Starting phenix.real_space_refine on Sun Oct 13 03:51:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/10_2024/8rtb_19485.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/10_2024/8rtb_19485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/10_2024/8rtb_19485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/10_2024/8rtb_19485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/10_2024/8rtb_19485.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/10_2024/8rtb_19485.cif" } resolution = 3.83 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= 0.007 sd= 0.029 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 57 5.16 5 C 9069 2.51 5 N 2413 2.21 5 O 2593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 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: 14132 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 835 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 5992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5992 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 36, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5284 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 630} Chain breaks: 5 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 367 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 49} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 450 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "F" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 279 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 240 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 350 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "J" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 335 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 10.22, per 1000 atoms: 0.72 Number of scatterers: 14132 At special positions: 0 Unit cell: (134.442, 89.628, 158.983, 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 57 16.00 O 2593 8.00 N 2413 7.00 C 9069 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: 3.32 Conformation dependent library (CDL) restraints added in 1.9 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 19 sheets defined 52.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'C' and resid 28 through 45 Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.019A pdb=" N TRP C 50 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 51 " --> pdb=" O TRP C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 51' Processing helix chain 'C' and resid 52 through 67 removed outlier: 3.950A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.788A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 4.071A pdb=" N TRP C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.791A pdb=" N SER A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 53 through 72 removed outlier: 3.576A pdb=" N PHE A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 132 through 140 removed outlier: 3.822A pdb=" N PHE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 171 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.934A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.834A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.946A pdb=" N TYR A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 266 removed outlier: 4.300A pdb=" N VAL A 262 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 266 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 297 Processing helix chain 'A' and resid 305 through 318 removed outlier: 4.066A pdb=" N ILE A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 removed outlier: 3.550A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 469 through 472 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 507 through 511 removed outlier: 4.527A pdb=" N GLN A 510 " --> pdb=" O ASN A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.534A pdb=" N LEU A 623 " --> pdb=" O THR A 620 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP A 624 " --> pdb=" O GLU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 642 removed outlier: 3.607A pdb=" N SER A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.519A pdb=" N ALA A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A 695 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.832A pdb=" N LYS A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 702 " --> pdb=" O ILE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 removed outlier: 3.635A pdb=" N TYR A 722 " --> pdb=" O ASP A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 738 Processing helix chain 'A' and resid 777 through 785 removed outlier: 4.305A pdb=" N VAL A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 801 removed outlier: 3.782A pdb=" N SER A 796 " --> pdb=" O GLU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 820 Proline residue: A 810 - end of helix Processing helix chain 'B' and resid 53 through 71 removed outlier: 3.926A pdb=" N VAL B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 71 " --> pdb=" O THR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 148 through 171 Processing helix chain 'B' and resid 191 through 202 removed outlier: 4.061A pdb=" N PHE B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 196 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 4.353A pdb=" N TYR B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 280 through 297 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.858A pdb=" N ASN B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 353 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 469 through 472 Processing helix chain 'B' and resid 484 through 491 Processing helix chain 'B' and resid 628 through 643 removed outlier: 3.584A pdb=" N MET B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 677 removed outlier: 4.195A pdb=" N ASP B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 695 removed outlier: 3.802A pdb=" N ALA B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.920A pdb=" N LYS B 700 " --> pdb=" O SER B 696 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 725 removed outlier: 3.630A pdb=" N TYR B 722 " --> pdb=" O ASP B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 739 removed outlier: 3.607A pdb=" N LEU B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 785 Processing helix chain 'B' and resid 787 through 802 Processing helix chain 'B' and resid 804 through 821 removed outlier: 4.283A pdb=" N TRP B 808 " --> pdb=" O ASP B 804 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) Proline residue: B 810 - end of helix Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 27 through 62 removed outlier: 4.357A pdb=" N SER E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 60 removed outlier: 3.644A pdb=" N TYR D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 61 Processing helix chain 'G' and resid 23 through 61 Processing helix chain 'H' and resid 43 through 69 Processing helix chain 'J' and resid 31 through 49 Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 60 through 82 removed outlier: 4.515A pdb=" N CYS J 67 " --> pdb=" O PHE J 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.587A pdb=" N ARG A 222 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.754A pdb=" N ILE A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 127 removed outlier: 3.534A pdb=" N SER A 40 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 38 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AA8, first strand: chain 'A' and resid 248 through 250 removed outlier: 3.523A pdb=" N ARG A 249 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 357 " --> pdb=" O ARG A 249 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.555A pdb=" N HIS A 326 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 415 through 417 Processing sheet with id=AB2, first strand: chain 'A' and resid 495 through 496 removed outlier: 5.897A pdb=" N ILE A 475 " --> pdb=" O TYR A 615 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE A 617 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA A 477 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 474 " --> pdb=" O MET A 650 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 652 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL A 476 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL A 684 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR A 651 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A 447 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N MET A 448 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A 709 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 767 through 768 removed outlier: 3.648A pdb=" N VAL A 768 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 22 through 27 removed outlier: 4.660A pdb=" N HIS B 24 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 177 through 178 removed outlier: 3.693A pdb=" N TYR B 38 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 121 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 331 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB7, first strand: chain 'B' and resid 277 through 278 Processing sheet with id=AB8, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.878A pdb=" N THR B 415 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 684 through 687 removed outlier: 6.002A pdb=" N THR B 447 " --> pdb=" O PHE B 685 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR B 687 " --> pdb=" O THR B 447 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 449 " --> pdb=" O THR B 687 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET B 448 " --> pdb=" O ILE B 710 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 615 through 618 removed outlier: 6.269A pdb=" N ALA B 477 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL B 476 " --> pdb=" O VAL B 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 703 hydrogen bonds defined for protein. 2004 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: 4.92 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4603 1.34 - 1.46: 2939 1.46 - 1.58: 6825 1.58 - 1.70: 1 1.70 - 1.81: 99 Bond restraints: 14467 Sorted by residual: bond pdb=" CB PRO A 497 " pdb=" CG PRO A 497 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" N PRO A 497 " pdb=" CA PRO A 497 " ideal model delta sigma weight residual 1.481 1.444 0.038 1.85e-02 2.92e+03 4.12e+00 bond pdb=" CD LYS H 65 " pdb=" CE LYS H 65 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CG GLU A 154 " pdb=" CD GLU A 154 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.86e+00 bond pdb=" CG1 ILE A 82 " pdb=" CD1 ILE A 82 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.81e+00 ... (remaining 14462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 19294 2.59 - 5.18: 286 5.18 - 7.77: 28 7.77 - 10.36: 2 10.36 - 12.95: 1 Bond angle restraints: 19611 Sorted by residual: angle pdb=" CA PRO A 497 " pdb=" N PRO A 497 " pdb=" CD PRO A 497 " ideal model delta sigma weight residual 112.00 99.05 12.95 1.40e+00 5.10e-01 8.56e+01 angle pdb=" C GLU F 31 " pdb=" N PHE F 32 " pdb=" CA PHE F 32 " ideal model delta sigma weight residual 120.68 113.22 7.46 1.70e+00 3.46e-01 1.93e+01 angle pdb=" CA TYR H 64 " pdb=" CB TYR H 64 " pdb=" CG TYR H 64 " ideal model delta sigma weight residual 113.90 121.50 -7.60 1.80e+00 3.09e-01 1.78e+01 angle pdb=" N VAL B 220 " pdb=" CA VAL B 220 " pdb=" C VAL B 220 " ideal model delta sigma weight residual 112.12 108.70 3.42 8.40e-01 1.42e+00 1.65e+01 angle pdb=" N VAL A 26 " pdb=" CA VAL A 26 " pdb=" C VAL A 26 " ideal model delta sigma weight residual 111.81 108.37 3.44 8.60e-01 1.35e+00 1.60e+01 ... (remaining 19606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7703 17.87 - 35.75: 727 35.75 - 53.62: 106 53.62 - 71.49: 18 71.49 - 89.36: 14 Dihedral angle restraints: 8568 sinusoidal: 3357 harmonic: 5211 Sorted by residual: dihedral pdb=" CA GLN A 305 " pdb=" C GLN A 305 " pdb=" N ILE A 306 " pdb=" CA ILE A 306 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA TYR A 664 " pdb=" C TYR A 664 " pdb=" N PHE A 665 " pdb=" CA PHE A 665 " ideal model delta harmonic sigma weight residual 180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASN B 314 " pdb=" C ASN B 314 " pdb=" N GLN B 315 " pdb=" CA GLN B 315 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 8565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1704 0.054 - 0.108: 381 0.108 - 0.162: 56 0.162 - 0.215: 5 0.215 - 0.269: 2 Chirality restraints: 2148 Sorted by residual: chirality pdb=" CB ILE A 82 " pdb=" CA ILE A 82 " pdb=" CG1 ILE A 82 " pdb=" CG2 ILE A 82 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 416 " pdb=" CA ILE A 416 " pdb=" CG1 ILE A 416 " pdb=" CG2 ILE A 416 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TYR D 18 " pdb=" N TYR D 18 " pdb=" C TYR D 18 " pdb=" CB TYR D 18 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2145 not shown) Planarity restraints: 2531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 20 " -0.073 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B 21 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 21 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 21 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 496 " -0.080 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO A 497 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 497 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 497 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 33 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO J 34 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO J 34 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO J 34 " 0.061 5.00e-02 4.00e+02 ... (remaining 2528 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 249 2.68 - 3.24: 14144 3.24 - 3.79: 21172 3.79 - 4.35: 27517 4.35 - 4.90: 46506 Nonbonded interactions: 109588 Sorted by model distance: nonbonded pdb=" NH2 ARG A 211 " pdb=" OD1 ASP B 252 " model vdw 2.126 3.120 nonbonded pdb=" NH1 ARG A 222 " pdb=" OD2 ASP B 362 " model vdw 2.132 3.120 nonbonded pdb=" O LEU A 609 " pdb=" OH TYR A 615 " model vdw 2.167 3.040 nonbonded pdb=" NZ LYS A 106 " pdb=" O ASP A 776 " model vdw 2.210 3.120 nonbonded pdb=" OG1 THR A 640 " pdb=" OH TYR A 651 " model vdw 2.213 3.040 ... (remaining 109583 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' and (resid 15 through 130 or (resid 147 through 150 and (name N or na \ me CA or name C or name O or name CB )) or resid 151 through 235 or resid 240 th \ rough 431 or (resid 432 through 433 and (name N or name CA or name C or name O o \ r name CB )) or resid 442 through 498 or resid 607 through 662 or (resid 663 and \ (name N or name CA or name C or name O or name CB )) or resid 664 through 688 o \ r (resid 689 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 90 through 691 or (resid 692 through 693 and (name N or name CA or name C or nam \ e O or name CB )) or resid 694 through 764 or (resid 765 and (name N or name CA \ or name C or name O or name CB )) or (resid 776 and (name N or name CA or name C \ or name O or name CB )) or resid 777 or (resid 778 and (name N or name CA or na \ me C or name O or name CB )) or resid 779 through 816 or (resid 817 through 818 \ and (name N or name CA or name C or name O or name CB )) or resid 819 or (resid \ 820 and (name N or name CA or name C or name O or name CB )) or resid 821)) selection = (chain 'B' and (resid 15 through 254 or (resid 255 and (name N or name CA or nam \ e C or name O or name CB )) or resid 256 through 607 or (resid 608 and (name N o \ r name CA or name C or name O or name CB )) or resid 609 through 720 or (resid 7 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 722 through \ 731 or (resid 732 and (name N or name CA or name C or name O or name CB )) or r \ esid 733 through 821)) } ncs_group { reference = (chain 'D' and ((resid 13 and (name N or name CA or name C or name O or name CB \ )) or resid 14 or (resid 15 and (name N or name CA or name C or name O or name C \ B )) or resid 16 through 33 or (resid 34 and (name N or name CA or name C or nam \ e O or name CB )) or resid 35 through 40 or (resid 41 and (name N or name CA or \ name C or name O or name CB )) or resid 42 through 47 or (resid 48 and (name N o \ r name CA or name C or name O or name CB )) or resid 49 through 62)) selection = chain 'E' } ncs_group { reference = (chain 'F' and ((resid 22 through 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 or (resid 31 and (name N or name CA or name C or name \ O or name CB )) or resid 32 or (resid 33 through 39 and (name N or name CA or na \ me C or name O or name CB )) or resid 40 or (resid 41 through 45 and (name N or \ name CA or name C or name O or name CB )) or resid 46 through 55 or (resid 56 an \ d (name N or name CA or name C or name O or name CB )) or resid 57 through 61 or \ (resid 62 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 22 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 57 or (resid 58 through 59 and (na \ me N or name CA or name C or name O or name CB )) or resid 60 through 62)) } 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: 8.270 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.810 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.163 14467 Z= 0.373 Angle : 0.789 12.955 19611 Z= 0.455 Chirality : 0.046 0.269 2148 Planarity : 0.007 0.113 2531 Dihedral : 14.187 89.364 5208 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.38 (0.20), residues: 1774 helix: 0.50 (0.18), residues: 824 sheet: -2.74 (0.32), residues: 265 loop : -1.83 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 50 HIS 0.008 0.001 HIS A 326 PHE 0.034 0.002 PHE A 520 TYR 0.043 0.002 TYR H 64 ARG 0.010 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.6817 (tp) cc_final: 0.6581 (tp) REVERT: A 305 GLN cc_start: 0.6633 (tp40) cc_final: 0.6410 (tp-100) REVERT: A 322 VAL cc_start: 0.7554 (t) cc_final: 0.7287 (t) REVERT: B 260 LEU cc_start: 0.7453 (pt) cc_final: 0.7142 (pp) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2795 time to fit residues: 136.0632 Evaluate side-chains 222 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 0.0170 chunk 160 optimal weight: 3.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 408 ASN B 428 ASN B 673 GLN B 705 GLN B 750 GLN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14467 Z= 0.238 Angle : 0.709 11.376 19611 Z= 0.361 Chirality : 0.043 0.226 2148 Planarity : 0.006 0.083 2531 Dihedral : 5.091 25.302 1953 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.99 % Allowed : 10.63 % Favored : 87.38 % 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: -0.91 (0.20), residues: 1774 helix: 0.85 (0.18), residues: 857 sheet: -2.44 (0.32), residues: 256 loop : -1.72 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 50 HIS 0.009 0.001 HIS B 274 PHE 0.025 0.002 PHE B 391 TYR 0.032 0.002 TYR D 18 ARG 0.008 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 253 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 TYR cc_start: 0.6752 (t80) cc_final: 0.6455 (t80) REVERT: D 18 TYR cc_start: 0.5884 (p90) cc_final: 0.5504 (p90) REVERT: J 40 LEU cc_start: 0.7751 (tp) cc_final: 0.7282 (tp) outliers start: 29 outliers final: 11 residues processed: 270 average time/residue: 0.2602 time to fit residues: 104.5667 Evaluate side-chains 230 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 219 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 54 optimal weight: 0.4980 chunk 129 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 GLN B 372 GLN B 750 GLN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3045 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: