Starting phenix.real_space_refine on Tue Nov 19 13:21:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/11_2024/6xn4_22267.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/11_2024/6xn4_22267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/11_2024/6xn4_22267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/11_2024/6xn4_22267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/11_2024/6xn4_22267.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/11_2024/6xn4_22267.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 48 5.16 5 C 12041 2.51 5 N 3263 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19273 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2227 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 275, 2225 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 275, 2225 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2272 Chain: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 736 Classifications: {'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 12} Link IDs: {'rna2p': 16, 'rna3p': 18} Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "D" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1089 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "T" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 644 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 25} Chain: "A" Number of atoms: 5984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5984 Classifications: {'peptide': 741} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 730} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2515 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 294} Chain breaks: 3 Time building chain proxies: 12.31, per 1000 atoms: 0.64 Number of scatterers: 19273 At special positions: 0 Unit cell: (109.548, 126.732, 183.654, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 64 15.00 O 3857 8.00 N 3263 7.00 C 12041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.01 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.43 Conformation dependent library (CDL) restraints added in 2.9 seconds 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4184 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 24 sheets defined 40.5% alpha, 12.8% beta 2 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 7.17 Creating SS restraints... Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.582A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.555A pdb=" N PHE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 4.073A pdb=" N LEU B 227 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 61 removed outlier: 3.543A pdb=" N LEU F 49 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.600A pdb=" N GLY F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 removed outlier: 3.546A pdb=" N ARG F 183 " --> pdb=" O HIS F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 157 through 174 removed outlier: 3.537A pdb=" N ASN H 164 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS H 166 " --> pdb=" O PHE H 162 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE H 174 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.797A pdb=" N LEU G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 157 through 173 Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.539A pdb=" N ILE C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.732A pdb=" N GLU C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'D' and resid 53 through 73 removed outlier: 4.369A pdb=" N VAL D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.554A pdb=" N ALA D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 removed outlier: 3.621A pdb=" N THR D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.506A pdb=" N TYR D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.657A pdb=" N LYS A 17 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 19 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 4.300A pdb=" N LYS A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 72 through 85 removed outlier: 4.116A pdb=" N THR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.801A pdb=" N LYS A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.522A pdb=" N TYR A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.848A pdb=" N VAL A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 224 removed outlier: 3.597A pdb=" N HIS A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 270 through 295 removed outlier: 4.081A pdb=" N ASP A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 Processing helix chain 'A' and resid 364 through 381 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 418 through 430 removed outlier: 3.878A pdb=" N SER A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.931A pdb=" N SER A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.679A pdb=" N GLU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 540 through 564 removed outlier: 3.920A pdb=" N THR A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.391A pdb=" N ASP A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 638 removed outlier: 3.710A pdb=" N ASP A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 674 through 682 removed outlier: 3.522A pdb=" N GLU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.654A pdb=" N GLY A 701 " --> pdb=" O ASP A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 727 through 739 Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.574A pdb=" N MET A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.514A pdb=" N THR J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 65 removed outlier: 3.803A pdb=" N VAL J 62 " --> pdb=" O PHE J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 76 Processing helix chain 'J' and resid 127 through 138 removed outlier: 3.684A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.637A pdb=" N ALA J 154 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 167 No H-bonds generated for 'chain 'J' and resid 165 through 167' Processing helix chain 'J' and resid 209 through 229 removed outlier: 3.650A pdb=" N ILE J 213 " --> pdb=" O THR J 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP J 228 " --> pdb=" O TYR J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 301 removed outlier: 4.047A pdb=" N GLN J 290 " --> pdb=" O LYS J 286 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG J 292 " --> pdb=" O ARG J 288 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU J 299 " --> pdb=" O SER J 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.649A pdb=" N PHE B 65 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 7 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 132 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AA5, first strand: chain 'B' and resid 274 through 277 removed outlier: 5.858A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 