Starting phenix.real_space_refine on Mon Sep 30 05:18:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igs_35439/09_2024/8igs_35439.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igs_35439/09_2024/8igs_35439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igs_35439/09_2024/8igs_35439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igs_35439/09_2024/8igs_35439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igs_35439/09_2024/8igs_35439.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igs_35439/09_2024/8igs_35439.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 73 5.49 5 Mg 1 5.21 5 S 108 5.16 5 C 15127 2.51 5 N 4343 2.21 5 O 4827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24481 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 9176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1167, 9176 Classifications: {'peptide': 1167} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1114} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 9022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1154, 9022 Classifications: {'peptide': 1154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 46, 'TRANS': 1105} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "L" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2500 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "N" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 759 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "J" 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 11303 SG CYS J 70 46.411 118.512 59.984 1.00172.53 S ATOM 11317 SG CYS J 72 47.558 122.071 60.408 1.00177.56 S ATOM 11425 SG CYS J 85 45.469 121.111 57.432 1.00176.10 S ATOM 11449 SG CYS J 88 48.983 119.555 57.657 1.00168.48 S ATOM 17131 SG CYS J 814 43.246 52.257 48.933 1.00113.72 S ATOM 17696 SG CYS J 888 45.573 55.084 49.953 1.00 91.01 S ATOM 17747 SG CYS J 895 43.205 53.458 52.529 1.00108.65 S ATOM 17768 SG CYS J 898 46.145 51.549 51.272 1.00110.03 S Time building chain proxies: 13.30, per 1000 atoms: 0.54 Number of scatterers: 24481 At special positions: 0 Unit cell: (132.09, 159.46, 141.61, 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 108 16.00 P 73 15.00 Mg 1 11.99 O 4827 8.00 N 4343 7.00 C 15127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.35 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J2002 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 70 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 85 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 72 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 88 " pdb=" ZN J2003 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 895 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 898 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 814 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 888 " Number of angles added : 12 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5418 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 36 sheets defined 46.5% alpha, 13.3% beta 36 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 10.08 Creating SS restraints... Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.517A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 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 228 Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.671A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.511A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 165 through 169 removed outlier: 3.501A pdb=" N GLY I 168 " --> pdb=" O HIS I 165 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS I 169 " --> pdb=" O SER I 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 165 through 169' Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.898A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 347 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.968A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 480 removed outlier: 4.317A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.693A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.783A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.599A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.937A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.671A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 899 through 907 Processing helix chain 'I' and resid 942 through 967 Processing helix chain 'I' and resid 1022 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.235A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.539A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.639A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.571A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.820A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.917A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.583A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.649A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 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 removed outlier: 3.771A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 192 removed outlier: 3.816A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 3.919A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 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 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.863A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 515 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.792A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.633A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.547A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.148A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 788 removed outlier: 3.660A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 805 Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.592A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.557A pdb=" N CYS J 888 " --> pdb=" O VAL J 885 " (cutoff:3.500A) Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.543A pdb=" N TYR J 899 " --> pdb=" O CYS J 895 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1138 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.370A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.888A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 4.016A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1353 Processing helix chain 'J' and resid 1361 through 1374 removed outlier: 4.443A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 13 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 75 Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 114 through 136 Processing helix chain 'L' and resid 137 through 153 Processing helix chain 'L' and resid 366 through 374 Processing helix chain 'L' and resid 375 through 392 removed outlier: 3.628A pdb=" N MET L 379 " --> pdb=" O ALA L 375 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 395 No H-bonds generated for 'chain 'L' and resid 393 through 395' Processing helix chain 'L' and resid 400 through 419 Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.842A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 Processing helix chain 'L' and resid 479 through 487 removed outlier: 3.882A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 500 Processing helix chain 'L' and resid 511 through 515 removed outlier: 3.668A pdb=" N ASP L 514 " --> pdb=" O ILE L 511 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU L 515 " --> pdb=" O GLY L 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 511 through 515' Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.763A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 Processing helix chain 'L' and resid 552 through 563 removed outlier: 3.588A pdb=" N PHE L 563 " --> pdb=" O LEU L 559 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 599 Processing helix chain 'L' and resid 604 through 610 Processing sheet with id=AA1, first strand: chain 'H' and resid 15 through 18 removed outlier: 4.451A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU H 17 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 53 through 61 removed outlier: 6.806A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'H' and resid 109 through 111 removed outlier: 6.802A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.699A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.206A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB1, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB2, first strand: chain 'I' and resid 154 through 157 Processing sheet with id=AB3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.427A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB5, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.473A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.666A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AB8, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB9, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.439A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AC2, first strand: chain 'I' and resid 830 through 831 Processing sheet with id=AC3, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.207A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.717A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AC6, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.412A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.656A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 4.092A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.612A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AD2, first strand: chain 'J' and resid 261 through 262 Processing sheet with id=AD3, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD4, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AD5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.713A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 848 through 849 removed outlier: 7.217A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 1187 through 1189 Processing sheet with id=AD9, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.748A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1055 hydrogen bonds defined for protein. 2991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 11.82 Time building geometry restraints manager: 7.28 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: 8009 1.34 - 1.46: 3883 1.46 - 1.58: 12774 1.58 - 1.70: 142 1.70 - 1.82: 191 Bond restraints: 24999 Sorted by residual: bond pdb=" N VAL I 196 " pdb=" CA VAL I 196 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.21e-02 6.83e+03 9.39e+00 bond pdb=" N ILE H 115 " pdb=" CA ILE H 115 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.19e-02 7.06e+03 9.18e+00 bond pdb=" N ARG J 764 " pdb=" CA ARG J 764 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.07e+00 bond pdb=" N ILE I 198 " pdb=" CA ILE I 198 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.93e+00 bond pdb=" N ILE K 13 " pdb=" CA ILE K 13 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.20e-02 6.94e+03 8.92e+00 ... (remaining 24994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 33142 1.61 - 3.21: 765 3.21 - 4.82: 127 4.82 - 6.42: 12 6.42 - 8.03: 3 Bond angle restraints: 34049 Sorted by residual: angle pdb=" C GLU J1327 " pdb=" CA GLU J1327 " pdb=" CB GLU J1327 " ideal model delta sigma weight residual 109.80 116.52 -6.72 1.23e+00 6.61e-01 2.99e+01 angle pdb=" N GLN I 490 " pdb=" CA GLN I 490 " pdb=" C GLN I 490 " ideal model delta sigma weight residual 114.75 109.25 5.50 1.26e+00 6.30e-01 1.91e+01 angle pdb=" N ARG J 764 " pdb=" CA ARG J 764 " pdb=" C ARG J 764 " ideal model delta sigma weight residual 111.07 106.58 4.49 1.07e+00 8.73e-01 1.76e+01 angle pdb=" CA GLY K 14 " pdb=" C GLY K 14 " pdb=" O GLY K 14 " ideal model delta sigma weight residual 121.88 118.72 3.16 7.80e-01 1.64e+00 1.64e+01 angle pdb=" N PHE K 17 " pdb=" CA PHE K 17 " pdb=" C PHE K 17 " ideal model delta sigma weight residual 113.55 108.50 5.05 1.26e+00 6.30e-01 1.61e+01 ... (remaining 34044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.02: 13662 26.02 - 52.03: 1316 52.03 - 78.05: 228 78.05 - 104.07: 27 104.07 - 130.09: 1 Dihedral angle restraints: 15234 sinusoidal: 6818 harmonic: 8416 Sorted by residual: dihedral pdb=" CA ASN K 15 " pdb=" C ASN K 15 " pdb=" N ARG K 16 " pdb=" CA ARG K 16 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA TYR I 47 " pdb=" C TYR I 47 " pdb=" N GLY I 48 " pdb=" CA GLY I 48 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 15231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3087 0.047 - 0.093: 572 0.093 - 0.140: 191 0.140 - 0.186: 9 0.186 - 0.233: 2 Chirality restraints: 3861 Sorted by residual: chirality pdb=" CA GLU J1327 " pdb=" N GLU J1327 " pdb=" C GLU J1327 " pdb=" CB GLU J1327 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL L 576 " pdb=" CA VAL L 576 " pdb=" CG1 VAL L 576 " pdb=" CG2 VAL L 576 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ASP I 728 " pdb=" N ASP I 728 " pdb=" C ASP I 728 " pdb=" CB ASP I 728 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 3858 not shown) Planarity restraints: 4202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU K 11 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C GLU K 11 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU K 11 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS K 12 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 68 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C TYR H 68 " 0.032 2.00e-02 2.50e+03 pdb=" O TYR H 68 " -0.012 2.00e-02 2.50e+03 pdb=" N SER H 69 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 43 " -0.023 2.00e-02 2.50e+03 1.02e-02 2.88e+00 pdb=" N9 DA N 43 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA N 43 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA N 43 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA N 43 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA N 43 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA N 43 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA N 43 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA N 43 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA N 43 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA N 43 " 0.003 2.00e-02 2.50e+03 ... (remaining 4199 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 219 2.56 - 3.15: 20343 3.15 - 3.73: 38742 3.73 - 4.32: 53555 4.32 - 4.90: 88632 Nonbonded interactions: 201491 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J2001 " model vdw 1.981 2.170 nonbonded pdb=" OG1 THR J 152 " pdb=" OE2 GLU J 175 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASP I 354 " pdb=" OG1 THR I 356 " model vdw 2.204 3.040 nonbonded pdb=" OG SER H 105 " pdb=" O ALA H 138 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP I 915 " pdb=" OG SER I 917 " model vdw 2.223 3.040 ... (remaining 201486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.050 Extract box with map and model: 1.140 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 67.510 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 0.039 24999 Z= 0.217 Angle : 0.592 8.029 34049 Z= 0.353 Chirality : 0.041 0.233 3861 Planarity : 0.003 0.038 4202 Dihedral : 19.319 130.087 9816 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.04 % Allowed : 19.60 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % 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: 0.31 (0.16), residues: 2905 helix: 1.71 (0.15), residues: 1199 sheet: -0.56 (0.29), residues: 314 loop : -0.97 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 807 HIS 0.004 0.001 HIS I 551 PHE 0.015 0.001 PHE J1325 TYR 0.020 0.001 TYR H 68 ARG 0.005 0.000 ARG J 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 2.812 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: H 200 LYS cc_start: 0.9288 (tttt) cc_final: 0.9022 (tttm) REVERT: I 197 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6246 (ttt90) REVERT: I 488 MET cc_start: 0.8662 (mmm) cc_final: 0.8393 (mmm) REVERT: I 516 ASP cc_start: 0.7979 (t0) cc_final: 0.7601 (t0) REVERT: I 902 LEU cc_start: 0.8858 (mm) cc_final: 0.8478 (tt) REVERT: J 644 MET cc_start: 0.9198 (mtm) cc_final: 0.8952 (mtm) REVERT: J 764 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8506 (ttt-90) REVERT: J 821 MET cc_start: 0.8291 (tpp) cc_final: 0.7958 (tpt) REVERT: J 822 MET cc_start: 0.8769 (tpp) cc_final: 0.8388 (mmm) REVERT: K 42 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8556 (mp0) REVERT: L 102 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8363 (mmm) outliers start: 26 outliers final: 4 residues processed: 187 average time/residue: 0.4267 time to fit residues: 120.0388 Evaluate side-chains 143 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain L residue 102 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 0.1980 chunk 231 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 267 optimal weight: 6.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 659 GLN I 811 ASN J 739 GLN J 777 HIS J 861 ASN K 15 ASN L 455 HIS L 518 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 24999 Z= 0.476 Angle : 0.681 7.818 34049 Z= 0.359 Chirality : 0.044 0.218 3861 Planarity : 0.004 0.044 4202 Dihedral : 15.896 120.149 4056 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.09 % Allowed : 19.40 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2905 helix: 1.59 (0.15), residues: 1224 sheet: -0.62 (0.27), residues: 336 loop : -1.06 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 807 HIS 0.006 0.001 HIS J 865 PHE 0.017 0.002 PHE I 405 TYR 0.015 0.002 TYR L 421 ARG 0.006 0.001 ARG I1211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 155 time to evaluate : 2.918 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: H 147 GLN cc_start: 0.8476 (mt0) cc_final: 0.8110 (mt0) REVERT: I 57 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8361 (t80) REVERT: I 488 MET cc_start: 0.8802 (mmm) cc_final: 0.8555 (mmm) REVERT: I 902 LEU cc_start: 0.8979 (mm) cc_final: 0.8702 (tt) REVERT: I 903 ARG cc_start: 0.8845 (ttm-80) cc_final: 0.8331 (mtp180) REVERT: J 100 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: J 821 MET cc_start: 0.8395 (tpp) cc_final: 0.8089 (tpt) REVERT: K 18 ASP cc_start: 0.8904 (m-30) cc_final: 0.8568 (m-30) REVERT: K 42 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8523 (mm-30) REVERT: K 61 ASN cc_start: 0.8021 (t0) cc_final: 0.7694 (t0) REVERT: K 72 GLN cc_start: 0.8275 (mt0) cc_final: 0.7934 (mt0) REVERT: L 489 MET cc_start: 0.8686 (mmm) cc_final: 0.8383 (mtp) outliers start: 77 outliers final: 34 residues processed: 221 average time/residue: 0.3460 time to fit residues: 122.9507 Evaluate side-chains 174 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 73 GLN Chi-restraints excluded: chain L residue 442 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 chunk 289 optimal weight: 20.0000 chunk 239 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 127 GLN I 811 ASN I1061 GLN J 365 GLN J 777 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24999 Z= 0.267 Angle : 0.575 7.642 34049 Z= 0.306 Chirality : 0.041 0.182 3861 Planarity : 0.004 0.043 4202 Dihedral : 15.781 116.990 4043 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.97 % Allowed : 20.40 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % 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: 0.32 (0.16), residues: 2905 helix: 1.70 (0.15), residues: 1223 sheet: -0.70 (0.27), residues: 332 loop : -0.94 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 807 HIS 0.005 0.001 HIS J 865 PHE 0.018 0.001 PHE I 57 TYR 0.020 0.001 TYR J 679 ARG 0.006 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 150 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.9012 (pp) REVERT: H 95 LYS cc_start: 0.9255 (mtpp) cc_final: 0.9001 (mtpp) REVERT: H 147 GLN cc_start: 0.8496 (mt0) cc_final: 0.8160 (mt0) REVERT: H 218 ARG cc_start: 0.6350 (tpt170) cc_final: 0.5260 (mmt180) REVERT: I 369 MET cc_start: 0.8380 (ppp) cc_final: 0.8144 (tmm) REVERT: I 488 MET cc_start: 0.8759 (mmm) cc_final: 0.8499 (mmm) REVERT: I 654 ASP cc_start: 0.8979 (m-30) cc_final: 0.8635 (m-30) REVERT: I 902 LEU cc_start: 0.9013 (mm) cc_final: 0.8802 (tp) REVERT: I 903 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8277 (mtp180) REVERT: J 100 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: J 821 MET cc_start: 0.8429 (tpp) cc_final: 0.8183 (tpt) REVERT: J 909 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9267 (tp) REVERT: K 42 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8425 (mp0) REVERT: K 61 ASN cc_start: 0.8113 (t0) cc_final: 0.7711 (t0) REVERT: K 65 ASP cc_start: 0.8553 (p0) cc_final: 0.8304 (p0) REVERT: L 100 MET cc_start: 0.8254 (mtt) cc_final: 0.7541 (mtm) REVERT: L 425 TYR cc_start: 0.6981 (m-80) cc_final: 0.6297 (m-80) outliers start: 74 outliers final: 42 residues processed: 215 average time/residue: 0.3604 time to fit residues: 125.0434 Evaluate side-chains 182 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 136 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 600 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 20.0000 chunk 201 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 269 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 186 ASN I 510 GLN I 811 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24999 Z= 0.336 Angle : 0.592 8.190 34049 Z= 0.314 Chirality : 0.041 0.165 3861 Planarity : 0.004 0.042 4202 Dihedral : 15.758 115.915 4041 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.25 % Allowed : 20.80 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % 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: 0.34 (0.16), residues: 2905 helix: 1.75 (0.15), residues: 1221 sheet: -0.73 (0.28), residues: 323 loop : -0.95 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 807 HIS 0.005 0.001 HIS J 865 PHE 0.019 0.001 PHE I 405 TYR 0.017 0.001 TYR J 679 ARG 0.004 0.000 ARG I 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 141 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8989 (pp) REVERT: H 95 LYS cc_start: 0.9274 (mtpp) cc_final: 0.9065 (mtpp) REVERT: H 147 GLN cc_start: 0.8544 (mt0) cc_final: 0.8223 (mt0) REVERT: H 218 ARG cc_start: 0.6580 (tpt170) cc_final: 0.5444 (mmt180) REVERT: I 369 MET cc_start: 0.8490 (ppp) cc_final: 0.8223 (tmm) REVERT: I 592 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8604 (ptm160) REVERT: I 654 ASP cc_start: 0.9013 (m-30) cc_final: 0.8675 (m-30) REVERT: I 903 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8656 (mmt-90) REVERT: I 1035 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9023 (ttmm) REVERT: J 100 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8231 (mt-10) REVERT: J 821 MET cc_start: 0.8425 (tpp) cc_final: 0.8172 (tpt) REVERT: J 909 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9287 (tp) REVERT: J 1366 HIS cc_start: 0.9196 (OUTLIER) cc_final: 0.8838 (m-70) REVERT: K 42 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8443 (mp0) REVERT: K 61 ASN cc_start: 0.8282 (t0) cc_final: 0.7818 (t0) REVERT: K 65 ASP cc_start: 0.8739 (p0) cc_final: 0.8021 (p0) REVERT: L 425 TYR cc_start: 0.7076 (m-80) cc_final: 0.6452 (m-80) outliers start: 81 outliers final: 52 residues processed: 214 average time/residue: 0.3601 time to fit residues: 122.2660 Evaluate side-chains 194 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 135 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 1035 LYS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 600 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 212 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 811 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24999 Z= 0.262 Angle : 0.560 8.948 34049 Z= 0.298 Chirality : 0.040 0.158 3861 Planarity : 0.004 0.042 4202 Dihedral : 15.681 114.046 4041 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.13 % Allowed : 21.53 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % 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: 0.42 (0.16), residues: 2905 helix: 1.82 (0.15), residues: 1221 sheet: -0.84 (0.27), residues: 332 loop : -0.87 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 807 HIS 0.004 0.001 HIS J 865 PHE 0.017 0.001 PHE I 405 TYR 0.018 0.001 TYR J 679 ARG 0.005 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 141 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8975 (pp) REVERT: H 66 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7342 (t-90) REVERT: H 68 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7316 (p90) REVERT: H 147 GLN cc_start: 0.8539 (mt0) cc_final: 0.8212 (mt0) REVERT: H 218 ARG cc_start: 0.6498 (tpt170) cc_final: 0.5302 (mmt180) REVERT: I 69 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7106 (mm-40) REVERT: I 369 MET cc_start: 0.8519 (ppp) cc_final: 0.8198 (tmm) REVERT: I 488 MET cc_start: 0.8699 (mmm) cc_final: 0.8258 (mmm) REVERT: I 510 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8049 (tp-100) REVERT: I 654 ASP cc_start: 0.8982 (m-30) cc_final: 0.8644 (m-30) REVERT: I 903 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8640 (mmt-90) REVERT: I 963 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: I 1035 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9100 (ttmm) REVERT: J 100 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: J 154 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8111 (mt) REVERT: J 821 MET cc_start: 0.8420 (tpp) cc_final: 0.8167 (tpt) REVERT: J 1366 HIS cc_start: 0.9187 (OUTLIER) cc_final: 0.8831 (m-70) REVERT: K 42 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8439 (mp0) REVERT: K 61 ASN cc_start: 0.8241 (t0) cc_final: 0.7760 (t0) REVERT: K 65 ASP cc_start: 0.8450 (p0) cc_final: 0.8221 (p0) REVERT: L 100 MET cc_start: 0.8332 (mtt) cc_final: 0.7765 (mtt) REVERT: L 425 TYR cc_start: 0.7024 (m-80) cc_final: 0.6407 (m-80) REVERT: L 507 MET cc_start: 0.9272 (tpp) cc_final: 0.8583 (tpp) outliers start: 78 outliers final: 48 residues processed: 212 average time/residue: 0.3456 time to fit residues: 118.1195 Evaluate side-chains 193 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 135 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 1035 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 600 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 10.0000 chunk 256 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 811 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 777 HIS ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24999 Z= 0.274 Angle : 0.563 9.425 34049 Z= 0.299 Chirality : 0.041 0.232 3861 Planarity : 0.004 0.053 4202 Dihedral : 15.626 112.785 4041 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.73 % Allowed : 21.29 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % 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: 0.46 (0.16), residues: 2905 helix: 1.86 (0.15), residues: 1224 sheet: -0.86 (0.28), residues: 332 loop : -0.85 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 807 HIS 0.004 0.001 HIS J 865 PHE 0.016 0.001 PHE I 405 TYR 0.017 0.001 TYR J 679 ARG 0.009 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 143 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8968 (pp) REVERT: H 66 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7477 (t-90) REVERT: H 68 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7375 (p90) REVERT: H 147 GLN cc_start: 0.8596 (mt0) cc_final: 0.8304 (mt0) REVERT: H 218 ARG cc_start: 0.6441 (tpt170) cc_final: 0.5212 (mmt180) REVERT: I 69 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7097 (mm-40) REVERT: I 369 MET cc_start: 0.8541 (ppp) cc_final: 0.8210 (tmm) REVERT: I 488 MET cc_start: 0.8568 (mmm) cc_final: 0.8327 (mmm) REVERT: I 510 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8068 (tp-100) REVERT: I 592 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8529 (ptm160) REVERT: I 654 ASP cc_start: 0.8978 (m-30) cc_final: 0.8643 (m-30) REVERT: I 740 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8554 (mt-10) REVERT: I 903 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8607 (mmt-90) REVERT: I 963 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: I 1035 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9075 (ttmm) REVERT: I 1168 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: J 100 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8242 (mt-10) REVERT: J 821 MET cc_start: 0.8404 (tpp) cc_final: 0.8154 (tpt) REVERT: J 1366 HIS cc_start: 0.9191 (OUTLIER) cc_final: 0.8822 (m-70) REVERT: K 5 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8476 (t) REVERT: K 42 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8440 (mp0) REVERT: K 61 ASN cc_start: 0.8254 (t0) cc_final: 0.7746 (t0) REVERT: L 100 MET cc_start: 0.8354 (mtt) cc_final: 0.7776 (mtt) REVERT: L 425 TYR cc_start: 0.7081 (m-80) cc_final: 0.6485 (m-80) REVERT: L 507 MET cc_start: 0.9295 (tpp) cc_final: 0.8604 (tpp) REVERT: L 580 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7283 (t80) outliers start: 93 outliers final: 63 residues processed: 226 average time/residue: 0.3495 time to fit residues: 127.4855 Evaluate side-chains 213 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 136 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 1035 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1168 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 658 GLU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 600 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 284 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 132 HIS I 811 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 504 GLN J 777 HIS ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24999 Z= 0.214 Angle : 0.541 10.387 34049 Z= 0.288 Chirality : 0.040 0.196 3861 Planarity : 0.003 0.042 4202 Dihedral : 15.552 111.548 4041 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.33 % Allowed : 21.61 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % 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: 0.54 (0.16), residues: 2905 helix: 1.92 (0.15), residues: 1223 sheet: -0.78 (0.28), residues: 322 loop : -0.81 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 807 HIS 0.004 0.001 HIS J 865 PHE 0.015 0.001 PHE I 57 TYR 0.017 0.001 TYR J 679 ARG 0.006 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 144 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8951 (pp) REVERT: H 66 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7524 (t-90) REVERT: H 147 GLN cc_start: 0.8583 (mt0) cc_final: 0.8286 (mt0) REVERT: H 218 ARG cc_start: 0.6487 (tpt170) cc_final: 0.5248 (mmt180) REVERT: I 69 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7078 (mm-40) REVERT: I 369 MET cc_start: 0.8555 (ppp) cc_final: 0.8250 (tmm) REVERT: I 488 MET cc_start: 0.8534 (mmm) cc_final: 0.8284 (mmm) REVERT: I 510 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8073 (tp-100) REVERT: I 542 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7145 (ptt180) REVERT: I 592 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8596 (ptm160) REVERT: I 654 ASP cc_start: 0.8965 (m-30) cc_final: 0.8651 (m-30) REVERT: I 740 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: I 903 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8613 (mmt-90) REVERT: I 963 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: I 1035 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8999 (ttmm) REVERT: J 100 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: J 504 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: J 821 MET cc_start: 0.8403 (tpp) cc_final: 0.8157 (tpt) REVERT: J 898 CYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9131 (m) REVERT: J 1366 HIS cc_start: 0.9174 (OUTLIER) cc_final: 0.8815 (m-70) REVERT: K 42 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8442 (mp0) REVERT: K 61 ASN cc_start: 0.8183 (t0) cc_final: 0.7904 (t0) REVERT: K 68 GLU cc_start: 0.8564 (pp20) cc_final: 0.8094 (pp20) REVERT: L 100 MET cc_start: 0.8359 (mtt) cc_final: 0.7731 (mtt) REVERT: L 395 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9029 (p) REVERT: L 425 TYR cc_start: 0.7155 (m-80) cc_final: 0.6486 (m-80) REVERT: L 474 MET cc_start: 0.8382 (ttm) cc_final: 0.8136 (ttm) REVERT: L 507 MET cc_start: 0.9294 (tpp) cc_final: 0.8633 (tpp) REVERT: L 580 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7395 (t80) outliers start: 83 outliers final: 50 residues processed: 218 average time/residue: 0.3664 time to fit residues: 128.9064 Evaluate side-chains 203 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 138 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 1035 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 600 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 6.9990 chunk 113 optimal weight: 0.3980 chunk 169 optimal weight: 0.0470 chunk 85 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 overall best weight: 1.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 132 HIS I 811 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 777 HIS ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24999 Z= 0.177 Angle : 0.525 10.847 34049 Z= 0.281 Chirality : 0.039 0.190 3861 Planarity : 0.003 0.041 4202 Dihedral : 15.432 110.024 4041 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.81 % Allowed : 22.25 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % 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: 0.61 (0.16), residues: 2905 helix: 1.98 (0.15), residues: 1222 sheet: -0.71 (0.28), residues: 322 loop : -0.78 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 807 HIS 0.003 0.001 HIS J 865 PHE 0.014 0.001 PHE I 405 TYR 0.017 0.001 TYR J 679 ARG 0.008 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 143 time to evaluate : 3.038 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: H 65 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8929 (pp) REVERT: H 66 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7439 (t-90) REVERT: H 147 GLN cc_start: 0.8572 (mt0) cc_final: 0.8290 (mt0) REVERT: H 218 ARG cc_start: 0.6535 (tpt170) cc_final: 0.5314 (mmt180) REVERT: I 69 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7068 (mm-40) REVERT: I 369 MET cc_start: 0.8499 (ppp) cc_final: 0.8231 (tmm) REVERT: I 488 MET cc_start: 0.8560 (mmm) cc_final: 0.8255 (mmm) REVERT: I 510 GLN cc_start: 0.8653 (tp-100) cc_final: 0.8040 (tp-100) REVERT: I 542 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7149 (ptt180) REVERT: I 592 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8615 (ptm160) REVERT: I 963 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: J 625 MET cc_start: 0.9314 (ttp) cc_final: 0.9059 (ttt) REVERT: J 743 MET cc_start: 0.8640 (ptp) cc_final: 0.8379 (ptp) REVERT: J 821 MET cc_start: 0.8386 (tpp) cc_final: 0.7933 (tpt) REVERT: J 1366 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8764 (m-70) REVERT: K 42 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8434 (mp0) REVERT: K 61 ASN cc_start: 0.8121 (t0) cc_final: 0.7901 (t0) REVERT: K 68 GLU cc_start: 0.8553 (pp20) cc_final: 0.8069 (pp20) REVERT: L 100 MET cc_start: 0.8360 (mtt) cc_final: 0.7734 (mtt) REVERT: L 395 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.9021 (p) REVERT: L 425 TYR cc_start: 0.7173 (m-80) cc_final: 0.6493 (m-80) REVERT: L 474 MET cc_start: 0.8391 (ttm) cc_final: 0.8145 (ttm) REVERT: L 507 MET cc_start: 0.9290 (tpp) cc_final: 0.8638 (tpp) REVERT: L 580 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7293 (t80) outliers start: 70 outliers final: 50 residues processed: 204 average time/residue: 0.3509 time to fit residues: 116.2361 Evaluate side-chains 196 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 137 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 658 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 600 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 10.0000 chunk 248 optimal weight: 0.4980 chunk 264 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 81 optimal weight: 0.0020 chunk 239 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 280 optimal weight: 20.0000 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 132 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I1220 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24999 Z= 0.143 Angle : 0.515 11.870 34049 Z= 0.274 Chirality : 0.039 0.198 3861 Planarity : 0.003 0.039 4202 Dihedral : 15.307 108.416 4041 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.41 % Allowed : 22.65 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % 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: 0.66 (0.16), residues: 2905 helix: 2.03 (0.15), residues: 1227 sheet: -0.63 (0.28), residues: 322 loop : -0.79 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 807 HIS 0.003 0.001 HIS L 600 PHE 0.030 0.001 PHE I1025 TYR 0.018 0.001 TYR J 679 ARG 0.007 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 149 time to evaluate : 3.206 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: H 65 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8893 (pp) REVERT: H 66 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7615 (t-90) REVERT: H 147 GLN cc_start: 0.8560 (mt0) cc_final: 0.8309 (mt0) REVERT: H 218 ARG cc_start: 0.6493 (tpt170) cc_final: 0.5196 (mmt180) REVERT: I 69 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7030 (mm110) REVERT: I 369 MET cc_start: 0.8475 (ppp) cc_final: 0.8214 (tmm) REVERT: I 488 MET cc_start: 0.8639 (mmm) cc_final: 0.8172 (mmm) REVERT: I 510 GLN cc_start: 0.8599 (tp-100) cc_final: 0.7976 (tp-100) REVERT: I 542 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7270 (ptt180) REVERT: I 592 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8627 (ptm160) REVERT: I 903 ARG cc_start: 0.8775 (mmt-90) cc_final: 0.8372 (mmt-90) REVERT: J 625 MET cc_start: 0.9291 (ttp) cc_final: 0.9068 (ttt) REVERT: J 743 MET cc_start: 0.8573 (ptp) cc_final: 0.8312 (ptp) REVERT: J 821 MET cc_start: 0.8367 (tpp) cc_final: 0.7940 (tpt) REVERT: J 1366 HIS cc_start: 0.9128 (OUTLIER) cc_final: 0.8762 (m-70) REVERT: K 61 ASN cc_start: 0.8030 (t0) cc_final: 0.7798 (t0) REVERT: L 100 MET cc_start: 0.8356 (mtt) cc_final: 0.7753 (mtt) REVERT: L 395 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8994 (p) REVERT: L 425 TYR cc_start: 0.7166 (m-80) cc_final: 0.6500 (m-80) REVERT: L 474 MET cc_start: 0.8396 (ttm) cc_final: 0.8157 (ttm) REVERT: L 507 MET cc_start: 0.9276 (tpp) cc_final: 0.8633 (tpp) REVERT: L 567 MET cc_start: 0.7700 (ptt) cc_final: 0.7355 (ppp) REVERT: L 580 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7317 (t80) outliers start: 60 outliers final: 39 residues processed: 202 average time/residue: 0.3694 time to fit residues: 120.9197 Evaluate side-chains 187 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 658 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 600 HIS Chi-restraints excluded: chain L residue 607 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 143 optimal weight: 0.0770 chunk 185 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS I 811 ASN J 294 ASN J 365 GLN J 777 HIS ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24999 Z= 0.206 Angle : 0.540 12.957 34049 Z= 0.284 Chirality : 0.040 0.188 3861 Planarity : 0.003 0.039 4202 Dihedral : 15.299 108.562 4041 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.37 % Allowed : 22.65 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % 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: 0.68 (0.16), residues: 2905 helix: 2.03 (0.15), residues: 1229 sheet: -0.64 (0.28), residues: 324 loop : -0.76 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 807 HIS 0.003 0.001 HIS L 600 PHE 0.013 0.001 PHE I 405 TYR 0.036 0.001 TYR H 177 ARG 0.007 0.000 ARG K 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 141 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8890 (pp) REVERT: H 66 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7560 (t-90) REVERT: H 147 GLN cc_start: 0.8623 (mt0) cc_final: 0.8353 (mt0) REVERT: H 218 ARG cc_start: 0.6531 (tpt170) cc_final: 0.5279 (mmt180) REVERT: I 69 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7024 (mm110) REVERT: I 369 MET cc_start: 0.8535 (ppp) cc_final: 0.8235 (tmm) REVERT: I 488 MET cc_start: 0.8664 (mmm) cc_final: 0.8072 (mmm) REVERT: I 510 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8077 (tp-100) REVERT: I 542 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7273 (ptt180) REVERT: I 592 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8599 (ptm160) REVERT: I 903 ARG cc_start: 0.8753 (mmt-90) cc_final: 0.8361 (mmt-90) REVERT: J 625 MET cc_start: 0.9318 (ttp) cc_final: 0.9079 (ttt) REVERT: J 821 MET cc_start: 0.8354 (tpp) cc_final: 0.7896 (tpt) REVERT: J 1366 HIS cc_start: 0.9156 (OUTLIER) cc_final: 0.8784 (m-70) REVERT: K 68 GLU cc_start: 0.8575 (pp20) cc_final: 0.8160 (pp20) REVERT: L 100 MET cc_start: 0.8353 (mtt) cc_final: 0.7728 (mtt) REVERT: L 395 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9030 (p) REVERT: L 425 TYR cc_start: 0.7183 (m-80) cc_final: 0.6514 (m-80) REVERT: L 474 MET cc_start: 0.8455 (ttm) cc_final: 0.8209 (ttm) REVERT: L 507 MET cc_start: 0.9280 (tpp) cc_final: 0.8646 (tpp) REVERT: L 580 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7371 (t80) outliers start: 59 outliers final: 46 residues processed: 193 average time/residue: 0.3545 time to fit residues: 111.5939 Evaluate side-chains 192 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 138 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 600 HIS Chi-restraints excluded: chain L residue 607 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 240 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 132 HIS I 811 ASN ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.079908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.056376 restraints weight = 68083.451| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.64 r_work: 0.2806 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24999 Z= 0.205 Angle : 0.545 12.655 34049 Z= 0.286 Chirality : 0.040 0.185 3861 Planarity : 0.003 0.038 4202 Dihedral : 15.301 108.195 4041 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.33 % Allowed : 22.73 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % 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: 0.68 (0.16), residues: 2905 helix: 2.04 (0.15), residues: 1228 sheet: -0.64 (0.28), residues: 324 loop : -0.77 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 807 HIS 0.009 0.001 HIS J 364 PHE 0.013 0.001 PHE I 405 TYR 0.036 0.001 TYR H 177 ARG 0.007 0.000 ARG K 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4398.51 seconds wall clock time: 79 minutes 49.72 seconds (4789.72 seconds total)