Starting phenix.real_space_refine on Wed Mar 20 07:28:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1s_29676/03_2024/8g1s_29676.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1s_29676/03_2024/8g1s_29676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1s_29676/03_2024/8g1s_29676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1s_29676/03_2024/8g1s_29676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1s_29676/03_2024/8g1s_29676.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1s_29676/03_2024/8g1s_29676.pdb" } resolution = 3.7 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= 0.002 sd= 0.057 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 92 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16476 2.51 5 N 4747 2.21 5 O 5366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 719": "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: 26788 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Inner-chain residues flagged as termini: ['pdbres=" DG A 26 "'] Classifications: {'DNA': 18} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 17} Chain: "B" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 609 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "G" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1708 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1693 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 997 Classifications: {'RNA': 47} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 16} Link IDs: {'rna2p': 13, 'rna3p': 33} Chain: "J" 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: 13.45, per 1000 atoms: 0.50 Number of scatterers: 26788 At special positions: 0 Unit cell: (137, 154, 162, 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 106 16.00 P 92 15.00 Mg 1 11.99 O 5366 8.00 N 4747 7.00 C 16476 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: 11.51 Conformation dependent library (CDL) restraints added in 4.4 seconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 43 sheets defined 36.7% alpha, 12.1% beta 26 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 8.26 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.601A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'H' and resid 35 through 50 removed outlier: 3.713A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 removed outlier: 3.894A pdb=" N LEU H 85 " --> pdb=" O ILE H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 228 through 232 Processing helix chain 'I' and resid 4 through 10 Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.972A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.618A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 246 removed outlier: 3.518A pdb=" N ARG I 245 " --> pdb=" O VAL I 242 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 242 through 246' Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 294 removed outlier: 4.026A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 345 through 354 removed outlier: 4.022A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR I 350 " --> pdb=" O TYR I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 479 Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 519 through 526 Processing helix chain 'I' and resid 544 through 549 Processing helix chain 'I' and resid 607 through 614 removed outlier: 4.036A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 675 through 685 Processing helix chain 'I' and resid 704 through 712 removed outlier: 3.773A pdb=" N SER I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) Processing helix chain 'I' and resid 819 through 825 removed outlier: 3.987A pdb=" N VAL I 823 " --> pdb=" O SER I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 858 through 865 removed outlier: 4.288A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU I 865 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 removed outlier: 3.652A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU I 967 " --> pdb=" O GLU I 963 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL I 978 " --> pdb=" O ARG I 974 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 990 removed outlier: 4.349A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1038 Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.532A pdb=" N MET I1131 " --> pdb=" O LYS I1127 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.527A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.532A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1280 removed outlier: 3.600A pdb=" N VAL I1275 " --> pdb=" O GLY I1271 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1309 Processing helix chain 'I' and resid 1320 through 1332 Processing helix chain 'J' and resid 28 through 33 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.546A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.641A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 229 Processing helix chain 'J' and resid 233 through 238 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 265 through 286 Processing helix chain 'J' and resid 288 through 309 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 403 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.524A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE J 411 " --> pdb=" O VAL J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 434 removed outlier: 3.545A pdb=" N ILE J 434 " --> pdb=" O ARG J 431 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 458 removed outlier: 3.561A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.550A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.616A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.505A pdb=" N GLY J 613 " --> pdb=" O TYR J 609 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.788A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 647 through 670 removed outlier: 3.964A pdb=" N HIS J 651 " --> pdb=" O PRO J 647 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.744A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.528A pdb=" N VAL J 839 " --> pdb=" O LEU J 835 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.769A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 4.077A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1314 through 1316 No H-bonds generated for 'chain 'J' and resid 1314 through 1316' Processing helix chain 'J' and resid 1319 through 1326 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 78 removed outlier: 3.566A pdb=" N ALA K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 15 Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.519A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 removed outlier: 3.668A pdb=" N ARG G 91 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 109 Processing sheet with id=AA5, first strand: chain 'G' and resid 180 through 182 removed outlier: 6.571A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 16 removed outlier: 4.189A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 31 through 32 removed outlier: 3.816A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 99 through 105 removed outlier: 3.583A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.937A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.649A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 66 through 69 Processing sheet with id=AB4, first strand: chain 'I' and resid 66 through 69 removed outlier: 6.258A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU I 100 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN I 120 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.672A pdb=" N ILE I 177 " --> pdb=" O GLY I 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 250 through 251 removed outlier: 4.379A pdb=" N ARG I 267 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.786A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.961A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 599 through 606 removed outlier: 5.235A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 718 removed outlier: 6.552A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP I 781 " --> pdb=" O ALA I 718 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 748 through 752 removed outlier: 5.763A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'I' and resid 1096 through 1098 removed outlier: 3.556A pdb=" N MET I 800 " --> pdb=" O MET I1230 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET I1230 " --> pdb=" O MET I 800 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 838 removed outlier: 6.441A pdb=" N LYS I1051 " --> pdb=" O VAL I 931 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL I 931 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR I1053 " --> pdb=" O ILE I 929 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR I 927 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.788A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1065 through 1066 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.692A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.302A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AD7, first strand: chain 'J' and resid 356 through 357 removed outlier: 6.107A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'J' and resid 547 through 556 removed outlier: 3.653A pdb=" N GLU J 556 " --> pdb=" O VAL J 564 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE1, first strand: chain 'J' and resid 842 through 843 removed outlier: 3.882A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.603A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 991 through 997 removed outlier: 4.795A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS J 959 " --> pdb=" O LYS J 983 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE J 985 " --> pdb=" O SER J 957 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU J1009 " --> pdb=" O ILE J 958 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1034 through 1036 Processing sheet with id=AE5, first strand: chain 'J' and resid 1046 through 1047 removed outlier: 3.635A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1161 through 1162 Processing sheet with id=AE7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.297A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 963 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 11.46 Time building geometry restraints manager: 12.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4499 1.31 - 1.44: 6988 1.44 - 1.56: 15532 1.56 - 1.69: 183 1.69 - 1.81: 184 Bond restraints: 27386 Sorted by residual: bond pdb=" CA ARG J 425 " pdb=" C ARG J 425 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.25e-02 6.40e+03 2.16e+01 bond pdb=" C ARG J 425 " pdb=" O ARG J 425 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.17e-02 7.31e+03 1.36e+01 bond pdb=" CA ARG J 425 " pdb=" CB ARG J 425 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.58e-02 4.01e+03 1.22e+01 bond pdb=" CD ARG J 425 " pdb=" NE ARG J 425 " ideal model delta sigma weight residual 1.458 1.428 0.030 1.40e-02 5.10e+03 4.67e+00 bond pdb=" C GLY J1360 " pdb=" O GLY J1360 " ideal model delta sigma weight residual 1.236 1.247 -0.011 5.30e-03 3.56e+04 4.44e+00 ... (remaining 27381 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.29: 862 105.29 - 112.47: 14341 112.47 - 119.65: 8909 119.65 - 126.83: 12844 126.83 - 134.01: 460 Bond angle restraints: 37416 Sorted by residual: angle pdb=" N VAL I1254 " pdb=" CA VAL I1254 " pdb=" C VAL I1254 " ideal model delta sigma weight residual 112.29 108.01 4.28 9.40e-01 1.13e+00 2.07e+01 angle pdb=" NE ARG J 425 " pdb=" CZ ARG J 425 " pdb=" NH1 ARG J 425 " ideal model delta sigma weight residual 121.50 118.04 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" C GLY I 45 " pdb=" N GLN I 46 " pdb=" CA GLN I 46 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C GLN I1257 " pdb=" N PRO I1258 " pdb=" CA PRO I1258 " ideal model delta sigma weight residual 119.84 123.42 -3.58 1.25e+00 6.40e-01 8.21e+00 angle pdb=" CA ARG J 425 " pdb=" CB ARG J 425 " pdb=" CG ARG J 425 " ideal model delta sigma weight residual 114.10 108.39 5.71 2.00e+00 2.50e-01 8.14e+00 ... (remaining 37411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.49: 16085 33.49 - 66.98: 595 66.98 - 100.47: 46 100.47 - 133.96: 0 133.96 - 167.45: 5 Dihedral angle restraints: 16731 sinusoidal: 7628 harmonic: 9103 Sorted by residual: dihedral pdb=" O4' C R 17 " pdb=" C1' C R 17 " pdb=" N1 C R 17 " pdb=" C2 C R 17 " ideal model delta sinusoidal sigma weight residual 200.00 55.70 144.30 1 1.50e+01 4.44e-03 7.73e+01 dihedral pdb=" O4' U R 15 " pdb=" C1' U R 15 " pdb=" N1 U R 15 " pdb=" C2 U R 15 " ideal model delta sinusoidal sigma weight residual 200.00 57.62 142.38 1 1.50e+01 4.44e-03 7.65e+01 dihedral pdb=" CA GLU J1343 " pdb=" C GLU J1343 " pdb=" N LEU J1344 " pdb=" CA LEU J1344 " ideal model delta harmonic sigma weight residual -180.00 -154.85 -25.15 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 16728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2970 0.035 - 0.070: 924 0.070 - 0.105: 327 0.105 - 0.140: 83 0.140 - 0.175: 5 Chirality restraints: 4309 Sorted by residual: chirality pdb=" CA ARG J 425 " pdb=" N ARG J 425 " pdb=" C ARG J 425 " pdb=" CB ARG J 425 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" C1' G R 46 " pdb=" O4' G R 46 " pdb=" C2' G R 46 " pdb=" N9 G R 46 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" C1' C R 17 " pdb=" O4' C R 17 " pdb=" C2' C R 17 " pdb=" N1 C R 17 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 4306 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN J 424 " -0.013 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ASN J 424 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN J 424 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG J 425 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G R 46 " -0.031 2.00e-02 2.50e+03 1.32e-02 5.26e+00 pdb=" N9 G R 46 " 0.031 2.00e-02 2.50e+03 pdb=" C8 G R 46 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G R 46 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G R 46 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G R 46 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G R 46 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G R 46 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G R 46 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G R 46 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G R 46 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G R 46 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 358 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO J 359 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 359 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 359 " -0.025 5.00e-02 4.00e+02 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 308 2.58 - 3.16: 23528 3.16 - 3.74: 44403 3.74 - 4.32: 59592 4.32 - 4.90: 95788 Nonbonded interactions: 223619 Sorted by model distance: nonbonded pdb=" NZ LYS I1306 " pdb=" O2' C R 17 " model vdw 2.004 2.520 nonbonded pdb=" N1 DG A 26 " pdb=" OE2 GLU I 541 " model vdw 2.049 2.520 nonbonded pdb=" OP1 DT B 19 " pdb=" CG LYS I1262 " model vdw 2.055 3.440 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1401 " model vdw 2.087 2.170 nonbonded pdb=" OH TYR I 123 " pdb=" OE2 GLU I 126 " model vdw 2.182 2.440 ... (remaining 223614 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 'G' and (resid 8 through 158 or resid 170 through 234)) selection = (chain 'H' and resid 8 through 234) } 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: 1.750 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: 6.750 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 75.410 Find NCS groups from input model: 1.020 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.003 0.058 27386 Z= 0.180 Angle : 0.579 8.927 37416 Z= 0.330 Chirality : 0.040 0.175 4309 Planarity : 0.004 0.046 4556 Dihedral : 16.068 167.451 10875 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.31 % Favored : 91.59 % Rotamer: Outliers : 1.07 % Allowed : 7.11 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 3152 helix: -0.07 (0.16), residues: 1087 sheet: -2.43 (0.27), residues: 365 loop : -1.82 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 580 HIS 0.003 0.001 HIS G 23 PHE 0.012 0.001 PHE J 260 TYR 0.013 0.001 TYR I1281 ARG 0.005 0.001 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 551 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 41 ASN cc_start: 0.8576 (t0) cc_final: 0.8335 (t0) REVERT: G 75 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8343 (tm-30) REVERT: G 194 GLN cc_start: 0.7245 (pp30) cc_final: 0.6959 (pp30) REVERT: H 100 LEU cc_start: 0.9175 (mp) cc_final: 0.8967 (mt) REVERT: H 185 TYR cc_start: 0.8681 (p90) cc_final: 0.8331 (p90) REVERT: I 84 GLU cc_start: 0.7882 (tp30) cc_final: 0.7393 (mm-30) REVERT: I 523 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6526 (mm-30) REVERT: I 568 ASN cc_start: 0.8396 (p0) cc_final: 0.8094 (p0) REVERT: I 654 ASP cc_start: 0.7373 (m-30) cc_final: 0.6939 (m-30) REVERT: I 739 ASP cc_start: 0.8279 (p0) cc_final: 0.7993 (p0) REVERT: I 820 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7732 (tm-30) REVERT: I 1018 TYR cc_start: 0.6946 (t80) cc_final: 0.6276 (m-80) REVERT: I 1023 HIS cc_start: 0.8008 (t-90) cc_final: 0.7770 (t-90) REVERT: I 1085 MET cc_start: 0.8727 (mmt) cc_final: 0.8494 (mmt) REVERT: I 1098 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8864 (mm) REVERT: I 1180 MET cc_start: 0.8903 (tpp) cc_final: 0.8386 (tpp) REVERT: I 1305 TYR cc_start: 0.8776 (t80) cc_final: 0.8548 (t80) REVERT: J 267 ASP cc_start: 0.8376 (p0) cc_final: 0.7891 (t70) REVERT: J 298 MET cc_start: 0.8439 (ptt) cc_final: 0.8189 (ptp) REVERT: J 698 MET cc_start: 0.9097 (mmm) cc_final: 0.8714 (tpp) REVERT: J 833 GLU cc_start: 0.6652 (mt-10) cc_final: 0.6451 (mt-10) REVERT: J 1121 LEU cc_start: 0.8639 (tp) cc_final: 0.8358 (mp) REVERT: K 8 ASP cc_start: 0.8414 (p0) cc_final: 0.7936 (p0) REVERT: K 47 THR cc_start: 0.9204 (m) cc_final: 0.8953 (m) outliers start: 29 outliers final: 6 residues processed: 574 average time/residue: 0.4190 time to fit residues: 364.5715 Evaluate side-chains 322 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 315 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 292 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 227 GLN I 519 ASN I 604 HIS I 618 GLN I1220 GLN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN ** J 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27386 Z= 0.209 Angle : 0.601 10.398 37416 Z= 0.312 Chirality : 0.042 0.185 4309 Planarity : 0.004 0.050 4556 Dihedral : 15.843 171.517 4682 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.88 % Favored : 93.08 % Rotamer: Outliers : 2.74 % Allowed : 14.37 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.15), residues: 3152 helix: 0.04 (0.16), residues: 1106 sheet: -2.42 (0.26), residues: 359 loop : -1.76 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 580 HIS 0.008 0.001 HIS I 343 PHE 0.014 0.001 PHE I 253 TYR 0.025 0.001 TYR G 185 ARG 0.007 0.000 ARG I1106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 374 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 75 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8395 (tm-30) REVERT: G 142 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7429 (mtm) REVERT: H 100 LEU cc_start: 0.8903 (mp) cc_final: 0.8682 (mt) REVERT: H 185 TYR cc_start: 0.8720 (p90) cc_final: 0.8385 (p90) REVERT: I 84 GLU cc_start: 0.7810 (tp30) cc_final: 0.7296 (mm-30) REVERT: I 568 ASN cc_start: 0.8620 (p0) cc_final: 0.8194 (p0) REVERT: I 820 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7794 (tm-30) REVERT: I 1018 TYR cc_start: 0.7156 (t80) cc_final: 0.6358 (m-80) REVERT: I 1098 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8709 (mm) REVERT: I 1141 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9031 (tt) REVERT: I 1180 MET cc_start: 0.8934 (tpp) cc_final: 0.8268 (tpp) REVERT: I 1290 MET cc_start: 0.8484 (mmt) cc_final: 0.8271 (mmt) REVERT: I 1304 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7970 (ttm) REVERT: J 157 GLN cc_start: 0.7636 (mt0) cc_final: 0.7294 (pp30) REVERT: J 267 ASP cc_start: 0.8372 (p0) cc_final: 0.8169 (p0) REVERT: J 298 MET cc_start: 0.8465 (ptt) cc_final: 0.8177 (ptp) REVERT: J 329 ASP cc_start: 0.8237 (m-30) cc_final: 0.7954 (m-30) REVERT: J 1003 LEU cc_start: 0.8310 (tp) cc_final: 0.8081 (tt) REVERT: J 1121 LEU cc_start: 0.8669 (tp) cc_final: 0.8383 (mp) REVERT: K 63 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8900 (mm) REVERT: K 75 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7820 (tm-30) outliers start: 74 outliers final: 34 residues processed: 427 average time/residue: 0.3600 time to fit residues: 250.3587 Evaluate side-chains 344 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 305 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 63 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** 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 306, in __init__ self.caller(self.refine_xyz) 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 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4861 > 50: distance: 76 - 92: 5.337 distance: 80 - 101: 22.499 distance: 84 - 109: 9.967 distance: 89 - 117: 5.177 distance: 93 - 94: 6.349 distance: 93 - 96: 4.798 distance: 94 - 95: 11.494 distance: 94 - 101: 21.455 distance: 95 - 125: 9.608 distance: 96 - 97: 8.602 distance: 97 - 98: 5.605 distance: 98 - 99: 8.097 distance: 99 - 100: 3.005 distance: 101 - 102: 33.890 distance: 102 - 103: 8.298 distance: 102 - 105: 19.781 distance: 103 - 104: 7.197 distance: 103 - 109: 10.451 distance: 104 - 133: 20.035 distance: 105 - 106: 6.187 distance: 106 - 107: 14.002 distance: 106 - 108: 4.085 distance: 109 - 110: 7.585 distance: 110 - 113: 6.706 distance: 111 - 112: 3.260 distance: 112 - 144: 5.131 distance: 113 - 114: 4.929 distance: 113 - 115: 7.020 distance: 118 - 121: 4.410 distance: 122 - 124: 3.089 distance: 125 - 126: 3.801 distance: 126 - 127: 6.089 distance: 126 - 129: 3.439 distance: 127 - 128: 4.404 distance: 129 - 130: 4.322 distance: 129 - 131: 5.657 distance: 130 - 132: 7.263 distance: 133 - 134: 3.299 distance: 134 - 137: 5.758 distance: 139 - 140: 3.388 distance: 141 - 143: 4.394 distance: 146 - 152: 3.919 distance: 148 - 149: 3.241 distance: 149 - 150: 4.941 distance: 149 - 151: 5.902 distance: 152 - 153: 4.380 distance: 153 - 154: 3.237 distance: 156 - 157: 3.602 distance: 157 - 158: 5.484 distance: 157 - 160: 3.264 distance: 158 - 159: 4.828 distance: 158 - 165: 7.496 distance: 160 - 161: 4.484 distance: 161 - 162: 4.128 distance: 162 - 163: 5.416 distance: 165 - 166: 5.111 distance: 166 - 167: 5.419 distance: 167 - 168: 20.624