94 through 96 removed outlier: 7.675A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 123 Processing sheet with id=AA9, first strand: chain 'H' and resid 94 through 95 removed outlier: 3.723A pdb=" N PHE H 146 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'H' and resid 115 through 123 Processing sheet with id=AB3, first strand: chain 'G' and resid 94 through 95 removed outlier: 6.447A pdb=" N VAL G 4 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL G 195 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU G 6 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU G 193 " --> pdb=" O GLU G 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AB5, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AB6, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.804A pdb=" N PHE C 42 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 304 through 305 removed outlier: 4.215A pdb=" N PHE A 247 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 352 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 249 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A 344 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 475 Processing sheet with id=AC1, first strand: chain 'A' and resid 568 through 570 removed outlier: 3.518A pdb=" N ALA A 651 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AC3, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AC4, first strand: chain 'J' and resid 22 through 23 removed outlier: 6.666A pdb=" N LEU J 184 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASP J 176 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU J 186 " --> pdb=" O LYS J 174 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN J 173 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 37 through 40 removed outlier: 3.897A pdb=" N TYR J 86 " --> pdb=" O MET J 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 314 through 315 729 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 6.47 Time building geometry restraints manager: 5.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6115 1.34 - 1.48: 5333 1.48 - 1.62: 8202 1.62 - 1.76: 4 1.76 - 1.89: 88 Bond restraints: 19742 Sorted by residual: bond pdb=" CA ASN J 141 " pdb=" C ASN J 141 " ideal model delta sigma weight residual 1.522 1.436 0.087 1.37e-02 5.33e+03 4.00e+01 bond pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.15e-02 7.56e+03 1.28e+01 bond pdb=" C LYS J 170 " pdb=" N VAL J 171 " ideal model delta sigma weight residual 1.329 1.289 0.040 1.46e-02 4.69e+03 7.61e+00 bond pdb=" CG1 ILE A 708 " pdb=" CD1 ILE A 708 " ideal model delta sigma weight residual 1.513 1.407 0.106 3.90e-02 6.57e+02 7.45e+00 bond pdb=" C GLN J 259 " pdb=" N PRO J 260 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.19e-02 7.06e+03 7.37e+00 ... (remaining 19737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 26473 4.07 - 8.15: 381 8.15 - 12.22: 30 12.22 - 16.30: 3 16.30 - 20.37: 1 Bond angle restraints: 26888 Sorted by residual: angle pdb=" CA CYS A 418 " pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " ideal model delta sigma weight residual 114.40 134.77 -20.37 2.30e+00 1.89e-01 7.84e+01 angle pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 123.91 136.92 -13.01 1.66e+00 3.63e-01 6.14e+01 angle pdb=" N ILE J 17 " pdb=" CA ILE J 17 " pdb=" C ILE J 17 " ideal model delta sigma weight residual 113.71 107.32 6.39 9.50e-01 1.11e+00 4.53e+01 angle pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" C ILE A 341 " ideal model delta sigma weight residual 113.71 107.52 6.19 9.50e-01 1.11e+00 4.24e+01 angle pdb=" N VAL A 199 " pdb=" CA VAL A 199 " pdb=" C VAL A 199 " ideal model delta sigma weight residual 113.10 107.33 5.77 9.70e-01 1.06e+00 3.54e+01 ... (remaining 26883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 11568 34.63 - 69.25: 374 69.25 - 103.88: 38 103.88 - 138.50: 4 138.50 - 173.13: 2 Dihedral angle restraints: 11986 sinusoidal: 5486 harmonic: 6500 Sorted by residual: dihedral pdb=" CA SER H 20 " pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta harmonic sigma weight residual 180.00 46.16 133.84 0 5.00e+00 4.00e-02 7.16e+02 dihedral pdb=" CA ILE H 26 " pdb=" C ILE H 26 " pdb=" N GLY H 27 " pdb=" CA GLY H 27 " ideal model delta harmonic sigma weight residual 180.00 116.21 63.79 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA ILE G 26 " pdb=" C ILE G 26 " pdb=" N GLY G 27 " pdb=" CA GLY G 27 " ideal model delta harmonic sigma weight residual 180.00 120.81 59.19 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 11983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2711 0.100 - 0.200: 299 0.200 - 0.300: 33 0.300 - 0.399: 4 0.399 - 0.499: 3 Chirality restraints: 3050 Sorted by residual: chirality pdb=" CB ILE A 708 " pdb=" CA ILE A 708 " pdb=" CG1 ILE A 708 " pdb=" CG2 ILE A 708 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" CB VAL B 131 " pdb=" CA VAL B 131 " pdb=" CG1 VAL B 131 " pdb=" CG2 VAL B 131 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C1' A T 29 " pdb=" O4' A T 29 " pdb=" C2' A T 29 " pdb=" N9 A T 29 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 3047 not shown) Planarity restraints: 3212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET H 15 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C MET H 15 " 0.065 2.00e-02 2.50e+03 pdb=" O MET H 15 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS H 16 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 137 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" CD GLU C 137 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU C 137 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU C 137 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 15 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C MET G 15 " 0.056 2.00e-02 2.50e+03 pdb=" O MET G 15 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS G 16 " -0.018 2.00e-02 2.50e+03 ... (remaining 3209 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1373 2.71 - 3.26: 19283 3.26 - 3.81: 34177 3.81 - 4.35: 41684 4.35 - 4.90: 68043 Nonbonded interactions: 164560 Sorted by model distance: nonbonded pdb=" OG SER B 128 " pdb=" OH TYR B 186 " model vdw 2.166 3.040 nonbonded pdb=" OH TYR B 232 " pdb=" O TYR A 383 " model vdw 2.200 3.040 nonbonded pdb=" OG SER F 47 " pdb=" OP1 A R 9 " model vdw 2.218 3.040 nonbonded pdb=" OG SER C 55 " pdb=" OP2 U T 22 " model vdw 2.240 3.040 nonbonded pdb=" OG SER H 47 " pdb=" OP1 A R 21 " model vdw 2.243 3.040 ... (remaining 164555 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 'C' and resid 12 through 146) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.190 Process input model: 50.190 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.090 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: