Starting phenix.real_space_refine on Tue Feb 20 22:29:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oty_13069/02_2024/7oty_13069_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oty_13069/02_2024/7oty_13069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oty_13069/02_2024/7oty_13069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oty_13069/02_2024/7oty_13069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oty_13069/02_2024/7oty_13069_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oty_13069/02_2024/7oty_13069_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 191 5.16 5 Cl 1 4.86 5 C 18628 2.51 5 N 4905 2.21 5 O 5308 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A GLU 916": "OE1" <-> "OE2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "A GLU 1265": "OE1" <-> "OE2" Residue "A GLU 1273": "OE1" <-> "OE2" Residue "A ARG 1321": "NH1" <-> "NH2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A ARG 1497": "NH1" <-> "NH2" Residue "A GLU 1516": "OE1" <-> "OE2" Residue "A GLU 1557": "OE1" <-> "OE2" Residue "A ARG 1608": "NH1" <-> "NH2" Residue "A GLU 1775": "OE1" <-> "OE2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1837": "NH1" <-> "NH2" Residue "A ARG 1854": "NH1" <-> "NH2" Residue "A ARG 1937": "NH1" <-> "NH2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A ARG 2090": "NH1" <-> "NH2" Residue "A ARG 2106": "NH1" <-> "NH2" Residue "A ARG 2120": "NH1" <-> "NH2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A GLU 2406": "OE1" <-> "OE2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A PHE 2461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2488": "OE1" <-> "OE2" Residue "A GLU 2828": "OE1" <-> "OE2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2922": "NH1" <-> "NH2" Residue "A GLU 2925": "OE1" <-> "OE2" Residue "A GLU 2990": "OE1" <-> "OE2" Residue "A GLU 3038": "OE1" <-> "OE2" Residue "A GLU 3137": "OE1" <-> "OE2" Residue "A ARG 3282": "NH1" <-> "NH2" Residue "A GLU 3295": "OE1" <-> "OE2" Residue "A GLU 3309": "OE1" <-> "OE2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3350": "OE1" <-> "OE2" Residue "A ARG 3357": "NH1" <-> "NH2" Residue "A ARG 3358": "NH1" <-> "NH2" Residue "A ARG 3380": "NH1" <-> "NH2" Residue "A GLU 3393": "OE1" <-> "OE2" Residue "A ARG 3425": "NH1" <-> "NH2" Residue "A GLU 3477": "OE1" <-> "OE2" Residue "A GLU 3519": "OE1" <-> "OE2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A GLU 3698": "OE1" <-> "OE2" Residue "A GLU 3700": "OE1" <-> "OE2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A GLU 3724": "OE1" <-> "OE2" Residue "A ARG 3725": "NH1" <-> "NH2" Residue "A ARG 3741": "NH1" <-> "NH2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A GLU 3747": "OE1" <-> "OE2" Residue "A PHE 3750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A GLU 3823": "OE1" <-> "OE2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A GLU 4030": "OE1" <-> "OE2" Residue "A ARG 4082": "NH1" <-> "NH2" Residue "A GLU 4093": "OE1" <-> "OE2" Residue "A ARG 4119": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29034 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 29034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3657, 29034 Unusual residues: {'1IX': 1} Classifications: {'peptide': 3656, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 158, 'TRANS': 3497, None: 1} Not linked: pdbres="UNK A6020 " pdbres="1IX A6101 " Chain breaks: 17 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'UNK:plan-1': 20, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 146 Time building chain proxies: 16.25, per 1000 atoms: 0.56 Number of scatterers: 29034 At special positions: 0 Unit cell: (125.184, 153.872, 182.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 191 16.00 F 1 9.00 O 5308 8.00 N 4905 7.00 C 18628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.26 Conformation dependent library (CDL) restraints added in 5.4 seconds 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 185 helices and 4 sheets defined 62.8% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.29 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 4.573A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 59 through 70 removed outlier: 3.711A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 96 removed outlier: 4.241A pdb=" N GLU A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 85 " --> pdb=" O CYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.986A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 removed outlier: 3.933A pdb=" N LEU A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N MET A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.868A pdb=" N LEU A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 192 through 206 removed outlier: 3.981A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.819A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 308 through 329 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 357 through 368 removed outlier: 3.797A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 407 through 421 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 432 through 444 Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 473 through 492 removed outlier: 4.118A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.715A pdb=" N VAL A 528 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP A 529 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 535 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 536 " --> pdb=" O HIS A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.989A pdb=" N ALA A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 Processing helix chain 'A' and resid 617 through 633 removed outlier: 3.701A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 659 Proline residue: A 644 - end of helix removed outlier: 5.338A pdb=" N TYR A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N SER A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.969A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 720 removed outlier: 4.401A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLN A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 735 removed outlier: 3.527A pdb=" N SER A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 758 removed outlier: 4.376A pdb=" N LEU A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 763 through 779 Processing helix chain 'A' and resid 782 through 795 Proline residue: A 787 - end of helix removed outlier: 4.720A pdb=" N LYS A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP A 791 " --> pdb=" O PRO A 787 " (cutoff:3.500A) Proline residue: A 794 - end of helix Processing helix chain 'A' and resid 848 through 861 Processing helix chain 'A' and resid 867 through 876 removed outlier: 4.968A pdb=" N VAL A 873 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A 874 " --> pdb=" O LEU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 920 Proline residue: A 912 - end of helix removed outlier: 3.839A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 946 removed outlier: 3.845A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 973 removed outlier: 3.607A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 978 through 996 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1008 through 1014 removed outlier: 3.896A pdb=" N LEU A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1043 Processing helix chain 'A' and resid 1046 through 1049 No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1072 through 1085 removed outlier: 3.640A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1116 removed outlier: 3.586A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1140 Processing helix chain 'A' and resid 1142 through 1145 No H-bonds generated for 'chain 'A' and resid 1142 through 1145' Processing helix chain 'A' and resid 1165 through 1177 removed outlier: 4.957A pdb=" N GLY A1177 " --> pdb=" O LEU A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1197 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1204 through 1214 Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.811A pdb=" N GLU A1225 " --> pdb=" O ASN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1272 Processing helix chain 'A' and resid 1278 through 1281 No H-bonds generated for 'chain 'A' and resid 1278 through 1281' Processing helix chain 'A' and resid 1290 through 1299 removed outlier: 4.041A pdb=" N GLU A1299 " --> pdb=" O ALA A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1350 removed outlier: 3.832A pdb=" N GLU A1328 " --> pdb=" O PRO A1324 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG A1329 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1359 removed outlier: 4.313A pdb=" N LEU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1355 through 1359' Processing helix chain 'A' and resid 1365 through 1382 removed outlier: 3.576A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Proline residue: A1379 - end of helix removed outlier: 4.737A pdb=" N ILE A1382 " --> pdb=" O GLU A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1408 Proline residue: A1396 - end of helix removed outlier: 3.730A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1420 removed outlier: 4.054A pdb=" N ASP A1413 " --> pdb=" O PRO A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1432 Processing helix chain 'A' and resid 1442 through 1461 Processing helix chain 'A' and resid 1464 through 1467 No H-bonds generated for 'chain 'A' and resid 1464 through 1467' Processing helix chain 'A' and resid 1477 through 1480 No H-bonds generated for 'chain 'A' and resid 1477 through 1480' Processing helix chain 'A' and resid 1482 through 1486 Processing helix chain 'A' and resid 1507 through 1520 Processing helix chain 'A' and resid 1525 through 1532 removed outlier: 3.921A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1573 removed outlier: 5.877A pdb=" N GLU A1565 " --> pdb=" O SER A1561 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A1566 " --> pdb=" O LEU A1562 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1584 removed outlier: 4.620A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1606 Processing helix chain 'A' and resid 1612 through 1624 Processing helix chain 'A' and resid 1626 through 1629 Processing helix chain 'A' and resid 1639 through 1655 Processing helix chain 'A' and resid 1668 through 1679 Processing helix chain 'A' and resid 1686 through 1692 Processing helix chain 'A' and resid 1696 through 1698 No H-bonds generated for 'chain 'A' and resid 1696 through 1698' Processing helix chain 'A' and resid 1707 through 1721 Processing helix chain 'A' and resid 1734 through 1753 Processing helix chain 'A' and resid 1756 through 1768 removed outlier: 3.792A pdb=" N ARG A1768 " --> pdb=" O GLU A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1787 removed outlier: 3.827A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1805 Processing helix chain 'A' and resid 1814 through 1821 removed outlier: 3.804A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1828 Processing helix chain 'A' and resid 1835 through 1852 removed outlier: 4.842A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1881 Processing helix chain 'A' and resid 1886 through 1889 No H-bonds generated for 'chain 'A' and resid 1886 through 1889' Processing helix chain 'A' and resid 1911 through 1924 removed outlier: 3.613A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1955 Processing helix chain 'A' and resid 1971 through 1973 No H-bonds generated for 'chain 'A' and resid 1971 through 1973' Processing helix chain 'A' and resid 2094 through 2106 removed outlier: 3.796A pdb=" N ARG A2106 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2134 removed outlier: 3.678A pdb=" N LYS A2132 " --> pdb=" O PHE A2128 " (cutoff:3.500A) Processing helix chain 'A' and resid 2140 through 2152 Processing helix chain 'A' and resid 2156 through 2171 Proline residue: A2159 - end of helix removed outlier: 4.305A pdb=" N LYS A2162 " --> pdb=" O PRO A2159 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU A2165 " --> pdb=" O LYS A2162 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A2166 " --> pdb=" O HIS A2163 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2184 through 2195 Processing helix chain 'A' and resid 2206 through 2221 removed outlier: 3.853A pdb=" N ARG A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2228 through 2244 Processing helix chain 'A' and resid 2255 through 2260 Processing helix chain 'A' and resid 2268 through 2282 Processing helix chain 'A' and resid 2297 through 2308 removed outlier: 3.843A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N MET A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2332 removed outlier: 3.674A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2354 removed outlier: 3.842A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2368 removed outlier: 3.744A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2377 removed outlier: 3.682A pdb=" N ARG A2377 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2379 through 2388 Proline residue: A2387 - end of helix Processing helix chain 'A' and resid 2392 through 2403 Processing helix chain 'A' and resid 2413 through 2417 Processing helix chain 'A' and resid 2420 through 2424 removed outlier: 3.542A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2420 through 2424' Processing helix chain 'A' and resid 2430 through 2445 Proline residue: A2444 - end of helix Processing helix chain 'A' and resid 2448 through 2458 removed outlier: 3.858A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2470 through 2483 removed outlier: 3.537A pdb=" N ASN A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2511 removed outlier: 4.080A pdb=" N LEU A2510 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE A2511 " --> pdb=" O ILE A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2515 through 2525 Processing helix chain 'A' and resid 2535 through 2545 removed outlier: 3.808A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2548 through 2563 removed outlier: 3.889A pdb=" N GLU A2551 " --> pdb=" O PRO A2548 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL A2552 " --> pdb=" O LYS A2549 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A2555 " --> pdb=" O VAL A2552 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A2558 " --> pdb=" O LEU A2555 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A2559 " --> pdb=" O SER A2556 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A2561 " --> pdb=" O ALA A2558 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2798 removed outlier: 5.334A pdb=" N THR A2792 " --> pdb=" O SER A2789 " (cutoff:3.500A) Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2802 through 2822 removed outlier: 4.414A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS A2822 " --> pdb=" O LYS A2818 " (cutoff:3.500A) Processing helix chain 'A' and resid 2826 through 2846 Processing helix chain 'A' and resid 2852 through 2864 Processing helix chain 'A' and resid 2873 through 2883 Processing helix chain 'A' and resid 2886 through 2898 Processing helix chain 'A' and resid 2918 through 2932 removed outlier: 3.598A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2946 removed outlier: 3.754A pdb=" N SER A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2952 through 2961 removed outlier: 3.584A pdb=" N ALA A2956 " --> pdb=" O ILE A2952 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A2957 " --> pdb=" O THR A2953 " (cutoff:3.500A) Processing helix chain 'A' and resid 2965 through 2976 Processing helix chain 'A' and resid 2988 through 3004 removed outlier: 3.995A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (cutoff:3.500A) Processing helix chain 'A' and resid 3008 through 3013 Processing helix chain 'A' and resid 3041 through 3054 Processing helix chain 'A' and resid 3060 through 3069 removed outlier: 3.608A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3075 through 3079 Processing helix chain 'A' and resid 3083 through 3093 removed outlier: 3.699A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3116 Processing helix chain 'A' and resid 3122 through 3131 removed outlier: 3.681A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) Processing helix chain 'A' and resid 3133 through 3145 removed outlier: 3.513A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3166 Processing helix chain 'A' and resid 3176 through 3193 Processing helix chain 'A' and resid 3231 through 3248 removed outlier: 3.626A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) Processing helix chain 'A' and resid 3252 through 3262 Processing helix chain 'A' and resid 3272 through 3286 removed outlier: 3.736A pdb=" N ARG A3282 " --> pdb=" O GLN A3278 " (cutoff:3.500A) Processing helix chain 'A' and resid 3294 through 3306 removed outlier: 4.115A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) Processing helix chain 'A' and resid 3323 through 3343 Processing helix chain 'A' and resid 3346 through 3351 removed outlier: 4.262A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) Processing helix chain 'A' and resid 3354 through 3363 removed outlier: 3.850A pdb=" N ILE A3359 " --> pdb=" O LYS A3355 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A3360 " --> pdb=" O ALA A3356 " (cutoff:3.500A) Processing helix chain 'A' and resid 3370 through 3392 Processing helix chain 'A' and resid 3406 through 3428 removed outlier: 3.674A pdb=" N ILE A3410 " --> pdb=" O ALA A3407 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A3413 " --> pdb=" O ILE A3410 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A3418 " --> pdb=" O THR A3415 " (cutoff:3.500A) Processing helix chain 'A' and resid 3442 through 3455 Processing helix chain 'A' and resid 3459 through 3462 No H-bonds generated for 'chain 'A' and resid 3459 through 3462' Processing helix chain 'A' and resid 3465 through 3471 removed outlier: 3.553A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A3470 " --> pdb=" O PRO A3466 " (cutoff:3.500A) Processing helix chain 'A' and resid 3476 through 3479 Processing helix chain 'A' and resid 3481 through 3489 removed outlier: 3.732A pdb=" N SER A3488 " --> pdb=" O THR A3484 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3494 through 3505 removed outlier: 4.781A pdb=" N SER A3500 " --> pdb=" O SER A3497 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL A3503 " --> pdb=" O SER A3500 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3524 removed outlier: 3.931A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3530 through 3537 Processing helix chain 'A' and resid 3548 through 3562 removed outlier: 5.017A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A3554 " --> pdb=" O LYS A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3577 removed outlier: 3.910A pdb=" N GLN A3577 " --> pdb=" O ASN A3573 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3593 Processing helix chain 'A' and resid 3605 through 3616 removed outlier: 4.016A pdb=" N LYS A3608 " --> pdb=" O ASN A3605 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A3609 " --> pdb=" O ILE A3606 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A3610 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A3615 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3627 through 3635 removed outlier: 3.943A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 No H-bonds generated for 'chain 'A' and resid 3640 through 3643' Processing helix chain 'A' and resid 3658 through 3670 removed outlier: 3.774A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3681 through 3684 No H-bonds generated for 'chain 'A' and resid 3681 through 3684' Processing helix chain 'A' and resid 3759 through 3777 Processing helix chain 'A' and resid 3779 through 3783 Processing helix chain 'A' and resid 3812 through 3819 removed outlier: 3.645A pdb=" N THR A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3822 through 3829 Processing helix chain 'A' and resid 3835 through 3845 removed outlier: 4.303A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3861 removed outlier: 3.640A pdb=" N TYR A3855 " --> pdb=" O VAL A3852 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A3859 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3876 removed outlier: 3.644A pdb=" N SER A3876 " --> pdb=" O ARG A3872 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3889 Processing helix chain 'A' and resid 3894 through 3918 Processing helix chain 'A' and resid 3948 through 3951 No H-bonds generated for 'chain 'A' and resid 3948 through 3951' Processing helix chain 'A' and resid 3965 through 3970 Processing helix chain 'A' and resid 3979 through 3993 Processing helix chain 'A' and resid 3995 through 4007 Processing helix chain 'A' and resid 4009 through 4011 No H-bonds generated for 'chain 'A' and resid 4009 through 4011' Processing helix chain 'A' and resid 4013 through 4023 removed outlier: 3.799A pdb=" N LYS A4022 " --> pdb=" O GLN A4018 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS A4023 " --> pdb=" O LYS A4019 " (cutoff:3.500A) Processing helix chain 'A' and resid 4041 through 4050 removed outlier: 3.641A pdb=" N TYR A4046 " --> pdb=" O GLN A4042 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4056 through 4067 Processing helix chain 'A' and resid 4074 through 4082 Processing helix chain 'A' and resid 4100 through 4112 Processing helix chain 'A' and resid 4114 through 4119 removed outlier: 3.908A pdb=" N ARG A4119 " --> pdb=" O ASN A4115 " (cutoff:3.500A) Processing helix chain 'A' and resid 6003 through 6009 Processing helix chain 'A' and resid 6011 through 6014 No H-bonds generated for 'chain 'A' and resid 6011 through 6014' Processing sheet with id= A, first strand: chain 'A' and resid 583 through 585 Processing sheet with id= B, first strand: chain 'A' and resid 893 through 895 Processing sheet with id= C, first strand: chain 'A' and resid 3736 through 3742 removed outlier: 3.840A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A3800 " --> pdb=" O THR A3797 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A3797 " --> pdb=" O LEU A3800 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 3809 through 3811 1374 hydrogen bonds defined for protein. 3819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.39 Time building geometry restraints manager: 13.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.17: 1 1.17 - 1.33: 8629 1.33 - 1.50: 10060 1.50 - 1.67: 10640 1.67 - 1.83: 299 Bond restraints: 29629 Sorted by residual: bond pdb=" C30 1IX A6101 " pdb=" O29 1IX A6101 " ideal model delta sigma weight residual 1.406 1.000 0.406 2.00e-02 2.50e+03 4.12e+02 bond pdb=" C11 1IX A6101 " pdb="CL1 1IX A6101 " ideal model delta sigma weight residual 1.728 1.825 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C LEU A1068 " pdb=" N HIS A1069 " ideal model delta sigma weight residual 1.331 1.237 0.094 2.07e-02 2.33e+03 2.05e+01 bond pdb=" C12 1IX A6101 " pdb=" C13 1IX A6101 " ideal model delta sigma weight residual 1.379 1.465 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C20 1IX A6101 " pdb=" C21 1IX A6101 " ideal model delta sigma weight residual 1.416 1.336 0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 29624 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.67: 533 104.67 - 112.42: 15256 112.42 - 120.18: 12667 120.18 - 127.93: 11355 127.93 - 135.69: 261 Bond angle restraints: 40072 Sorted by residual: angle pdb=" C28 1IX A6101 " pdb=" O29 1IX A6101 " pdb=" C30 1IX A6101 " ideal model delta sigma weight residual 109.87 135.69 -25.82 3.00e+00 1.11e-01 7.41e+01 angle pdb=" N GLN A3494 " pdb=" CA GLN A3494 " pdb=" C GLN A3494 " ideal model delta sigma weight residual 110.97 102.87 8.10 1.09e+00 8.42e-01 5.52e+01 angle pdb=" N CYS A3492 " pdb=" CA CYS A3492 " pdb=" C CYS A3492 " ideal model delta sigma weight residual 107.73 119.81 -12.08 1.80e+00 3.09e-01 4.51e+01 angle pdb=" N LYS A3753 " pdb=" CA LYS A3753 " pdb=" C LYS A3753 " ideal model delta sigma weight residual 109.96 100.00 9.96 1.50e+00 4.44e-01 4.41e+01 angle pdb=" C LEU A1884 " pdb=" N PRO A1885 " pdb=" CA PRO A1885 " ideal model delta sigma weight residual 120.85 113.97 6.88 1.08e+00 8.57e-01 4.06e+01 ... (remaining 40067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 16199 17.82 - 35.63: 1554 35.63 - 53.45: 269 53.45 - 71.27: 42 71.27 - 89.08: 22 Dihedral angle restraints: 18086 sinusoidal: 7329 harmonic: 10757 Sorted by residual: dihedral pdb=" C CYS A3492 " pdb=" N CYS A3492 " pdb=" CA CYS A3492 " pdb=" CB CYS A3492 " ideal model delta harmonic sigma weight residual -122.60 -137.16 14.56 0 2.50e+00 1.60e-01 3.39e+01 dihedral pdb=" CA ILE A2785 " pdb=" C ILE A2785 " pdb=" N LYS A2786 " pdb=" CA LYS A2786 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU A3714 " pdb=" C GLU A3714 " pdb=" N TYR A3715 " pdb=" CA TYR A3715 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 18083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 4426 0.131 - 0.263: 133 0.263 - 0.394: 5 0.394 - 0.525: 0 0.525 - 0.656: 1 Chirality restraints: 4565 Sorted by residual: chirality pdb=" CA CYS A3492 " pdb=" N CYS A3492 " pdb=" C CYS A3492 " pdb=" CB CYS A3492 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA GLU A3693 " pdb=" N GLU A3693 " pdb=" C GLU A3693 " pdb=" CB GLU A3693 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA GLU A 775 " pdb=" N GLU A 775 " pdb=" C GLU A 775 " pdb=" CB GLU A 775 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 4562 not shown) Planarity restraints: 5084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A3684 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO A3685 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A3685 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A3685 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A3520 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" CD GLU A3520 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU A3520 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU A3520 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A2135 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO A2136 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A2136 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A2136 " 0.044 5.00e-02 4.00e+02 ... (remaining 5081 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 2 1.92 - 2.67: 762 2.67 - 3.41: 44374 3.41 - 4.16: 69743 4.16 - 4.90: 128594 Nonbonded interactions: 243475 Sorted by model distance: nonbonded pdb=" SG CYS A1255 " pdb=" CE2 PHE A3694 " model vdw 1.177 3.700 nonbonded pdb=" SG CYS A1255 " pdb=" CD2 PHE A3694 " model vdw 1.822 3.700 nonbonded pdb=" CB CYS A1255 " pdb=" CE2 PHE A3694 " model vdw 1.948 3.740 nonbonded pdb=" O TYR A1243 " pdb=" NH1 ARG A1245 " model vdw 2.079 2.520 nonbonded pdb=" O ALA A1078 " pdb=" OH TYR A1107 " model vdw 2.083 2.440 ... (remaining 243470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 max=1.00 mean=0.95 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: 2.320 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: 5.820 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 81.420 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.013 0.406 29629 Z= 0.831 Angle : 1.081 25.820 40072 Z= 0.578 Chirality : 0.061 0.656 4565 Planarity : 0.006 0.086 5084 Dihedral : 14.426 89.081 11074 Min Nonbonded Distance : 1.177 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.13 % Favored : 89.67 % Rotamer: Outliers : 0.75 % Allowed : 0.72 % Favored : 98.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.13), residues: 3602 helix: -0.82 (0.10), residues: 2377 sheet: -1.72 (0.70), residues: 54 loop : -2.65 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A3686 HIS 0.022 0.003 HIS A 993 PHE 0.037 0.004 PHE A4011 TYR 0.034 0.004 TYR A 366 ARG 0.018 0.002 ARG A3708 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 321 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1004 GLN cc_start: 0.7468 (mp10) cc_final: 0.7182 (mp10) REVERT: A 1155 ARG cc_start: 0.6858 (mtp-110) cc_final: 0.6588 (ttm-80) REVERT: A 1812 LEU cc_start: 0.7089 (mt) cc_final: 0.6812 (pp) REVERT: A 2185 MET cc_start: 0.8098 (tpt) cc_final: 0.7864 (tpt) REVERT: A 2269 ASP cc_start: 0.7067 (p0) cc_final: 0.6626 (p0) REVERT: A 2307 MET cc_start: 0.7921 (mpp) cc_final: 0.7046 (mpt) REVERT: A 2328 ARG cc_start: 0.7846 (tmt-80) cc_final: 0.7491 (tpt90) REVERT: A 3695 LEU cc_start: 0.4516 (OUTLIER) cc_final: 0.4293 (tt) REVERT: A 4039 TYR cc_start: 0.5627 (t80) cc_final: 0.5281 (t80) outliers start: 24 outliers final: 4 residues processed: 335 average time/residue: 1.3723 time to fit residues: 546.5006 Evaluate side-chains 249 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 244 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1863 PHE Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3695 LEU Chi-restraints excluded: chain A residue 3803 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 186 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 286 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 331 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2305 ASN A2365 ASN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2795 GLN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN ** A3390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3577 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29629 Z= 0.204 Angle : 0.682 8.842 40072 Z= 0.344 Chirality : 0.042 0.169 4565 Planarity : 0.005 0.058 5084 Dihedral : 5.856 47.913 3953 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.89 % Favored : 92.98 % Rotamer: Outliers : 1.28 % Allowed : 9.39 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3602 helix: -0.08 (0.11), residues: 2375 sheet: -1.52 (0.71), residues: 51 loop : -2.29 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A3588 HIS 0.008 0.001 HIS A 993 PHE 0.027 0.002 PHE A2823 TYR 0.033 0.002 TYR A3540 ARG 0.004 0.000 ARG A1806 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 293 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 775 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: A 1369 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7702 (mmt) REVERT: A 2185 MET cc_start: 0.7938 (tpt) cc_final: 0.7729 (tpt) REVERT: A 2307 MET cc_start: 0.7690 (mpp) cc_final: 0.6770 (mpt) REVERT: A 2328 ARG cc_start: 0.7711 (tmt-80) cc_final: 0.7467 (tpt90) REVERT: A 2374 LEU cc_start: 0.8515 (tp) cc_final: 0.8162 (tt) REVERT: A 2396 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7219 (tm) REVERT: A 2443 MET cc_start: 0.7873 (ttm) cc_final: 0.7642 (ttm) REVERT: A 3176 MET cc_start: 0.8873 (mmm) cc_final: 0.8650 (mmm) REVERT: A 4005 PHE cc_start: 0.7839 (t80) cc_final: 0.7578 (t80) outliers start: 41 outliers final: 10 residues processed: 307 average time/residue: 1.3688 time to fit residues: 500.2429 Evaluate side-chains 261 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 248 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2274 ILE Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3625 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 275 optimal weight: 0.7980 chunk 225 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 295 optimal weight: 0.6980 chunk 329 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN A 982 GLN ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1435 ASN ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 GLN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2977 ASN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3390 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29629 Z= 0.182 Angle : 0.617 12.269 40072 Z= 0.309 Chirality : 0.040 0.163 4565 Planarity : 0.004 0.046 5084 Dihedral : 5.164 44.237 3945 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.47 % Favored : 92.39 % Rotamer: Outliers : 1.97 % Allowed : 12.02 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3602 helix: 0.27 (0.11), residues: 2397 sheet: -1.57 (0.68), residues: 51 loop : -2.23 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A3588 HIS 0.007 0.001 HIS A 993 PHE 0.022 0.001 PHE A1923 TYR 0.027 0.001 TYR A3540 ARG 0.007 0.000 ARG A1155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 278 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.4506 (mm) REVERT: A 395 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8027 (ttp) REVERT: A 1369 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6858 (mpt) REVERT: A 1576 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: A 2307 MET cc_start: 0.7526 (mpp) cc_final: 0.6513 (mpt) REVERT: A 2328 ARG cc_start: 0.7701 (tmt-80) cc_final: 0.7476 (tpt90) REVERT: A 2374 LEU cc_start: 0.8594 (tp) cc_final: 0.8227 (mp) REVERT: A 2396 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7063 (tm) REVERT: A 2443 MET cc_start: 0.7863 (ttm) cc_final: 0.7609 (ttm) REVERT: A 3080 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8023 (pp) REVERT: A 3176 MET cc_start: 0.8859 (mmm) cc_final: 0.8560 (mmm) REVERT: A 3609 MET cc_start: 0.3503 (ptp) cc_final: 0.2642 (mmm) outliers start: 63 outliers final: 17 residues processed: 306 average time/residue: 1.3692 time to fit residues: 501.1866 Evaluate side-chains 268 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1477 HIS Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2274 ILE Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 328 optimal weight: 3.9990 chunk 249 optimal weight: 0.7980 chunk 172 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 222 optimal weight: 0.0060 chunk 333 optimal weight: 0.0980 chunk 352 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 315 optimal weight: 0.0670 chunk 95 optimal weight: 0.8980 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 GLN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29629 Z= 0.148 Angle : 0.587 12.161 40072 Z= 0.292 Chirality : 0.039 0.237 4565 Planarity : 0.004 0.044 5084 Dihedral : 4.853 43.172 3945 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.41 % Favored : 93.45 % Rotamer: Outliers : 1.97 % Allowed : 14.21 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3602 helix: 0.53 (0.11), residues: 2383 sheet: -1.41 (0.67), residues: 49 loop : -2.08 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A3588 HIS 0.005 0.001 HIS A2787 PHE 0.021 0.001 PHE A1805 TYR 0.022 0.001 TYR A3540 ARG 0.010 0.000 ARG A3474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 278 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.4896 (OUTLIER) cc_final: 0.4480 (mm) REVERT: A 395 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7998 (ttp) REVERT: A 550 PHE cc_start: 0.5333 (p90) cc_final: 0.5117 (p90) REVERT: A 1369 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7487 (mmt) REVERT: A 1576 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: A 2185 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7483 (tpt) REVERT: A 2276 LEU cc_start: 0.9024 (mt) cc_final: 0.8824 (mt) REVERT: A 2307 MET cc_start: 0.7281 (mpp) cc_final: 0.6116 (mpt) REVERT: A 2374 LEU cc_start: 0.8682 (tp) cc_final: 0.8331 (mp) REVERT: A 2443 MET cc_start: 0.7799 (ttm) cc_final: 0.7525 (ttm) REVERT: A 3493 TRP cc_start: 0.5869 (OUTLIER) cc_final: 0.5438 (p90) REVERT: A 3609 MET cc_start: 0.3317 (ptp) cc_final: 0.2568 (mmm) REVERT: A 3797 THR cc_start: 0.8146 (m) cc_final: 0.7872 (m) REVERT: A 4023 LYS cc_start: 0.5475 (OUTLIER) cc_final: 0.5247 (ttmt) outliers start: 63 outliers final: 18 residues processed: 316 average time/residue: 1.3951 time to fit residues: 527.5694 Evaluate side-chains 272 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 247 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2185 MET Chi-restraints excluded: chain A residue 2274 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3493 TRP Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 4023 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 262 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 0.8980 chunk 316 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4018 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29629 Z= 0.210 Angle : 0.608 9.015 40072 Z= 0.302 Chirality : 0.040 0.199 4565 Planarity : 0.004 0.049 5084 Dihedral : 4.757 26.363 3943 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.30 % Favored : 92.62 % Rotamer: Outliers : 2.25 % Allowed : 15.53 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3602 helix: 0.54 (0.11), residues: 2387 sheet: -1.44 (0.70), residues: 51 loop : -2.08 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A3588 HIS 0.006 0.001 HIS A 993 PHE 0.025 0.001 PHE A1805 TYR 0.026 0.001 TYR A3540 ARG 0.009 0.000 ARG A 971 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 263 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.4925 (OUTLIER) cc_final: 0.4459 (mm) REVERT: A 395 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8078 (ttp) REVERT: A 550 PHE cc_start: 0.5119 (p90) cc_final: 0.4909 (p90) REVERT: A 1369 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6841 (mpt) REVERT: A 1576 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: A 1812 LEU cc_start: 0.6537 (tt) cc_final: 0.6165 (pt) REVERT: A 2185 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7536 (tpt) REVERT: A 2276 LEU cc_start: 0.9032 (mt) cc_final: 0.8822 (mt) REVERT: A 2307 MET cc_start: 0.7343 (mpp) cc_final: 0.6096 (mpt) REVERT: A 2328 ARG cc_start: 0.8092 (tpt90) cc_final: 0.7808 (tpm170) REVERT: A 2443 MET cc_start: 0.7881 (ttm) cc_final: 0.7573 (ttm) REVERT: A 3080 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8149 (pt) REVERT: A 3609 MET cc_start: 0.3269 (ptp) cc_final: 0.2510 (mmm) outliers start: 72 outliers final: 26 residues processed: 305 average time/residue: 1.3511 time to fit residues: 498.2940 Evaluate side-chains 278 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 246 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2185 MET Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2334 LYS Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3245 SER Chi-restraints excluded: chain A residue 3890 MET Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 0.7980 chunk 317 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 353 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 116 optimal weight: 0.0060 chunk 185 optimal weight: 5.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 GLN ** A2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3104 GLN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29629 Z= 0.195 Angle : 0.604 10.178 40072 Z= 0.299 Chirality : 0.040 0.216 4565 Planarity : 0.004 0.057 5084 Dihedral : 4.718 25.904 3943 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 2.54 % Allowed : 16.34 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3602 helix: 0.58 (0.11), residues: 2386 sheet: -1.47 (0.69), residues: 51 loop : -2.07 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A3588 HIS 0.005 0.001 HIS A 993 PHE 0.026 0.001 PHE A1805 TYR 0.024 0.001 TYR A3540 ARG 0.011 0.000 ARG A 971 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 257 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4544 (mm) REVERT: A 144 MET cc_start: 0.2640 (OUTLIER) cc_final: 0.1395 (pmm) REVERT: A 189 MET cc_start: 0.4823 (OUTLIER) cc_final: 0.4575 (mmm) REVERT: A 395 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8085 (ttp) REVERT: A 1369 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.6835 (mpt) REVERT: A 1403 MET cc_start: 0.7568 (mtm) cc_final: 0.7355 (mtt) REVERT: A 1576 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6874 (m-30) REVERT: A 1812 LEU cc_start: 0.6619 (tt) cc_final: 0.6274 (pt) REVERT: A 2185 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7479 (tpt) REVERT: A 2307 MET cc_start: 0.7320 (mpp) cc_final: 0.6129 (mpt) REVERT: A 2443 MET cc_start: 0.7859 (ttm) cc_final: 0.7536 (ttm) REVERT: A 3159 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6725 (ptp90) REVERT: A 3609 MET cc_start: 0.3692 (ptp) cc_final: 0.3068 (mtm) outliers start: 81 outliers final: 29 residues processed: 307 average time/residue: 1.3129 time to fit residues: 486.0466 Evaluate side-chains 279 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 242 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2185 MET Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2334 LYS Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3245 SER Chi-restraints excluded: chain A residue 3451 LEU Chi-restraints excluded: chain A residue 3890 MET Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 chunk 257 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 297 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 351 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 chunk 214 optimal weight: 0.0020 chunk 162 optimal weight: 0.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 GLN A2414 GLN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3104 GLN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29629 Z= 0.186 Angle : 0.604 9.294 40072 Z= 0.299 Chirality : 0.040 0.262 4565 Planarity : 0.004 0.050 5084 Dihedral : 4.661 25.718 3943 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.78 % Rotamer: Outliers : 2.32 % Allowed : 17.41 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3602 helix: 0.59 (0.11), residues: 2392 sheet: -1.40 (0.70), residues: 51 loop : -2.01 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A3588 HIS 0.006 0.001 HIS A 334 PHE 0.044 0.001 PHE A1672 TYR 0.023 0.001 TYR A3540 ARG 0.008 0.000 ARG A2328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 256 time to evaluate : 3.461 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: A 131 LEU cc_start: 0.4626 (OUTLIER) cc_final: 0.4133 (mm) REVERT: A 144 MET cc_start: 0.2624 (OUTLIER) cc_final: 0.1409 (pmm) REVERT: A 189 MET cc_start: 0.4816 (OUTLIER) cc_final: 0.4567 (mmm) REVERT: A 395 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8094 (ttp) REVERT: A 775 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: A 1244 LEU cc_start: 0.3279 (OUTLIER) cc_final: 0.2986 (pp) REVERT: A 1403 MET cc_start: 0.7530 (mtm) cc_final: 0.7320 (mtt) REVERT: A 1510 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7090 (tp) REVERT: A 1576 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6917 (m-30) REVERT: A 1812 LEU cc_start: 0.6548 (tt) cc_final: 0.6175 (pt) REVERT: A 2307 MET cc_start: 0.7365 (mpp) cc_final: 0.6169 (mpt) REVERT: A 2443 MET cc_start: 0.7845 (ttm) cc_final: 0.7521 (ttm) REVERT: A 3159 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6658 (ptp90) REVERT: A 3609 MET cc_start: 0.3642 (ptp) cc_final: 0.2876 (mtt) outliers start: 74 outliers final: 33 residues processed: 303 average time/residue: 1.3825 time to fit residues: 505.1338 Evaluate side-chains 282 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 240 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3245 SER Chi-restraints excluded: chain A residue 3451 LEU Chi-restraints excluded: chain A residue 3667 LEU Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3890 MET Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29629 Z= 0.281 Angle : 0.651 10.329 40072 Z= 0.322 Chirality : 0.042 0.303 4565 Planarity : 0.004 0.052 5084 Dihedral : 4.819 25.694 3943 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 2.19 % Allowed : 17.88 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3602 helix: 0.47 (0.11), residues: 2381 sheet: -1.27 (0.68), residues: 58 loop : -2.11 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A3588 HIS 0.006 0.001 HIS A 993 PHE 0.030 0.002 PHE A1672 TYR 0.027 0.002 TYR A3540 ARG 0.005 0.000 ARG A 971 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 248 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.4446 (OUTLIER) cc_final: 0.3849 (mm) REVERT: A 144 MET cc_start: 0.2721 (OUTLIER) cc_final: 0.1450 (pmm) REVERT: A 189 MET cc_start: 0.4724 (OUTLIER) cc_final: 0.4495 (mmm) REVERT: A 395 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8046 (ttp) REVERT: A 2307 MET cc_start: 0.7369 (mpp) cc_final: 0.6254 (mpt) REVERT: A 2443 MET cc_start: 0.7702 (ttm) cc_final: 0.7379 (ttm) REVERT: A 3159 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6674 (ptp90) REVERT: A 3609 MET cc_start: 0.3564 (ptp) cc_final: 0.3080 (mtt) outliers start: 70 outliers final: 34 residues processed: 293 average time/residue: 1.3768 time to fit residues: 483.4317 Evaluate side-chains 272 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 233 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2122 LEU Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2501 LEU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3245 SER Chi-restraints excluded: chain A residue 3451 LEU Chi-restraints excluded: chain A residue 3687 MET Chi-restraints excluded: chain A residue 3890 MET Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 3.9990 chunk 337 optimal weight: 0.4980 chunk 307 optimal weight: 0.8980 chunk 327 optimal weight: 0.6980 chunk 336 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 257 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 296 optimal weight: 0.9990 chunk 310 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 ASN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29629 Z= 0.168 Angle : 0.620 12.781 40072 Z= 0.307 Chirality : 0.040 0.270 4565 Planarity : 0.004 0.048 5084 Dihedral : 4.632 25.987 3943 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.20 % Rotamer: Outliers : 1.88 % Allowed : 18.38 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3602 helix: 0.64 (0.11), residues: 2373 sheet: -1.04 (0.69), residues: 60 loop : -2.07 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP A3588 HIS 0.007 0.001 HIS A 334 PHE 0.028 0.001 PHE A1805 TYR 0.024 0.001 TYR A3013 ARG 0.008 0.000 ARG A1712 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 258 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.4421 (OUTLIER) cc_final: 0.3839 (mm) REVERT: A 144 MET cc_start: 0.2687 (OUTLIER) cc_final: 0.1431 (pmm) REVERT: A 395 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8048 (ttp) REVERT: A 2185 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7330 (tpt) REVERT: A 2232 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7440 (mmm-85) REVERT: A 2307 MET cc_start: 0.7229 (mpp) cc_final: 0.6135 (mpt) REVERT: A 2443 MET cc_start: 0.7802 (ttm) cc_final: 0.7507 (ttm) REVERT: A 3159 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6630 (ptp90) REVERT: A 3609 MET cc_start: 0.3312 (ptp) cc_final: 0.2749 (mtt) REVERT: A 4108 MET cc_start: 0.7852 (mtp) cc_final: 0.7352 (mmt) outliers start: 60 outliers final: 29 residues processed: 297 average time/residue: 1.3804 time to fit residues: 489.8243 Evaluate side-chains 273 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 239 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2122 LEU Chi-restraints excluded: chain A residue 2185 MET Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2392 VAL Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2501 LEU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3451 LEU Chi-restraints excluded: chain A residue 3667 LEU Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 0.0170 chunk 215 optimal weight: 3.9990 chunk 346 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 240 optimal weight: 0.7980 chunk 363 optimal weight: 3.9990 chunk 334 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 223 optimal weight: 0.5980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2787 HIS A3104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29629 Z= 0.187 Angle : 0.632 12.364 40072 Z= 0.311 Chirality : 0.040 0.253 4565 Planarity : 0.004 0.050 5084 Dihedral : 4.582 25.884 3943 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.89 % Favored : 93.06 % Rotamer: Outliers : 1.44 % Allowed : 19.07 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3602 helix: 0.65 (0.11), residues: 2372 sheet: -1.00 (0.69), residues: 60 loop : -2.07 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A3588 HIS 0.009 0.001 HIS A 334 PHE 0.026 0.001 PHE A1805 TYR 0.022 0.001 TYR A3540 ARG 0.008 0.000 ARG A2522 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 248 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.4184 (OUTLIER) cc_final: 0.3617 (mm) REVERT: A 144 MET cc_start: 0.2701 (OUTLIER) cc_final: 0.1419 (pmm) REVERT: A 395 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8061 (ttp) REVERT: A 1369 MET cc_start: 0.7458 (mpt) cc_final: 0.7144 (mmt) REVERT: A 2185 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7341 (tpt) REVERT: A 2307 MET cc_start: 0.7305 (mpp) cc_final: 0.6249 (mpt) REVERT: A 2443 MET cc_start: 0.7796 (ttm) cc_final: 0.7537 (ttm) REVERT: A 3159 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6645 (ptp90) REVERT: A 3609 MET cc_start: 0.3246 (ptp) cc_final: 0.2706 (mtt) REVERT: A 4108 MET cc_start: 0.8015 (mtp) cc_final: 0.7712 (mmt) outliers start: 46 outliers final: 27 residues processed: 279 average time/residue: 1.3889 time to fit residues: 467.3265 Evaluate side-chains 269 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 2103 HIS Chi-restraints excluded: chain A residue 2185 MET Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2321 GLU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2501 LEU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3451 LEU Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3898 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3972 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 9.9990 chunk 230 optimal weight: 0.0270 chunk 308 optimal weight: 0.6980 chunk 88 optimal weight: 0.0670 chunk 266 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 290 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2787 HIS A3104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.184090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.144652 restraints weight = 44493.203| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.22 r_work: 0.3784 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29629 Z= 0.169 Angle : 0.635 15.677 40072 Z= 0.311 Chirality : 0.040 0.257 4565 Planarity : 0.004 0.048 5084 Dihedral : 4.522 25.976 3943 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.17 % Rotamer: Outliers : 1.41 % Allowed : 19.44 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3602 helix: 0.71 (0.11), residues: 2365 sheet: -1.01 (0.69), residues: 60 loop : -2.01 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.001 TRP A3588 HIS 0.010 0.001 HIS A 334 PHE 0.040 0.001 PHE A2257 TYR 0.024 0.001 TYR A3013 ARG 0.015 0.000 ARG A1420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9165.97 seconds wall clock time: 165 minutes 15.48 seconds (9915.48 seconds total)