Starting phenix.real_space_refine on Thu Mar 21 10:38:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4e_24148/03_2024/7n4e_24148_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4e_24148/03_2024/7n4e_24148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4e_24148/03_2024/7n4e_24148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4e_24148/03_2024/7n4e_24148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4e_24148/03_2024/7n4e_24148_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4e_24148/03_2024/7n4e_24148_neut.pdb" } resolution = 3.8 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= 0.001 sd= 0.007 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 89 5.49 5 Mg 1 5.21 5 S 125 5.16 5 C 18412 2.51 5 N 5284 2.21 5 O 5909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 320": "OD1" <-> "OD2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 446": "OD1" <-> "OD2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C ASP 654": "OD1" <-> "OD2" Residue "C ASP 739": "OD1" <-> "OD2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 813": "OE1" <-> "OE2" Residue "C PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 949": "OE1" <-> "OE2" Residue "C TYR 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1240": "OD1" <-> "OD2" Residue "C TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D ASP 622": "OD1" <-> "OD2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "D ASP 802": "OD1" <-> "OD2" Residue "D GLU 833": "OE1" <-> "OE2" Residue "D PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1007": "OD1" <-> "OD2" Residue "D PHE 1037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1143": "OD1" <-> "OD2" Residue "D TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1293": "OE1" <-> "OE2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "F ASP 267": "OD1" <-> "OD2" Residue "F GLU 336": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29822 Number of models: 1 Model: "" Number of chains: 10 Chain: "1" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 785 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain breaks: 1 Chain: "2" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 830 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain breaks: 1 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10568 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10319 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1271} Chain breaks: 2 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2943 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 9, 'TRANS': 349} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16208 SG CYS D 72 98.609 126.868 120.725 1.00 98.14 S ATOM 22665 SG CYS D 898 103.092 62.630 90.623 1.00 47.28 S Time building chain proxies: 15.29, per 1000 atoms: 0.51 Number of scatterers: 29822 At special positions: 0 Unit cell: (144.48, 159.6, 198.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 125 16.00 P 89 15.00 Mg 1 11.99 O 5909 8.00 N 5284 7.00 C 18412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 12.07 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6598 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 45 sheets defined 43.4% alpha, 14.7% beta 26 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 10.12 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.892A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.055A 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 154 through 162 removed outlier: 3.853A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 234 removed outlier: 3.728A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 51 removed outlier: 3.892A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 4.056A 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 154 through 162 removed outlier: 3.854A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 3.728A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.704A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.764A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.992A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.861A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.724A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 549' Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.645A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.919A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.671A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 902 removed outlier: 4.123A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 905 No H-bonds generated for 'chain 'C' and resid 903 through 905' Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 removed outlier: 3.986A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 3.995A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1138 through 1150 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.614A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.650A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.634A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 210 through 231 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 286 removed outlier: 3.903A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.608A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.537A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (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 505 through 515 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.744A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.591A pdb=" N ILE 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 636 removed outlier: 3.829A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.610A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.557A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.077A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1063 through 1067 removed outlier: 3.565A pdb=" N ARG D1067 " --> pdb=" O SER D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.688A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.548A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.346A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 4.484A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D1375 " --> pdb=" O ARG D1371 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 76 removed outlier: 3.507A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 114 through 136 Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 157 through 161 removed outlier: 4.275A pdb=" N LEU F 161 " --> pdb=" O ARG F 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 157 through 161' Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 237 through 237 No H-bonds generated for 'chain 'F' and resid 237 through 237' Processing helix chain 'F' and resid 243 through 256 Processing helix chain 'F' and resid 262 through 292 removed outlier: 3.528A pdb=" N PHE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 4.237A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 Processing helix chain 'F' and resid 327 through 332 removed outlier: 3.641A pdb=" N HIS F 331 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP F 332 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 382 Processing helix chain 'F' and resid 383 through 392 removed outlier: 3.632A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 400 through 419 Processing helix chain 'F' and resid 420 through 424 removed outlier: 4.031A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 447 removed outlier: 3.821A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP F 445 " --> pdb=" O ARG F 441 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA F 447 " --> pdb=" O ILE F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 4.110A pdb=" N ILE F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 removed outlier: 4.185A pdb=" N LEU F 488 " --> pdb=" O ALA F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 4.811A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 104 removed outlier: 7.220A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (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: 6.499A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 17 removed outlier: 4.811A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 104 removed outlier: 7.220A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (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 108 through 111 removed outlier: 6.499A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.514A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.835A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 96 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLU C 106 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LYS C 115 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.502A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.786A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AB8, first strand: chain 'C' and resid 284 through 287 removed outlier: 4.208A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.947A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.753A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.753A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.957A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1065 through 1066 removed outlier: 7.498A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.990A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.750A pdb=" N THR C 888 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.811A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.224A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.796A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.520A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 5.184A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 148 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.834A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 547 through 557 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 958 through 961 removed outlier: 6.710A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 965 through 966 removed outlier: 3.724A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1024 through 1026 Processing sheet with id=AE5, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.917A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AE7, first strand: chain 'D' and resid 1164 through 1167 removed outlier: 6.776A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.582A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D1267 " --> pdb=" O THR D1301 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 162 through 164 removed outlier: 7.075A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 13.59 Time building geometry restraints manager: 13.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9550 1.34 - 1.46: 4396 1.46 - 1.58: 16111 1.58 - 1.70: 172 1.70 - 1.82: 219 Bond restraints: 30448 Sorted by residual: bond pdb=" O3' DT 1 59 " pdb=" P DA 1 60 " ideal model delta sigma weight residual 1.607 1.501 0.106 1.50e-02 4.44e+03 4.98e+01 bond pdb=" C1' DG 1 27 " pdb=" N9 DG 1 27 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1' DA 1 23 " pdb=" N9 DA 1 23 " ideal model delta sigma weight residual 1.460 1.397 0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" C1' DA 2 36 " pdb=" N9 DA 2 36 " ideal model delta sigma weight residual 1.460 1.398 0.062 2.00e-02 2.50e+03 9.65e+00 bond pdb=" C1' DA 2 37 " pdb=" N9 DA 2 37 " ideal model delta sigma weight residual 1.460 1.400 0.060 2.00e-02 2.50e+03 9.13e+00 ... (remaining 30443 not shown) Histogram of bond angle deviations from ideal: 96.82 - 104.88: 819 104.88 - 112.94: 16655 112.94 - 121.00: 15138 121.00 - 129.06: 8694 129.06 - 137.12: 175 Bond angle restraints: 41481 Sorted by residual: angle pdb=" C3' DT 1 59 " pdb=" O3' DT 1 59 " pdb=" P DA 1 60 " ideal model delta sigma weight residual 120.20 134.23 -14.03 1.50e+00 4.44e-01 8.75e+01 angle pdb=" C MET D 822 " pdb=" N THR D 823 " pdb=" CA THR D 823 " ideal model delta sigma weight residual 122.36 137.12 -14.76 2.42e+00 1.71e-01 3.72e+01 angle pdb=" CB ARG A 191 " pdb=" CG ARG A 191 " pdb=" CD ARG A 191 " ideal model delta sigma weight residual 111.30 123.80 -12.50 2.30e+00 1.89e-01 2.95e+01 angle pdb=" CB ARG B 191 " pdb=" CG ARG B 191 " pdb=" CD ARG B 191 " ideal model delta sigma weight residual 111.30 123.77 -12.47 2.30e+00 1.89e-01 2.94e+01 angle pdb=" N VAL D 706 " pdb=" CA VAL D 706 " pdb=" C VAL D 706 " ideal model delta sigma weight residual 113.43 107.69 5.74 1.09e+00 8.42e-01 2.78e+01 ... (remaining 41476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 17597 33.19 - 66.38: 928 66.38 - 99.57: 54 99.57 - 132.76: 0 132.76 - 165.95: 1 Dihedral angle restraints: 18580 sinusoidal: 8338 harmonic: 10242 Sorted by residual: dihedral pdb=" CG ARG B 45 " pdb=" CD ARG B 45 " pdb=" NE ARG B 45 " pdb=" CZ ARG B 45 " ideal model delta sinusoidal sigma weight residual 90.00 6.03 83.97 2 1.50e+01 4.44e-03 2.11e+01 dihedral pdb=" CG ARG A 45 " pdb=" CD ARG A 45 " pdb=" NE ARG A 45 " pdb=" CZ ARG A 45 " ideal model delta sinusoidal sigma weight residual 90.00 6.05 83.95 2 1.50e+01 4.44e-03 2.11e+01 dihedral pdb=" CA GLU A 97 " pdb=" C GLU A 97 " pdb=" N VAL A 98 " pdb=" CA VAL A 98 " ideal model delta harmonic sigma weight residual 180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 18577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4059 0.064 - 0.129: 634 0.129 - 0.193: 23 0.193 - 0.257: 7 0.257 - 0.322: 2 Chirality restraints: 4725 Sorted by residual: chirality pdb=" C3' DT 2 2 " pdb=" C4' DT 2 2 " pdb=" O3' DT 2 2 " pdb=" C2' DT 2 2 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB ILE D1106 " pdb=" CA ILE D1106 " pdb=" CG1 ILE D1106 " pdb=" CG2 ILE D1106 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS D 321 " pdb=" N LYS D 321 " pdb=" C LYS D 321 " pdb=" CB LYS D 321 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 4722 not shown) Planarity restraints: 5115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 45 " 0.382 9.50e-02 1.11e+02 1.72e-01 1.96e+01 pdb=" NE ARG A 45 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 45 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 45 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 45 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 45 " 0.382 9.50e-02 1.11e+02 1.71e-01 1.95e+01 pdb=" NE ARG B 45 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 45 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 45 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 45 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 55 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.14e+00 pdb=" CD GLU E 55 " 0.049 2.00e-02 2.50e+03 pdb=" OE1 GLU E 55 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU E 55 " -0.018 2.00e-02 2.50e+03 ... (remaining 5112 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 64 2.34 - 2.98: 14570 2.98 - 3.62: 44443 3.62 - 4.26: 66245 4.26 - 4.90: 109371 Nonbonded interactions: 234693 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb=" OD2 ASP D 464 " model vdw 1.705 3.040 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1501 " model vdw 2.020 2.310 nonbonded pdb=" O SER D 884 " pdb="ZN ZN D1502 " model vdw 2.037 2.230 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.050 2.170 nonbonded pdb=" O ARG C 542 " pdb=" NE ARG C 542 " model vdw 2.077 2.520 ... (remaining 234688 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 6 through 233) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 3.600 Check model and map are aligned: 0.450 Set scattering table: 0.300 Process input model: 91.180 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 0.106 30448 Z= 0.243 Angle : 0.720 14.761 41481 Z= 0.413 Chirality : 0.045 0.322 4725 Planarity : 0.005 0.172 5115 Dihedral : 17.756 165.952 11982 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.45 % Allowed : 1.22 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.65 (0.14), residues: 3539 helix: 0.73 (0.14), residues: 1404 sheet: -0.18 (0.27), residues: 353 loop : -1.47 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 33 HIS 0.004 0.001 HIS C 273 PHE 0.016 0.001 PHE B 231 TYR 0.015 0.001 TYR D 679 ARG 0.022 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 254 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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