O GLU A 850 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 855 " --> pdb=" O MET A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 891 removed outlier: 3.665A pdb=" N GLN A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 removed outlier: 4.391A pdb=" N GLU A 900 " --> pdb=" O GLY A 896 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 901 " --> pdb=" O GLU A 897 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 909 " --> pdb=" O ASP A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 938 removed outlier: 3.547A pdb=" N ILE A 916 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 929 " --> pdb=" O THR A 925 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 930 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.914A pdb=" N GLU B 23 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.640A pdb=" N HIS B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.510A pdb=" N GLU B 68 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 69 " --> pdb=" O LEU B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 69' Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.970A pdb=" N PHE B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 112 Processing helix chain 'B' and resid 118 through 136 removed outlier: 4.123A pdb=" N GLN B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.534A pdb=" N MET B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 184 removed outlier: 3.765A pdb=" N ILE B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 176 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.535A pdb=" N ALA B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.707A pdb=" N ASP B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 removed outlier: 4.006A pdb=" N ARG B 229 " --> pdb=" O LYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 269 through 313 removed outlier: 3.874A pdb=" N SER B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 321 through 343 removed outlier: 3.618A pdb=" N LYS B 325 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 329 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 356 through 370 removed outlier: 3.645A pdb=" N VAL B 360 " --> pdb=" O TRP B 356 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 390 removed outlier: 3.934A pdb=" N ASN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TYR B 387 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 398 Processing helix chain 'B' and resid 407 through 424 removed outlier: 3.813A pdb=" N GLU B 422 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 471 removed outlier: 3.516A pdb=" N LEU B 459 " --> pdb=" O HIS B 455 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 461 " --> pdb=" O TYR B 457 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B 470 " --> pdb=" O ARG B 466 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.635A pdb=" N TYR B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 484 through 489' Processing helix chain 'B' and resid 491 through 499 removed outlier: 5.178A pdb=" N GLU B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 530 removed outlier: 3.825A pdb=" N TYR B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 570 removed outlier: 4.181A pdb=" N ALA B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 586 Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 602 through 618 removed outlier: 3.793A pdb=" N ASN B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.691A pdb=" N THR B 629 " --> pdb=" O MET B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 641 removed outlier: 4.003A pdb=" N MET B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 664 removed outlier: 3.627A pdb=" N ASN B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 664 " --> pdb=" O PHE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 4.030A pdb=" N SER B 668 " --> pdb=" O LYS B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 737 removed outlier: 4.670A pdb=" N LEU B 730 " --> pdb=" O ALA B 726 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N HIS B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 766 removed outlier: 4.462A pdb=" N THR B 756 " --> pdb=" O THR B 752 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 808 removed outlier: 3.521A pdb=" N ILE B 807 " --> pdb=" O ASN B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 812 removed outlier: 3.845A pdb=" N GLU B 812 " --> pdb=" O GLU B 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 809 through 812' Processing helix chain 'B' and resid 813 through 824 Processing helix chain 'B' and resid 827 through 838 Processing helix chain 'B' and resid 841 through 866 removed outlier: 3.712A pdb=" N MET B 851 " --> pdb=" O ALA B 847 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 854 " --> pdb=" O GLU B 850 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 855 " --> pdb=" O MET B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 891 removed outlier: 3.637A pdb=" N GLN B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 907 removed outlier: 4.477A pdb=" N GLU B 900 " --> pdb=" O GLY B 896 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 901 " --> pdb=" O GLU B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 938 removed outlier: 3.783A pdb=" N GLU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 930 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 933 " --> pdb=" O GLU B 929 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 403 Processing sheet with id=AA2, first strand: chain 'A' and resid 573 through 574 removed outlier: 7.632A pdb=" N ILE A 573 " --> pdb=" O ASN A 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 720 through 722 removed outlier: 6.524A pdb=" N LYS A 720 " --> pdb=" O ARG A 769 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 573 through 574 removed outlier: 7.649A pdb=" N ILE B 573 " --> pdb=" O ASN B 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 720 through 722 removed outlier: 6.561A pdb=" N LYS B 720 " --> pdb=" O ARG B 769 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 758 hydrogen bonds defined for protein. 2235 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 3.08 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: 4622 1.34 - 1.46: 2806 1.46 - 1.58: 6860 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 14370 Sorted by residual: bond pdb=" CB GLN B 188 " pdb=" CG GLN B 188 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" C TYR A 61 " pdb=" N PRO A 62 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 bond pdb=" C TYR B 61 " pdb=" N PRO B 62 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.48e+00 bond pdb=" CA GLY B 939 " pdb=" C GLY B 939 " ideal model delta sigma weight residual 1.510 1.528 -0.018 1.46e-02 4.69e+03 1.48e+00 bond pdb=" CA GLY A 939 " pdb=" C GLY A 939 " ideal model delta sigma weight residual 1.510 1.527 -0.018 1.46e-02 4.69e+03 1.45e+00 ... (remaining 14365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 18775 1.76 - 3.52: 509 3.52 - 5.28: 96 5.28 - 7.04: 26 7.04 - 8.80: 14 Bond angle restraints: 19420 Sorted by residual: angle pdb=" C ILE B 202 " pdb=" N ASN B 203 " pdb=" CA ASN B 203 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.09e+01 angle pdb=" N ILE B 59 " pdb=" CA ILE B 59 " pdb=" C ILE B 59 " ideal model delta sigma weight residual 112.96 108.42 4.54 1.00e+00 1.00e+00 2.06e+01 angle pdb=" CA ARG B 384 " pdb=" CB ARG B 384 " pdb=" CG ARG B 384 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 angle pdb=" C ILE A 202 " pdb=" N ASN A 203 " pdb=" CA ASN A 203 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 angle pdb=" CA LYS B 564 " pdb=" CB LYS B 564 " pdb=" CG LYS B 564 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 ... (remaining 19415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7753 17.91 - 35.82: 755 35.82 - 53.72: 119 53.72 - 71.63: 28 71.63 - 89.54: 11 Dihedral angle restraints: 8666 sinusoidal: 3580 harmonic: 5086 Sorted by residual: dihedral pdb=" CA VAL A 360 " pdb=" C VAL A 360 " pdb=" N GLU A 361 " pdb=" CA GLU A 361 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU B 458 " pdb=" CG GLU B 458 " pdb=" CD GLU B 458 " pdb=" OE1 GLU B 458 " ideal model delta sinusoidal sigma weight residual 0.00 -88.84 88.84 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA GLU A 358 " pdb=" C GLU A 358 " pdb=" N MET A 359 " pdb=" CA MET A 359 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 8663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1668 0.052 - 0.105: 410 0.105 - 0.157: 68 0.157 - 0.209: 10 0.209 - 0.261: 2 Chirality restraints: 2158 Sorted by residual: chirality pdb=" CB THR A 750 " pdb=" CA THR A 750 " pdb=" OG1 THR A 750 " pdb=" CG2 THR A 750 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB THR B 750 " pdb=" CA THR B 750 " pdb=" OG1 THR B 750 " pdb=" CG2 THR B 750 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA GLU B 283 " pdb=" N GLU B 283 " pdb=" C GLU B 283 " pdb=" CB GLU B 283 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2155 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 501 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO B 502 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 501 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A 502 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 891 " -0.021 2.00e-02 2.50e+03 1.74e-02 5.29e+00 pdb=" CG PHE B 891 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 891 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 891 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 891 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 891 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 891 " -0.003 2.00e-02 2.50e+03 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3628 2.80 - 3.32: 13263 3.32 - 3.85: 22903 3.85 - 4.37: 26257 4.37 - 4.90: 44035 Nonbonded interactions: 110086 Sorted by model distance: nonbonded pdb=" O TYR A 819 " pdb=" OG1 THR A 823 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR A 385 " pdb=" OE2 GLU A 458 " model vdw 2.278 3.040 nonbonded pdb=" O HIS B 481 " pdb=" OH TYR B 488 " model vdw 2.283 3.040 nonbonded pdb=" O HIS A 481 " pdb=" OH TYR A 488 " model vdw 2.319 3.040 nonbonded pdb=" O TYR A 391 " pdb=" OG1 THR A 394 " model vdw 2.329 3.040 ... (remaining 110081 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 28.390 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: