Starting phenix.real_space_refine on Sun Nov 17 15:35:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/11_2024/7qd8_13910.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/11_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_13910/11_2024/7qd8_13910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/11_2024/7qd8_13910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/11_2024/7qd8_13910.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd8_13910/11_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-5513/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: 9.28, per 1000 atoms: 0.66 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: 3.57 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: 1.31 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: 4.48 Time building geometry restraints manager: 4.13 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 34.110 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 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 : 0.004 0.044 14370 Z= 0.256 Angle : 0.745 8.805 19420 Z= 0.393 Chirality : 0.047 0.261 2158 Planarity : 0.005 0.066 2476 Dihedral : 14.487 89.540 5374 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -1.83 (0.18), residues: 1706 helix: -1.15 (0.14), residues: 1128 sheet: None (None), residues: 0 loop : -0.98 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 102 HIS 0.007 0.001 HIS A 43 PHE 0.040 0.002 PHE B 891 TYR 0.027 0.002 TYR A 811 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7955 (tptp) cc_final: 0.7591 (tppt) REVERT: A 39 LEU cc_start: 0.8649 (mm) cc_final: 0.8439 (mm) REVERT: A 456 TYR cc_start: 0.5074 (m-10) cc_final: 0.4102 (t80) REVERT: B 274 TYR cc_start: 0.3873 (m-10) cc_final: 0.3536 (m-80) REVERT: B 819 TYR cc_start: 0.5661 (t80) cc_final: 0.5349 (t80) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1713 time to fit residues: 41.7855 Evaluate side-chains 127 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 134 optimal weight: 0.0370 chunk 52 optimal weight: 0.0870 chunk 81 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 116 ASN A 217 GLN B 43 HIS B 83 GLN B 116 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14370 Z= 0.138 Angle : 0.478 7.347 19420 Z= 0.252 Chirality : 0.037 0.159 2158 Planarity : 0.004 0.054 2476 Dihedral : 4.109 15.710 1898 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.53 % Allowed : 7.28 % Favored : 92.19 % 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: -0.60 (0.19), residues: 1706 helix: -0.06 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.87 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 923 HIS 0.009 0.001 HIS A 38 PHE 0.020 0.001 PHE A 329 TYR 0.014 0.001 TYR B 387 ARG 0.002 0.000 ARG B 727 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 1.627 Fit side-chains revert: symmetry clash REVERT: A 295 ILE cc_start: 0.7770 (mm) cc_final: 0.7486 (mm) REVERT: A 456 TYR cc_start: 0.5407 (m-10) cc_final: 0.4542 (t80) outliers start: 8 outliers final: 1 residues processed: 146 average time/residue: 0.2217 time to fit residues: 52.0296 Evaluate side-chains 120 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 0.0070 chunk 129 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 156 optimal weight: 0.3980 chunk 169 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 overall best weight: 1.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 296 HIS ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14370 Z= 0.195 Angle : 0.507 7.974 19420 Z= 0.264 Chirality : 0.039 0.162 2158 Planarity : 0.003 0.048 2476 Dihedral : 4.096 15.798 1898 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.99 % Allowed : 11.46 % Favored : 87.55 % 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: -0.08 (0.20), residues: 1706 helix: 0.33 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -0.61 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 528 HIS 0.010 0.001 HIS A 38 PHE 0.019 0.002 PHE B 891 TYR 0.022 0.001 TYR B 819 ARG 0.002 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.741 Fit side-chains revert: symmetry clash REVERT: A 295 ILE cc_start: 0.7811 (mm) cc_final: 0.7528 (mm) REVERT: A 456 TYR cc_start: 0.5556 (m-10) cc_final: 0.4556 (t80) REVERT: A 891 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.5858 (m-10) REVERT: B 891 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.5458 (m-10) outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 0.2105 time to fit residues: 47.6073 Evaluate side-chains 127 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14370 Z= 0.216 Angle : 0.518 12.327 19420 Z= 0.269 Chirality : 0.039 0.159 2158 Planarity : 0.003 0.043 2476 Dihedral : 4.150 16.043 1898 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.85 % Allowed : 13.05 % Favored : 85.10 % 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: 0.04 (0.20), residues: 1706 helix: 0.42 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -0.56 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 528 HIS 0.006 0.001 HIS A 38 PHE 0.018 0.002 PHE B 891 TYR 0.019 0.001 TYR A 819 ARG 0.002 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.511 Fit side-chains revert: symmetry clash REVERT: A 193 GLN cc_start: 0.6005 (OUTLIER) cc_final: 0.5349 (pp30) REVERT: A 456 TYR cc_start: 0.5782 (m-10) cc_final: 0.4643 (t80) REVERT: A 891 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.5842 (m-10) REVERT: B 891 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.5544 (m-10) outliers start: 28 outliers final: 15 residues processed: 149 average time/residue: 0.2215 time to fit residues: 52.6864 Evaluate side-chains 142 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.0570 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 116 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 HIS B 83 GLN B 116 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14370 Z= 0.136 Angle : 0.481 11.361 19420 Z= 0.242 Chirality : 0.037 0.154 2158 Planarity : 0.003 0.033 2476 Dihedral : 3.812 14.617 1898 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.79 % Allowed : 14.70 % Favored : 83.51 % 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: 0.34 (0.20), residues: 1706 helix: 0.67 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -0.52 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 923 HIS 0.006 0.001 HIS A 38 PHE 0.015 0.001 PHE B 436 TYR 0.016 0.001 TYR B 819 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: A 456 TYR cc_start: 0.5621 (m-10) cc_final: 0.4512 (t80) REVERT: A 891 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.5706 (m-10) REVERT: B 891 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.5412 (m-10) outliers start: 27 outliers final: 18 residues processed: 155 average time/residue: 0.2240 time to fit residues: 55.4558 Evaluate side-chains 146 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 41 optimal weight: 0.0060 chunk 166 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14370 Z= 0.147 Angle : 0.484 11.922 19420 Z= 0.244 Chirality : 0.037 0.152 2158 Planarity : 0.003 0.029 2476 Dihedral : 3.782 14.911 1898 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.66 % Allowed : 15.76 % Favored : 82.58 % 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: 0.49 (0.20), residues: 1706 helix: 0.81 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -0.51 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 210 HIS 0.008 0.001 HIS A 38 PHE 0.015 0.001 PHE B 891 TYR 0.012 0.001 TYR A 391 ARG 0.003 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 TYR cc_start: 0.5587 (m-10) cc_final: 0.4496 (t80) REVERT: A 891 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.5705 (m-10) REVERT: B 377 TYR cc_start: 0.6101 (m-80) cc_final: 0.5345 (m-10) REVERT: B 891 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.5446 (m-10) outliers start: 25 outliers final: 17 residues processed: 152 average time/residue: 0.2264 time to fit residues: 54.6290 Evaluate side-chains 149 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 165 optimal weight: 0.0770 chunk 103 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 0.0030 overall best weight: 0.4948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.2133 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: