Starting phenix.real_space_refine on Wed Mar 20 06:00:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xya_33515/03_2024/7xya_33515.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xya_33515/03_2024/7xya_33515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xya_33515/03_2024/7xya_33515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xya_33515/03_2024/7xya_33515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xya_33515/03_2024/7xya_33515.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xya_33515/03_2024/7xya_33515.pdb" } resolution = 3.3 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= 0.001 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: 6 Type Number sf(0) Gaussians P 126 5.49 5 Mg 1 5.21 5 S 84 5.16 5 C 16219 2.51 5 N 4891 2.21 5 O 5229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 554": "OD1" <-> "OD2" Residue "C PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 606": "OD1" <-> "OD2" Residue "C PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 654": "OD1" <-> "OD2" Residue "C ASP 680": "OD1" <-> "OD2" Residue "C ASP 733": "OD1" <-> "OD2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1101": "OD1" <-> "OD2" Residue "C ASP 1112": "OD1" <-> "OD2" Residue "C GLU 1174": "OE1" <-> "OE2" Residue "C GLU 1207": "OE1" <-> "OE2" Residue "C ASP 1256": "OD1" <-> "OD2" Residue "C TYR 1266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1304": "OE1" <-> "OE2" Residue "C ASP 1325": "OD1" <-> "OD2" Residue "C GLU 1344": "OE1" <-> "OE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D ASP 284": "OD1" <-> "OD2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 532": "OE1" <-> "OE2" Residue "D TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "D GLU 811": "OE1" <-> "OE2" Residue "D GLU 817": "OE1" <-> "OE2" Residue "D PHE 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 878": "OD1" <-> "OD2" Residue "D PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F GLU 282": "OE1" <-> "OE2" Residue "F PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 373": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26550 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1583 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1499 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 1, 'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 7936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 7936 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 369} Link IDs: {'PTRANS': 49, 'TRANS': 1140} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1406 Unresolved non-hydrogen angles: 1792 Unresolved non-hydrogen dihedrals: 1109 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 10, 'ASN:plan1': 18, 'TRP:plan': 1, 'ASP:plan': 42, 'PHE:plan': 16, 'GLU:plan': 56, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 814 Chain: "D" Number of atoms: 9270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 9270 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 60, 'TRANS': 1277} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1154 Unresolved non-hydrogen angles: 1470 Unresolved non-hydrogen dihedrals: 917 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 24, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 55, 'ASP:plan': 43} Unresolved non-hydrogen planarities: 690 Chain: "E" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 460 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "F" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2418 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 2 Chain: "N" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1196 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "R" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "T" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1195 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 783 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 647 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 1, 'TRP:plan': 5, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 301 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.91, per 1000 atoms: 0.56 Number of scatterers: 26550 At special positions: 0 Unit cell: (147.87, 159.96, 159.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 126 15.00 Mg 1 11.99 O 5229 8.00 N 4891 7.00 C 16219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 888 " - pdb=" SG CYS D 895 " distance=2.30 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 14.17 Conformation dependent library (CDL) restraints added in 5.3 seconds 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6442 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 45 sheets defined 44.1% alpha, 13.2% beta 53 base pairs and 98 stacking pairs defined. Time for finding SS restraints: 9.09 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.181A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.712A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.572A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 211 through 227 removed outlier: 3.820A pdb=" N LEU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.089A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 210 through 217 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 350 through 357 Processing helix chain 'C' and resid 363 through 376 Processing helix chain 'C' and resid 382 through 396 removed outlier: 4.064A pdb=" N SER C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 Processing helix chain 'C' and resid 426 through 443 removed outlier: 4.023A pdb=" N ILE C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 484 Processing helix chain 'C' and resid 493 through 498 removed outlier: 3.671A pdb=" N ILE C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 514 removed outlier: 3.615A pdb=" N SER C 514 " --> pdb=" O PHE C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'C' and resid 544 through 548 removed outlier: 3.608A pdb=" N ALA C 548 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 removed outlier: 3.545A pdb=" N TYR C 560 " --> pdb=" O PRO C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 617 removed outlier: 3.708A pdb=" N ALA C 617 " --> pdb=" O ILE C 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 614 through 617' Processing helix chain 'C' and resid 661 through 665 removed outlier: 3.838A pdb=" N VAL C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 673 Processing helix chain 'C' and resid 675 through 679 Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 708 through 717 removed outlier: 4.471A pdb=" N ASN C 712 " --> pdb=" O GLY C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 863 through 870 Processing helix chain 'C' and resid 947 through 984 Processing helix chain 'C' and resid 1021 through 1055 removed outlier: 3.606A pdb=" N GLN C1055 " --> pdb=" O ARG C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 4.138A pdb=" N SER C1122 " --> pdb=" O LEU C1118 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C1123 " --> pdb=" O GLY C1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1118 through 1123' Processing helix chain 'C' and resid 1126 through 1151 Processing helix chain 'C' and resid 1154 through 1167 Processing helix chain 'C' and resid 1182 through 1192 Processing helix chain 'C' and resid 1206 through 1217 Processing helix chain 'C' and resid 1286 through 1296 Processing helix chain 'C' and resid 1299 through 1308 Processing helix chain 'C' and resid 1312 through 1326 removed outlier: 3.819A pdb=" N THR C1317 " --> pdb=" O VAL C1313 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS C1318 " --> pdb=" O ASN C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1348 removed outlier: 3.756A pdb=" N ASN C1339 " --> pdb=" O PRO C1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.922A pdb=" N TRP D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP D 410 " --> pdb=" O PRO D 406 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.503A pdb=" N VAL D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 635 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.360A pdb=" N ARG D 652 " --> pdb=" O ASP D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.582A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS D 703 " --> pdb=" O ALA D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.645A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.780A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.576A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1051 through 1055 removed outlier: 3.573A pdb=" N THR D1054 " --> pdb=" O ASP D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.738A pdb=" N ILE D1220 " --> pdb=" O ASN D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.510A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.340A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1292 removed outlier: 3.630A pdb=" N LEU D1292 " --> pdb=" O GLU D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.988A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1375 Processing helix chain 'E' and resid 8 through 14 Processing helix chain 'E' and resid 16 through 32 removed outlier: 3.804A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'F' and resid 98 through 109 removed outlier: 3.837A pdb=" N THR F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 138 removed outlier: 3.684A pdb=" N GLN F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 155 Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.617A pdb=" N VAL F 163 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 238 removed outlier: 3.785A pdb=" N ALA F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 261 Processing helix chain 'F' and resid 266 through 300 removed outlier: 3.558A pdb=" N ARG F 300 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 310 Processing helix chain 'F' and resid 317 through 327 removed outlier: 3.738A pdb=" N LYS F 327 " --> pdb=" O VAL F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 335 removed outlier: 3.516A pdb=" N GLU F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 356 Processing helix chain 'F' and resid 358 through 396 removed outlier: 4.905A pdb=" N ARG F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU F 390 " --> pdb=" O ALA F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 404 through 422 Processing helix chain 'F' and resid 430 through 450 removed outlier: 4.134A pdb=" N TYR F 434 " --> pdb=" O LYS F 430 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP F 437 " --> pdb=" O THR F 433 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP F 438 " --> pdb=" O TYR F 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 25 through 35 Processing helix chain 'G' and resid 50 through 69 Processing helix chain 'G' and resid 72 through 84 Processing helix chain 'G' and resid 86 through 101 Processing helix chain 'G' and resid 105 through 120 Processing helix chain 'G' and resid 126 through 135 Processing helix chain 'G' and resid 137 through 170 removed outlier: 4.276A pdb=" N GLU G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Proline residue: G 166 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 7.097A pdb=" N ASP A 198 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 6.085A pdb=" N ALA A 146 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL A 56 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 148 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N CYS A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.554A pdb=" N ALA A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 18 removed outlier: 3.762A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP B 198 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 61 removed outlier: 6.785A pdb=" N LYS B 144 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA B 59 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS B 142 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE B 61 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASN B 140 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.061A pdb=" N LYS C 13 " --> pdb=" O ALA C1198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 70 through 74 removed outlier: 4.045A pdb=" N LYS C 119 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB6, first strand: chain 'C' and resid 456 through 458 Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.717A pdb=" N CYS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AB9, first strand: chain 'C' and resid 585 through 586 removed outlier: 5.097A pdb=" N GLU C 607 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AC2, first strand: chain 'C' and resid 721 through 722 removed outlier: 6.619A pdb=" N VAL C 721 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 755 through 757 removed outlier: 6.873A pdb=" N ARG C 736 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL C 732 " --> pdb=" O ARG C 736 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 738 " --> pdb=" O ASP C 730 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 762 through 763 Processing sheet with id=AC5, first strand: chain 'C' and resid 794 through 795 Processing sheet with id=AC6, first strand: chain 'C' and resid 1083 through 1084 removed outlier: 4.548A pdb=" N THR C1241 " --> pdb=" O PHE C 809 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N ILE C1113 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG C 806 " --> pdb=" O ILE C1113 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU C1115 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA C 808 " --> pdb=" O LEU C1115 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS C 822 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE C 821 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C1096 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 823 " --> pdb=" O ILE C1096 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1083 through 1084 Processing sheet with id=AC8, first strand: chain 'C' and resid 835 through 846 removed outlier: 4.342A pdb=" N LYS C1065 " --> pdb=" O ALA C 845 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP C 935 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA C1072 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL C 933 " --> pdb=" O ALA C1072 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N LYS C1074 " --> pdb=" O GLY C 931 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N GLY C 931 " --> pdb=" O LYS C1074 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD1, first strand: chain 'C' and resid 892 through 893 Processing sheet with id=AD2, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.562A pdb=" N CYS D 366 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 7.380A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1350 through 1353 removed outlier: 3.684A pdb=" N GLU C1353 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.329A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N SER D 109 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N VAL D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 removed outlier: 4.722A pdb=" N GLY D 558 " --> pdb=" O GLN D 562 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.429A pdb=" N VAL D 848 " --> pdb=" O ILE D 857 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 991 through 996 removed outlier: 3.789A pdb=" N GLU D 993 " --> pdb=" O VAL D 984 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AE4, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 3.746A pdb=" N GLY D1033 " --> pdb=" O VAL D1115 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1036 through 1038 Processing sheet with id=AE6, first strand: chain 'D' and resid 1046 through 1047 Processing sheet with id=AE7, first strand: chain 'D' and resid 1155 through 1156 removed outlier: 6.706A pdb=" N ILE D1155 " --> pdb=" O ILE D1210 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1172 through 1174 Processing sheet with id=AE9, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 7.218A pdb=" N LYS D1301 " --> pdb=" O SER D1267 " (cutoff:3.500A) 1285 hydrogen bonds defined for protein. 3645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 98 stacking parallelities Total time for adding SS restraints: 13.13 Time building geometry restraints manager: 13.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4936 1.33 - 1.45: 6707 1.45 - 1.57: 15114 1.57 - 1.70: 250 1.70 - 1.82: 150 Bond restraints: 27157 Sorted by residual: bond pdb=" N VAL D 253 " pdb=" CA VAL D 253 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.92e+01 bond pdb=" N ILE C 887 " pdb=" CA ILE C 887 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.23e-02 6.61e+03 1.17e+01 bond pdb=" N VAL C 889 " pdb=" CA VAL C 889 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N LEU C 18 " pdb=" CA LEU C 18 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.18e-02 7.18e+03 9.00e+00 bond pdb=" N LYS C 919 " pdb=" CA LYS C 919 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 8.92e+00 ... (remaining 27152 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.57: 1012 105.57 - 112.68: 14841 112.68 - 119.79: 8569 119.79 - 126.90: 12508 126.90 - 134.01: 520 Bond angle restraints: 37450 Sorted by residual: angle pdb=" C PRO C 350 " pdb=" CA PRO C 350 " pdb=" CB PRO C 350 " ideal model delta sigma weight residual 112.64 104.82 7.82 1.43e+00 4.89e-01 2.99e+01 angle pdb=" N THR C 921 " pdb=" CA THR C 921 " pdb=" C THR C 921 " ideal model delta sigma weight residual 112.59 106.00 6.59 1.22e+00 6.72e-01 2.92e+01 angle pdb=" CA GLY C1281 " pdb=" C GLY C1281 " pdb=" O GLY C1281 " ideal model delta sigma weight residual 122.23 118.59 3.64 6.90e-01 2.10e+00 2.78e+01 angle pdb=" CA LYS C1277 " pdb=" C LYS C1277 " pdb=" O LYS C1277 " ideal model delta sigma weight residual 120.70 114.78 5.92 1.15e+00 7.56e-01 2.65e+01 angle pdb=" C LEU C1274 " pdb=" N GLY C1275 " pdb=" CA GLY C1275 " ideal model delta sigma weight residual 121.46 116.75 4.71 9.50e-01 1.11e+00 2.46e+01 ... (remaining 37445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.09: 14752 27.09 - 54.18: 1203 54.18 - 81.27: 202 81.27 - 108.36: 11 108.36 - 135.45: 2 Dihedral angle restraints: 16170 sinusoidal: 6212 harmonic: 9958 Sorted by residual: dihedral pdb=" CB CYS D 888 " pdb=" SG CYS D 888 " pdb=" SG CYS D 895 " pdb=" CB CYS D 895 " ideal model delta sinusoidal sigma weight residual 93.00 -177.48 -89.52 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CA LYS F 327 " pdb=" C LYS F 327 " pdb=" N PRO F 328 " pdb=" CA PRO F 328 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA CYS D 898 " pdb=" C CYS D 898 " pdb=" N TYR D 899 " pdb=" CA TYR D 899 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 16167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3860 0.060 - 0.120: 566 0.120 - 0.180: 45 0.180 - 0.240: 7 0.240 - 0.300: 5 Chirality restraints: 4483 Sorted by residual: chirality pdb=" CA LYS C1277 " pdb=" N LYS C1277 " pdb=" C LYS C1277 " pdb=" CB LYS C1277 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA GLN C1279 " pdb=" N GLN C1279 " pdb=" C GLN C1279 " pdb=" CB GLN C1279 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA THR C 921 " pdb=" N THR C 921 " pdb=" C THR C 921 " pdb=" CB THR C 921 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4480 not shown) Planarity restraints: 4495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 651 " 0.065 5.00e-02 4.00e+02 9.54e-02 1.45e+01 pdb=" N PRO C 652 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO C 652 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 652 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 845 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.87e+00 pdb=" C ALA C 845 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA C 845 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG C 846 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 16 " 0.013 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C SER C 16 " -0.048 2.00e-02 2.50e+03 pdb=" O SER C 16 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS C 17 " 0.016 2.00e-02 2.50e+03 ... (remaining 4492 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 193 2.55 - 3.14: 20815 3.14 - 3.72: 43690 3.72 - 4.31: 55778 4.31 - 4.90: 92275 Nonbonded interactions: 212751 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1601 " model vdw 1.962 2.170 nonbonded pdb=" O3' A R 18 " pdb="MG MG D1601 " model vdw 1.989 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1601 " model vdw 2.016 2.170 nonbonded pdb=" NZ LYS C1082 " pdb=" O ASP D 462 " model vdw 2.201 2.520 nonbonded pdb=" NE2 HIS C1087 " pdb=" OE1 GLU C1131 " model vdw 2.203 2.520 ... (remaining 212746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or (resid 16 and (name N or name \ CA or name C or name O or name CB )) or resid 17 through 57 or (resid 58 throug \ h 62 and (name N or name CA or name C or name O or name CB )) or resid 63 or (re \ sid 64 through 66 and (name N or name CA or name C or name O or name CB )) or re \ sid 67 or (resid 68 and (name N or name CA or name C or name O or name CB )) or \ resid 69 through 74 or (resid 75 and (name N or name CA or name C or name O or n \ ame CB )) or resid 76 through 79 or (resid 80 and (name N or name CA or name C o \ r name O or name CB )) or resid 81 through 89 or (resid 90 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2)) or resid 91 through 9 \ 2 or (resid 93 and (name N or name CA or name C or name O or name CB )) or resid \ 94 or (resid 95 and (name N or name CA or name C or name O or name CB or name C \ G )) or resid 96 through 104 or (resid 105 and (name N or name CA or name C or n \ ame O or name CB )) or resid 109 through 113 or (resid 114 and (name N or name C \ A or name C or name O or name CB )) or resid 115 through 118 or (resid 119 and ( \ name N or name CA or name C or name O or name CB )) or resid 120 through 134 or \ resid 139 through 141 or (resid 142 and (name N or name CA or name C or name O o \ r name CB )) or resid 143 through 157 or (resid 169 and (name N or name CA or na \ me C or name O or name CB )) or resid 170 through 182 or (resid 183 and (name N \ or name CA or name C or name O or name CB )) or resid 184 through 217 or (resid \ 218 through 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 230)) selection = (chain 'B' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or resid 15 through 25 or (resid \ 26 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2)) or resid 27 through 31 or (resid 32 and (name N or name CA or name C or name \ O or name CB )) or resid 33 through 71 or (resid 72 and (name N or name CA or n \ ame C or name O or name CB )) or resid 73 through 116 or (resid 117 and (name N \ or name CA or name C or name O or name CB )) or resid 118 through 126 or (resid \ 127 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 128 through 139 or (resid 140 and (name N or name CA or name C or name O or nam \ e CB or name CG )) or resid 141 through 151 or (resid 152 and (name N or name CA \ or name C or name O or name CB )) or resid 153 through 193 or (resid 194 throug \ h 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 212 or (resid 213 through 215 and (name N or name CA or name C or name O or \ name CB )) or resid 216 through 230)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.400 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 81.600 Find NCS groups from input model: 1.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 0.109 27157 Z= 0.255 Angle : 0.678 9.933 37450 Z= 0.410 Chirality : 0.043 0.300 4483 Planarity : 0.004 0.095 4495 Dihedral : 19.124 135.446 9725 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 1.00 % Allowed : 19.63 % Favored : 79.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.71 % 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: -0.19 (0.14), residues: 3441 helix: 1.34 (0.14), residues: 1422 sheet: -0.54 (0.27), residues: 401 loop : -1.39 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 41 HIS 0.009 0.001 HIS D 430 PHE 0.020 0.002 PHE F 306 TYR 0.014 0.001 TYR D 679 ARG 0.011 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 261 MET cc_start: 0.4331 (tmm) cc_final: 0.4102 (tmm) REVERT: F 383 MET cc_start: 0.8895 (tpp) cc_final: 0.8534 (ttt) outliers start: 20 outliers final: 10 residues processed: 199 average time/residue: 0.3458 time to fit residues: 114.9514 Evaluate side-chains 183 residues out of total 2917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain E residue 22 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN B 188 ASN C 524 ASN C 623 GLN C 837 HIS ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1322 ASN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 566 ASN D1218 HIS D1235 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27157 Z= 0.333 Angle : 0.595 8.527 37450 Z= 0.319 Chirality : 0.042 0.162 4483 Planarity : 0.004 0.046 4495 Dihedral : 18.616 135.984 5139 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.48 % Rotamer: Outliers : 4.02 % Allowed : 17.92 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % 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: -0.11 (0.14), residues: 3441 helix: 1.41 (0.14), residues: 1453 sheet: -0.67 (0.26), residues: 391 loop : -1.34 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 41 HIS 0.022 0.002 HIS C 556 PHE 0.020 0.002 PHE F 306 TYR 0.020 0.002 TYR D 679 ARG 0.020 0.001 ARG C 547 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 179 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7953 (tp40) REVERT: C 690 MET cc_start: 0.9107 (tpp) cc_final: 0.8680 (mtm) REVERT: C 1285 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: D 22 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9068 (tp) REVERT: D 239 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9052 (pp) REVERT: D 1372 GLN cc_start: 0.8441 (pt0) cc_final: 0.8115 (pp30) REVERT: F 261 MET cc_start: 0.4754 (tmm) cc_final: 0.4492 (tmm) REVERT: F 356 GLU cc_start: 0.6473 (mm-30) cc_final: 0.6077 (pt0) outliers start: 80 outliers final: 43 residues processed: 244 average time/residue: 0.3404 time to fit residues: 138.6528 Evaluate side-chains 217 residues out of total 2917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 170 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 1067 VAL Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1285 PHE Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1311 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 359 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 268 optimal weight: 50.0000 chunk 219 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 322 optimal weight: 10.0000 chunk 348 optimal weight: 50.0000 chunk 287 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 259 optimal weight: 0.0010 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN B 140 ASN C 837 HIS ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1271 GLN D 277 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27157 Z= 0.223 Angle : 0.526 7.316 37450 Z= 0.284 Chirality : 0.040 0.212 4483 Planarity : 0.003 0.050 4495 Dihedral : 18.469 135.960 5131 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 3.82 % Allowed : 19.03 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % 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 (0.14), residues: 3441 helix: 1.64 (0.14), residues: 1456 sheet: -0.86 (0.25), residues: 412 loop : -1.23 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 41 HIS 0.014 0.001 HIS C 556 PHE 0.016 0.001 PHE F 310 TYR 0.017 0.001 TYR D 679 ARG 0.006 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 177 time to evaluate : 3.047 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.9465 (OUTLIER) cc_final: 0.9248 (t) REVERT: A 224 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7661 (tp40) REVERT: B 224 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: C 140 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7455 (p90) REVERT: C 1285 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: C 1337 SER cc_start: 0.9363 (OUTLIER) cc_final: 0.8848 (m) REVERT: D 239 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9074 (pp) REVERT: D 822 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8694 (mtp) REVERT: F 261 MET cc_start: 0.4835 (tmm) cc_final: 0.4589 (tmm) REVERT: F 356 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6216 (pt0) outliers start: 76 outliers final: 46 residues processed: 237 average time/residue: 0.3417 time to fit residues: 137.7833 Evaluate side-chains 216 residues out of total 2917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 162 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1187 LEU Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1285 PHE Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1311 ASP Chi-restraints excluded: chain C residue 1337 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 881 VAL Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 319 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 324 optimal weight: 9.9990 chunk 343 optimal weight: 50.0000 chunk 169 optimal weight: 9.9990 chunk 307 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN C 803 GLN C 837 HIS C1125 ASN C1163 HIS C1175 ASN D 266 ASN D 277 ASN D 489 ASN D 921 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 27157 Z= 0.449 Angle : 0.656 8.782 37450 Z= 0.349 Chirality : 0.044 0.186 4483 Planarity : 0.005 0.058 4495 Dihedral : 18.530 136.870 5130 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.98 % Rotamer: Outliers : 5.62 % Allowed : 18.93 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % 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: -0.24 (0.14), residues: 3441 helix: 1.34 (0.14), residues: 1466 sheet: -0.95 (0.25), residues: 390 loop : -1.43 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 41 HIS 0.009 0.002 HIS D 777 PHE 0.024 0.002 PHE F 310 TYR 0.026 0.002 TYR D 140 ARG 0.008 0.001 ARG D 901 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 172 time to evaluate : 2.657 Fit side-chains revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8427 (tp-100) cc_final: 0.8051 (tp40) REVERT: A 144 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8653 (ttpp) REVERT: A 224 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7716 (tp40) REVERT: B 25 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8637 (mtmt) REVERT: B 224 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: C 7 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7299 (pt0) REVERT: C 192 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.7610 (t80) REVERT: C 1285 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: D 20 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8923 (mt) REVERT: D 239 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9077 (pp) REVERT: F 356 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6448 (pt0) outliers start: 112 outliers final: 69 residues processed: 264 average time/residue: 0.3338 time to fit residues: 148.4010 Evaluate side-chains 235 residues out of total 2917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 158 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 803 GLN Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 1067 VAL Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain C residue 1285 PHE Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1352 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 881 VAL Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 167 TYR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 416 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 20.0000 chunk 194 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 255 optimal weight: 30.0000 chunk 141 optimal weight: 9.9990 chunk 292 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 30.0000 chunk 307 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN C 837 HIS ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27157 Z= 0.350 Angle : 0.587 7.729 37450 Z= 0.316 Chirality : 0.042 0.169 4483 Planarity : 0.004 0.054 4495 Dihedral : 18.490 136.988 5130 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 5.47 % Allowed : 19.93 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % 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: -0.14 (0.14), residues: 3441 helix: 1.49 (0.14), residues: 1453 sheet: -1.01 (0.25), residues: 407 loop : -1.37 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 41 HIS 0.006 0.001 HIS D 777 PHE 0.020 0.002 PHE F 310 TYR 0.018 0.002 TYR D 679 ARG 0.006 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 163 time to evaluate : 3.008 Fit side-chains Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable