Starting phenix.real_space_refine on Thu Mar 5 18:27:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8igs_35439/03_2026/8igs_35439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8igs_35439/03_2026/8igs_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/cci-nas-00/data/ceres_data/8igs_35439/03_2026/8igs_35439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8igs_35439/03_2026/8igs_35439.map" model { file = "/net/cci-nas-00/data/ceres_data/8igs_35439/03_2026/8igs_35439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8igs_35439/03_2026/8igs_35439.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.25, per 1000 atoms: 0.21 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: 2.20 Conformation dependent library (CDL) restraints added in 968.5 milliseconds 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: 2.88 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: 5.45 Time building geometry restraints manager: 2.90 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.770 ------------------------------------------------------------------------------- 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 25007 Z= 0.185 Angle : 0.595 8.441 34061 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 : 5.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG J 314 TYR 0.020 0.001 TYR H 68 PHE 0.015 0.001 PHE J1325 TRP 0.010 0.001 TRP I 807 HIS 0.004 0.001 HIS I 551 Details of bonding type rmsd covalent geometry : bond 0.00334 (24999) covalent geometry : angle 0.59164 (34049) hydrogen bonds : bond 0.14876 ( 1135) hydrogen bonds : angle 6.14809 ( 3159) metal coordination : bond 0.00617 ( 8) metal coordination : angle 3.50252 ( 12) *********************** 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 to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.843 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: 0.1871 time to fit residues: 52.9030 Evaluate side-chains 143 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 3.8104 ------------------------------------------------------------------------------- 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 I1061 GLN J 365 GLN J 739 GLN J 777 HIS J 861 ASN K 15 ASN L 455 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.079230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.055174 restraints weight = 68045.765| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.60 r_work: 0.2779 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25007 Z= 0.217 Angle : 0.616 8.203 34061 Z= 0.325 Chirality : 0.042 0.186 3861 Planarity : 0.004 0.042 4202 Dihedral : 15.810 119.441 4056 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.77 % Allowed : 19.36 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2905 helix: 1.69 (0.15), residues: 1226 sheet: -0.57 (0.27), residues: 336 loop : -0.99 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 67 TYR 0.017 0.001 TYR L 421 PHE 0.022 0.002 PHE I 57 TRP 0.008 0.001 TRP J 115 HIS 0.005 0.001 HIS J 865 Details of bonding type rmsd covalent geometry : bond 0.00501 (24999) covalent geometry : angle 0.61325 (34049) hydrogen bonds : bond 0.04352 ( 1135) hydrogen bonds : angle 4.75225 ( 3159) metal coordination : bond 0.01319 ( 8) metal coordination : angle 3.02977 ( 12) *********************** 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 225 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 156 time to evaluate : 0.822 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: 0.8478 (mt0) cc_final: 0.8128 (mt0) REVERT: I 654 ASP cc_start: 0.8765 (m-30) cc_final: 0.8485 (m-30) REVERT: I 902 LEU cc_start: 0.8927 (mm) cc_final: 0.8663 (tt) REVERT: I 903 ARG cc_start: 0.8977 (ttm-80) cc_final: 0.8364 (mtp180) REVERT: J 100 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: J 821 MET cc_start: 0.8375 (tpp) cc_final: 0.8101 (tpt) REVERT: J 822 MET cc_start: 0.8495 (tpp) cc_final: 0.8076 (mmm) REVERT: K 42 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8628 (mm-30) REVERT: K 61 ASN cc_start: 0.8062 (t0) cc_final: 0.7693 (t0) REVERT: K 72 GLN cc_start: 0.8294 (mt0) cc_final: 0.8027 (mt0) REVERT: L 395 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8939 (p) REVERT: L 489 MET cc_start: 0.8744 (mmm) cc_final: 0.8484 (mtp) REVERT: L 551 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6729 (mm) outliers start: 69 outliers final: 24 residues processed: 215 average time/residue: 0.1590 time to fit residues: 55.7384 Evaluate side-chains 167 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 121 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 187 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 799 ASN 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 227 PHE Chi-restraints excluded: chain J residue 392 THR 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 K residue 8 ASP Chi-restraints excluded: chain K residue 73 GLN Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 551 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 4.9990 chunk 202 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 151 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 127 GLN I 811 ASN J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.079482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.055499 restraints weight = 67724.523| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.63 r_work: 0.2796 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25007 Z= 0.175 Angle : 0.564 6.973 34061 Z= 0.300 Chirality : 0.041 0.181 3861 Planarity : 0.004 0.043 4202 Dihedral : 15.699 117.428 4041 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.97 % Allowed : 20.16 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2905 helix: 1.76 (0.15), residues: 1223 sheet: -0.61 (0.28), residues: 322 loop : -0.91 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 373 TYR 0.020 0.001 TYR J 679 PHE 0.014 0.001 PHE I 57 TRP 0.011 0.001 TRP I 807 HIS 0.004 0.001 HIS J 865 Details of bonding type rmsd covalent geometry : bond 0.00401 (24999) covalent geometry : angle 0.56221 (34049) hydrogen bonds : bond 0.03789 ( 1135) hydrogen bonds : angle 4.56278 ( 3159) metal coordination : bond 0.00996 ( 8) metal coordination : angle 2.58761 ( 12) *********************** 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 223 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 149 time to evaluate : 0.790 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: 0.9201 (OUTLIER) cc_final: 0.8980 (pp) REVERT: H 147 GLN cc_start: 0.8513 (mt0) cc_final: 0.8144 (mt0) REVERT: H 218 ARG cc_start: 0.6482 (tpt170) cc_final: 0.5343 (mmt180) REVERT: I 369 MET cc_start: 0.8166 (ppp) cc_final: 0.7855 (tmm) REVERT: I 481 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7097 (pp) REVERT: I 510 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8177 (tp-100) REVERT: I 654 ASP cc_start: 0.8756 (m-30) cc_final: 0.8480 (m-30) REVERT: I 903 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8175 (mmm-85) REVERT: J 100 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: J 545 HIS cc_start: 0.9163 (OUTLIER) cc_final: 0.8957 (p-80) REVERT: J 821 MET cc_start: 0.8412 (tpp) cc_final: 0.8164 (tpt) REVERT: J 909 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9282 (tp) REVERT: K 42 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8568 (mp0) REVERT: K 61 ASN cc_start: 0.8146 (t0) cc_final: 0.7866 (t0) REVERT: L 395 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8983 (p) REVERT: L 425 TYR cc_start: 0.7040 (m-80) cc_final: 0.6360 (m-80) REVERT: L 474 MET cc_start: 0.8418 (ttm) cc_final: 0.8076 (ttm) REVERT: L 551 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6484 (mm) outliers start: 74 outliers final: 44 residues processed: 213 average time/residue: 0.1519 time to fit residues: 52.4891 Evaluate side-chains 190 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 121 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE 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 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 903 ARG 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 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 545 HIS 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 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 L residue 112 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 551 LEU 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 24 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 234 optimal weight: 0.0070 overall best weight: 4.0006 ------------------------------------------------------------------------------- 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 777 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.078406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.054441 restraints weight = 68112.043| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.59 r_work: 0.2776 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25007 Z= 0.221 Angle : 0.590 7.606 34061 Z= 0.312 Chirality : 0.041 0.177 3861 Planarity : 0.004 0.041 4202 Dihedral : 15.715 116.032 4041 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.41 % Allowed : 20.60 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2905 helix: 1.75 (0.15), residues: 1221 sheet: -0.61 (0.28), residues: 317 loop : -0.89 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.017 0.001 TYR J 679 PHE 0.018 0.001 PHE I 405 TRP 0.010 0.001 TRP I 807 HIS 0.005 0.001 HIS J 865 Details of bonding type rmsd covalent geometry : bond 0.00512 (24999) covalent geometry : angle 0.58826 (34049) hydrogen bonds : bond 0.03923 ( 1135) hydrogen bonds : angle 4.51342 ( 3159) metal coordination : bond 0.01191 ( 8) metal coordination : angle 2.39602 ( 12) *********************** 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 226 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 141 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8927 (pp) REVERT: H 95 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8907 (mtpp) REVERT: H 147 GLN cc_start: 0.8568 (mt0) cc_final: 0.8268 (mt0) REVERT: H 218 ARG cc_start: 0.6457 (tpt170) cc_final: 0.5285 (mmt180) REVERT: I 69 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7150 (mm110) REVERT: I 369 MET cc_start: 0.8360 (ppp) cc_final: 0.8070 (tmm) REVERT: I 510 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8289 (tp-100) REVERT: I 592 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8673 (ptm160) REVERT: I 654 ASP cc_start: 0.8774 (m-30) cc_final: 0.8510 (m-30) REVERT: I 903 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8750 (mmt-90) REVERT: I 963 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: J 100 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: J 821 MET cc_start: 0.8412 (tpp) cc_final: 0.8118 (tpt) REVERT: J 909 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9306 (tp) REVERT: J 1366 HIS cc_start: 0.9006 (OUTLIER) cc_final: 0.8665 (m-70) REVERT: K 42 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8571 (mp0) REVERT: K 61 ASN cc_start: 0.8243 (t0) cc_final: 0.7862 (t0) REVERT: K 65 ASP cc_start: 0.8690 (p0) cc_final: 0.8085 (p0) REVERT: L 425 TYR cc_start: 0.7188 (m-80) cc_final: 0.6574 (m-80) REVERT: L 474 MET cc_start: 0.8382 (ttm) cc_final: 0.8029 (ttm) REVERT: L 507 MET cc_start: 0.9188 (tpp) cc_final: 0.8519 (tpp) outliers start: 85 outliers final: 54 residues processed: 217 average time/residue: 0.1521 time to fit residues: 52.5874 Evaluate side-chains 196 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 134 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 103 ASN 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 90 VAL 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 561 ILE 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 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 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 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 392 THR 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 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 13 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 80 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 81 optimal weight: 0.0670 chunk 5 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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 777 HIS K 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.078250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.054424 restraints weight = 67764.636| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.60 r_work: 0.2762 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25007 Z= 0.212 Angle : 0.583 8.696 34061 Z= 0.308 Chirality : 0.041 0.175 3861 Planarity : 0.004 0.042 4202 Dihedral : 15.693 114.558 4041 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.57 % Allowed : 21.29 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.16), residues: 2905 helix: 1.80 (0.15), residues: 1220 sheet: -0.71 (0.28), residues: 319 loop : -0.90 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 67 TYR 0.017 0.001 TYR J 679 PHE 0.018 0.001 PHE I 405 TRP 0.008 0.001 TRP I 807 HIS 0.005 0.001 HIS J 865 Details of bonding type rmsd covalent geometry : bond 0.00489 (24999) covalent geometry : angle 0.58073 (34049) hydrogen bonds : bond 0.03801 ( 1135) hydrogen bonds : angle 4.45779 ( 3159) metal coordination : bond 0.01065 ( 8) metal coordination : angle 2.51638 ( 12) *********************** 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 227 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 138 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8913 (pp) REVERT: H 66 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7373 (t-90) REVERT: H 95 LYS cc_start: 0.9189 (mtpp) cc_final: 0.8965 (mtpp) REVERT: H 147 GLN cc_start: 0.8577 (mt0) cc_final: 0.8276 (mt0) REVERT: H 218 ARG cc_start: 0.6508 (tpt170) cc_final: 0.5280 (mmt180) REVERT: I 369 MET cc_start: 0.8402 (ppp) cc_final: 0.8128 (tmm) REVERT: I 488 MET cc_start: 0.8670 (mmm) cc_final: 0.8393 (mmm) REVERT: I 492 MET cc_start: 0.8481 (mmm) cc_final: 0.8085 (mmt) REVERT: I 510 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8308 (tp-100) REVERT: I 654 ASP cc_start: 0.8768 (m-30) cc_final: 0.8510 (m-30) REVERT: I 903 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8815 (mmt-90) REVERT: I 963 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: I 1035 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9026 (ttmm) REVERT: J 100 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: J 821 MET cc_start: 0.8405 (tpp) cc_final: 0.8162 (tpt) REVERT: J 909 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9294 (tp) REVERT: J 1366 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8657 (m-70) REVERT: K 42 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8545 (mp0) REVERT: K 61 ASN cc_start: 0.8289 (t0) cc_final: 0.7867 (t0) REVERT: K 65 ASP cc_start: 0.8425 (p0) cc_final: 0.8209 (p0) REVERT: L 425 TYR cc_start: 0.7154 (m-80) cc_final: 0.6543 (m-80) REVERT: L 474 MET cc_start: 0.8418 (ttm) cc_final: 0.8056 (ttm) REVERT: L 507 MET cc_start: 0.9173 (tpp) cc_final: 0.8529 (tpp) outliers start: 89 outliers final: 55 residues processed: 216 average time/residue: 0.1496 time to fit residues: 52.8030 Evaluate side-chains 199 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 136 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 121 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 90 VAL 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 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 90 VAL 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 352 ARG Chi-restraints excluded: chain J residue 392 THR 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 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 K residue 13 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 216 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 127 GLN I 811 ASN I1220 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.079941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.056219 restraints weight = 67798.307| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.60 r_work: 0.2807 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25007 Z= 0.122 Angle : 0.530 9.305 34061 Z= 0.281 Chirality : 0.040 0.228 3861 Planarity : 0.003 0.041 4202 Dihedral : 15.500 111.658 4041 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.41 % Allowed : 22.09 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2905 helix: 1.90 (0.15), residues: 1228 sheet: -0.74 (0.28), residues: 320 loop : -0.83 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 191 TYR 0.019 0.001 TYR J 679 PHE 0.014 0.001 PHE I 405 TRP 0.011 0.001 TRP I 807 HIS 0.003 0.001 HIS J 865 Details of bonding type rmsd covalent geometry : bond 0.00277 (24999) covalent geometry : angle 0.52831 (34049) hydrogen bonds : bond 0.03238 ( 1135) hydrogen bonds : angle 4.26880 ( 3159) metal coordination : bond 0.00499 ( 8) metal coordination : angle 2.02816 ( 12) *********************** 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 213 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7328 (t-90) REVERT: H 147 GLN cc_start: 0.8541 (mt0) cc_final: 0.8269 (mt0) REVERT: H 218 ARG cc_start: 0.6494 (tpt170) cc_final: 0.5177 (mmt180) REVERT: I 369 MET cc_start: 0.8311 (ppp) cc_final: 0.8078 (tmm) REVERT: I 475 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8346 (p) REVERT: I 492 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8020 (mmt) REVERT: I 510 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8262 (tp-100) REVERT: I 592 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8694 (ptm160) REVERT: I 1035 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8937 (ttmm) REVERT: I 1332 SER cc_start: 0.9405 (t) cc_final: 0.9186 (t) REVERT: J 821 MET cc_start: 0.8380 (tpp) cc_final: 0.7948 (tpt) REVERT: J 1366 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8572 (m-70) REVERT: K 42 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8553 (mp0) REVERT: K 61 ASN cc_start: 0.8181 (t0) cc_final: 0.7726 (t0) REVERT: K 66 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8622 (t) REVERT: K 68 GLU cc_start: 0.8600 (pp20) cc_final: 0.8331 (pp20) REVERT: L 100 MET cc_start: 0.8233 (mtt) cc_final: 0.7659 (mtt) REVERT: L 395 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8991 (p) REVERT: L 425 TYR cc_start: 0.7142 (m-80) cc_final: 0.6553 (m-80) REVERT: L 474 MET cc_start: 0.8414 (ttm) cc_final: 0.8091 (ttm) REVERT: L 507 MET cc_start: 0.9155 (tpp) cc_final: 0.8555 (tpp) REVERT: L 580 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7254 (t80) outliers start: 60 outliers final: 39 residues processed: 206 average time/residue: 0.1527 time to fit residues: 50.9959 Evaluate side-chains 187 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 127 GLN Chi-restraints excluded: chain I residue 90 VAL 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 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 493 ILE 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 799 ASN Chi-restraints excluded: chain I residue 819 SER 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 46 TYR Chi-restraints excluded: chain J residue 90 VAL 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 256 ASP Chi-restraints excluded: chain J residue 342 LEU 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 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 K residue 66 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 442 SER 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 221 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 J 294 ASN J 777 HIS K 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.078750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.054963 restraints weight = 68162.620| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.59 r_work: 0.2777 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25007 Z= 0.184 Angle : 0.562 10.183 34061 Z= 0.297 Chirality : 0.040 0.183 3861 Planarity : 0.004 0.054 4202 Dihedral : 15.501 111.923 4041 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.37 % Allowed : 21.89 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.16), residues: 2905 helix: 1.94 (0.15), residues: 1223 sheet: -0.75 (0.28), residues: 322 loop : -0.81 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 378 TYR 0.016 0.001 TYR J 679 PHE 0.016 0.001 PHE I 57 TRP 0.008 0.001 TRP I 807 HIS 0.004 0.001 HIS J 865 Details of bonding type rmsd covalent geometry : bond 0.00424 (24999) covalent geometry : angle 0.56095 (34049) hydrogen bonds : bond 0.03550 ( 1135) hydrogen bonds : angle 4.29188 ( 3159) metal coordination : bond 0.00871 ( 8) metal coordination : angle 2.16398 ( 12) *********************** 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 225 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 141 time to evaluate : 0.858 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: 0.9148 (OUTLIER) cc_final: 0.8936 (pp) REVERT: H 66 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7337 (t-90) REVERT: H 147 GLN cc_start: 0.8570 (mt0) cc_final: 0.8279 (mt0) REVERT: H 218 ARG cc_start: 0.6555 (tpt170) cc_final: 0.5323 (mmt180) REVERT: I 369 MET cc_start: 0.8336 (ppp) cc_final: 0.8063 (tmm) REVERT: I 510 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8369 (tp-100) REVERT: I 542 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7419 (ptt180) REVERT: I 592 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8714 (ptm160) REVERT: I 903 ARG cc_start: 0.8958 (mmt-90) cc_final: 0.8525 (mmt-90) REVERT: I 963 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: I 1035 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9013 (ttmm) REVERT: J 100 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: J 180 MET cc_start: 0.6744 (mtp) cc_final: 0.6456 (ttt) REVERT: J 821 MET cc_start: 0.8387 (tpp) cc_final: 0.8142 (tpt) REVERT: J 1366 HIS cc_start: 0.8991 (OUTLIER) cc_final: 0.8647 (m-70) REVERT: K 42 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8562 (mp0) REVERT: K 61 ASN cc_start: 0.8201 (t0) cc_final: 0.7929 (t0) REVERT: L 425 TYR cc_start: 0.7259 (m-80) cc_final: 0.6584 (m-80) REVERT: L 474 MET cc_start: 0.8505 (ttm) cc_final: 0.8165 (ttm) REVERT: L 507 MET cc_start: 0.9159 (tpp) cc_final: 0.8569 (tpp) REVERT: L 580 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7224 (t80) outliers start: 84 outliers final: 60 residues processed: 216 average time/residue: 0.1538 time to fit residues: 53.6620 Evaluate side-chains 206 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 137 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 19 VAL 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 120 ASP 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 90 VAL 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 456 VAL 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 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 799 ASN 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 901 LEU 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 72 CYS Chi-restraints excluded: chain J residue 90 VAL 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 352 ARG 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 746 LEU 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 442 SER 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 215 optimal weight: 3.9990 chunk 263 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 288 optimal weight: 8.9990 chunk 276 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 365 GLN J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.078672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.054955 restraints weight = 68238.049| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.59 r_work: 0.2779 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25007 Z= 0.176 Angle : 0.565 13.719 34061 Z= 0.297 Chirality : 0.040 0.185 3861 Planarity : 0.004 0.038 4202 Dihedral : 15.496 111.122 4041 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.33 % Allowed : 21.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2905 helix: 1.93 (0.15), residues: 1224 sheet: -0.75 (0.28), residues: 320 loop : -0.83 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.015 0.001 TYR J 679 PHE 0.015 0.001 PHE I 405 TRP 0.008 0.001 TRP I 807 HIS 0.004 0.001 HIS J 865 Details of bonding type rmsd covalent geometry : bond 0.00406 (24999) covalent geometry : angle 0.56311 (34049) hydrogen bonds : bond 0.03532 ( 1135) hydrogen bonds : angle 4.28927 ( 3159) metal coordination : bond 0.00859 ( 8) metal coordination : angle 2.29036 ( 12) *********************** 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 220 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 137 time to evaluate : 0.983 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: 0.9140 (OUTLIER) cc_final: 0.8931 (pp) REVERT: H 66 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.7356 (t-90) REVERT: H 147 GLN cc_start: 0.8557 (mt0) cc_final: 0.8259 (mt0) REVERT: H 218 ARG cc_start: 0.6485 (tpt170) cc_final: 0.5184 (mmt180) REVERT: I 369 MET cc_start: 0.8373 (ppp) cc_final: 0.8112 (tmm) REVERT: I 510 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8359 (tp-100) REVERT: I 542 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7451 (ptt180) REVERT: I 592 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8720 (ptm160) REVERT: I 903 ARG cc_start: 0.8846 (mmt-90) cc_final: 0.8460 (mmt-90) REVERT: I 963 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: I 1035 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9024 (ttmm) REVERT: I 1168 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: J 100 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: J 743 MET cc_start: 0.8784 (ptp) cc_final: 0.8536 (ptp) REVERT: J 821 MET cc_start: 0.8366 (tpp) cc_final: 0.8129 (tpt) REVERT: J 1366 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8632 (m-70) REVERT: K 5 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8372 (t) REVERT: K 42 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8557 (mp0) REVERT: K 61 ASN cc_start: 0.8178 (t0) cc_final: 0.7927 (t0) REVERT: K 68 GLU cc_start: 0.8611 (pp20) cc_final: 0.8202 (pp20) REVERT: K 74 GLU cc_start: 0.8411 (pp20) cc_final: 0.8029 (pp20) REVERT: L 395 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8986 (p) REVERT: L 425 TYR cc_start: 0.7292 (m-80) cc_final: 0.6606 (m-80) REVERT: L 474 MET cc_start: 0.8494 (ttm) cc_final: 0.8150 (ttm) REVERT: L 507 MET cc_start: 0.9160 (tpp) cc_final: 0.8569 (tpp) REVERT: L 568 ASN cc_start: 0.7785 (t0) cc_final: 0.7550 (t0) REVERT: L 580 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7162 (t80) outliers start: 83 outliers final: 62 residues processed: 213 average time/residue: 0.1544 time to fit residues: 53.6902 Evaluate side-chains 208 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 134 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 19 VAL 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 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 90 VAL 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 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 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 901 LEU 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 90 VAL 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 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 746 LEU 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 930 LEU 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 K residue 5 THR Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 442 SER 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 293 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 H 147 GLN H 186 ASN I 811 ASN ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J 817 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.077537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.053774 restraints weight = 68458.919| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.58 r_work: 0.2746 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 25007 Z= 0.248 Angle : 0.621 13.968 34061 Z= 0.324 Chirality : 0.042 0.179 3861 Planarity : 0.004 0.038 4202 Dihedral : 15.603 111.492 4041 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.61 % Allowed : 21.93 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 2905 helix: 1.83 (0.15), residues: 1231 sheet: -0.78 (0.29), residues: 317 loop : -0.90 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.015 0.001 TYR J 631 PHE 0.019 0.002 PHE I 405 TRP 0.009 0.001 TRP I 807 HIS 0.008 0.001 HIS J 364 Details of bonding type rmsd covalent geometry : bond 0.00574 (24999) covalent geometry : angle 0.61816 (34049) hydrogen bonds : bond 0.03969 ( 1135) hydrogen bonds : angle 4.38839 ( 3159) metal coordination : bond 0.01224 ( 8) metal coordination : angle 3.09045 ( 12) *********************** 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 230 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 140 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8893 (pp) REVERT: H 66 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7325 (t-90) REVERT: H 147 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8340 (mt0) REVERT: H 218 ARG cc_start: 0.6443 (tpt170) cc_final: 0.5205 (mmt180) REVERT: I 369 MET cc_start: 0.8397 (ppp) cc_final: 0.8081 (tmm) REVERT: I 492 MET cc_start: 0.8520 (mmm) cc_final: 0.8302 (mmm) REVERT: I 510 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8381 (tp-100) REVERT: I 542 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7395 (ptt180) REVERT: I 592 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8670 (ptm160) REVERT: I 903 ARG cc_start: 0.8820 (mmt-90) cc_final: 0.8436 (mmt-90) REVERT: I 963 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: I 1035 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8959 (ttmm) REVERT: I 1168 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: J 100 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8463 (mt-10) REVERT: J 743 MET cc_start: 0.8852 (ptp) cc_final: 0.8611 (ptp) REVERT: J 821 MET cc_start: 0.8371 (tpp) cc_final: 0.8054 (tpt) REVERT: J 909 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9301 (tp) REVERT: J 1366 HIS cc_start: 0.9011 (OUTLIER) cc_final: 0.8638 (m-70) REVERT: K 42 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8545 (mp0) REVERT: K 68 GLU cc_start: 0.8711 (pp20) cc_final: 0.8281 (pp20) REVERT: L 425 TYR cc_start: 0.7332 (m-80) cc_final: 0.6636 (m-80) REVERT: L 474 MET cc_start: 0.8518 (ttm) cc_final: 0.8158 (ttm) REVERT: L 507 MET cc_start: 0.9154 (tpp) cc_final: 0.8533 (tpp) REVERT: L 567 MET cc_start: 0.7855 (ptt) cc_final: 0.7307 (ppp) REVERT: L 568 ASN cc_start: 0.7805 (t0) cc_final: 0.7478 (t0) REVERT: L 580 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7354 (t80) outliers start: 90 outliers final: 60 residues processed: 220 average time/residue: 0.1516 time to fit residues: 54.7656 Evaluate side-chains 206 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 134 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 90 VAL 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 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 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 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 901 LEU 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 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP 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 746 LEU 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 930 LEU 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 62 GLN Chi-restraints excluded: chain L residue 442 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 82 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 246 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 235 optimal weight: 30.0000 chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 365 GLN J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.079437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.055852 restraints weight = 67848.306| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.60 r_work: 0.2797 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25007 Z= 0.120 Angle : 0.554 13.818 34061 Z= 0.291 Chirality : 0.040 0.190 3861 Planarity : 0.003 0.040 4202 Dihedral : 15.483 108.745 4041 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.37 % Allowed : 23.13 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2905 helix: 1.91 (0.15), residues: 1226 sheet: -0.73 (0.29), residues: 320 loop : -0.83 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 148 TYR 0.016 0.001 TYR J 679 PHE 0.015 0.001 PHE I 57 TRP 0.013 0.001 TRP I 807 HIS 0.003 0.001 HIS J 865 Details of bonding type rmsd covalent geometry : bond 0.00271 (24999) covalent geometry : angle 0.55251 (34049) hydrogen bonds : bond 0.03302 ( 1135) hydrogen bonds : angle 4.24866 ( 3159) metal coordination : bond 0.00537 ( 8) metal coordination : angle 2.26087 ( 12) ********************** 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 199 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 140 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7318 (t-90) REVERT: H 147 GLN cc_start: 0.8543 (mt0) cc_final: 0.8304 (mt0) REVERT: H 218 ARG cc_start: 0.6400 (tpt170) cc_final: 0.5113 (mmt180) REVERT: I 369 MET cc_start: 0.8303 (ppp) cc_final: 0.8084 (tmm) REVERT: I 510 GLN cc_start: 0.8817 (tp-100) cc_final: 0.8355 (tp-100) REVERT: I 542 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7518 (ptt180) REVERT: I 592 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8696 (ptm160) REVERT: I 903 ARG cc_start: 0.8782 (mmt-90) cc_final: 0.8406 (mmt-90) REVERT: I 1035 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8942 (ttmm) REVERT: J 821 MET cc_start: 0.8339 (tpp) cc_final: 0.7954 (tpt) REVERT: J 1366 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8609 (m-70) REVERT: K 42 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8564 (mp0) REVERT: K 68 GLU cc_start: 0.8616 (pp20) cc_final: 0.8182 (pp20) REVERT: K 74 GLU cc_start: 0.8128 (pp20) cc_final: 0.7637 (pp20) REVERT: L 100 MET cc_start: 0.8257 (mtt) cc_final: 0.7445 (mtm) REVERT: L 395 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.9011 (p) REVERT: L 425 TYR cc_start: 0.7303 (m-80) cc_final: 0.6630 (m-80) REVERT: L 474 MET cc_start: 0.8508 (ttm) cc_final: 0.8169 (ttm) REVERT: L 507 MET cc_start: 0.9157 (tpp) cc_final: 0.8543 (tpp) REVERT: L 567 MET cc_start: 0.7928 (ptt) cc_final: 0.7468 (ppp) REVERT: L 568 ASN cc_start: 0.7720 (t0) cc_final: 0.7386 (t0) REVERT: L 580 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7444 (t80) outliers start: 59 outliers final: 44 residues processed: 194 average time/residue: 0.1478 time to fit residues: 47.2689 Evaluate side-chains 184 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 LEU 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 I residue 21 VAL Chi-restraints excluded: chain I residue 90 VAL 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 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 811 ASN Chi-restraints excluded: chain I residue 819 SER 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 72 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL 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 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 1366 HIS Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 442 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 288 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 143 optimal weight: 0.0170 chunk 104 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- 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 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.079384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.055817 restraints weight = 68068.805| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.61 r_work: 0.2798 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 25007 Z= 0.202 Angle : 0.770 59.199 34061 Z= 0.450 Chirality : 0.043 0.820 3861 Planarity : 0.004 0.133 4202 Dihedral : 15.506 108.751 4041 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.37 % Allowed : 23.05 % Favored : 74.58 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2905 helix: 1.90 (0.15), residues: 1225 sheet: -0.73 (0.29), residues: 320 loop : -0.84 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 67 TYR 0.016 0.001 TYR J 679 PHE 0.015 0.001 PHE I 57 TRP 0.012 0.001 TRP I 807 HIS 0.003 0.001 HIS J 865 Details of bonding type rmsd covalent geometry : bond 0.00437 (24999) covalent geometry : angle 0.76869 (34049) hydrogen bonds : bond 0.03322 ( 1135) hydrogen bonds : angle 4.24791 ( 3159) metal coordination : bond 0.00586 ( 8) metal coordination : angle 2.24432 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4766.37 seconds wall clock time: 82 minutes 35.81 seconds (4955.81 seconds total)