Starting phenix.real_space_refine on Tue Feb 20 22:31:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otw_13068/02_2024/7otw_13068_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otw_13068/02_2024/7otw_13068.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otw_13068/02_2024/7otw_13068_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otw_13068/02_2024/7otw_13068_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otw_13068/02_2024/7otw_13068_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otw_13068/02_2024/7otw_13068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otw_13068/02_2024/7otw_13068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otw_13068/02_2024/7otw_13068_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otw_13068/02_2024/7otw_13068_updated.pdb" } resolution = 2.99 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= 0.042 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: 4 Type Number sf(0) Gaussians S 191 5.16 5 C 18627 2.51 5 N 4911 2.21 5 O 5309 1.98 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 159": "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 628": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "A GLU 1093": "OE1" <-> "OE2" Residue "A GLU 1118": "OE1" <-> "OE2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A TYR 1243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "A ARG 1321": "NH1" <-> "NH2" Residue "A GLU 1416": "OE1" <-> "OE2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A ARG 1497": "NH1" <-> "NH2" Residue "A GLU 1516": "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 GLU 2154": "OE1" <-> "OE2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A GLU 2236": "OE1" <-> "OE2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A GLU 2321": "OE1" <-> "OE2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A GLU 2819": "OE1" <-> "OE2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2922": "NH1" <-> "NH2" Residue "A GLU 2925": "OE1" <-> "OE2" Residue "A GLU 3007": "OE1" <-> "OE2" Residue "A GLU 3033": "OE1" <-> "OE2" Residue "A GLU 3137": "OE1" <-> "OE2" Residue "A ARG 3282": "NH1" <-> "NH2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" 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 3427": "OE1" <-> "OE2" Residue "A GLU 3428": "OE1" <-> "OE2" Residue "A GLU 3519": "OE1" <-> "OE2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" 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 GLU 3745": "OE1" <-> "OE2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A GLU 3747": "OE1" <-> "OE2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A PHE 3904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3933": "OE1" <-> "OE2" Residue "A TYR 3981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4008": "OE1" <-> "OE2" Residue "A GLU 4030": "OE1" <-> "OE2" Residue "A GLU 4069": "OE1" <-> "OE2" Residue "A ARG 4082": "NH1" <-> "NH2" Residue "A GLU 4093": "OE1" <-> "OE2" Residue "A GLU 4100": "OE1" <-> "OE2" Residue "A ARG 4119": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29038 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 29038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3657, 29038 Unusual residues: {'MBW': 1} Classifications: {'peptide': 3656, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 158, 'TRANS': 3497, None: 1} Not linked: pdbres="UNK A6020 " pdbres="MBW A6101 " Chain breaks: 17 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 190 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': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 137 Time building chain proxies: 15.16, per 1000 atoms: 0.52 Number of scatterers: 29038 At special positions: 0 Unit cell: (125.184, 152.568, 183.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 191 16.00 O 5309 8.00 N 4911 7.00 C 18627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.07 Conformation dependent library (CDL) restraints added in 6.0 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: 182 helices and 3 sheets defined 63.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.04 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 5.289A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 Processing helix chain 'A' and resid 50 through 72 removed outlier: 4.423A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 Processing helix chain 'A' and resid 104 through 117 removed outlier: 4.230A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 removed outlier: 3.612A pdb=" N LEU A 135 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 137 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 141 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.841A pdb=" N LEU A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.998A pdb=" N LEU A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 182 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 removed outlier: 4.178A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.833A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.918A pdb=" N ASN A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 258 through 261 No H-bonds generated for 'chain 'A' and resid 258 through 261' 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 291 through 302 removed outlier: 4.662A pdb=" N VAL A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 329 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 407 through 423 Proline residue: A 411 - end of helix removed outlier: 3.667A pdb=" N LEU A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR A 423 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 446 Proline residue: A 433 - end of helix removed outlier: 3.640A pdb=" N PHE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.781A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 492 removed outlier: 4.188A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 removed outlier: 4.284A pdb=" N ASP A 529 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.678A pdb=" N ALA A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 578 Processing helix chain 'A' and resid 617 through 633 removed outlier: 3.635A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 3.990A 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: 5.592A pdb=" N TYR A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 678 removed outlier: 3.849A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 720 removed outlier: 3.639A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 738 through 743 removed outlier: 4.106A pdb=" N LEU A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 760 Proline residue: A 750 - end of helix removed outlier: 3.905A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 779 Processing helix chain 'A' and resid 782 through 800 Proline residue: A 787 - end of helix removed outlier: 4.737A pdb=" N LYS A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP A 791 " --> pdb=" O PRO A 787 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 3.930A pdb=" N ASP A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR A 799 " --> pdb=" O CYS A 795 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 849 through 861 Processing helix chain 'A' and resid 867 through 876 removed outlier: 3.591A pdb=" N LEU A 871 " --> pdb=" O LYS A 868 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL A 873 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 874 " --> pdb=" O LEU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 908 through 920 Proline residue: A 912 - end of helix removed outlier: 3.769A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 946 Processing helix chain 'A' and resid 959 through 973 removed outlier: 4.008A 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 1011 No H-bonds generated for 'chain 'A' and resid 1008 through 1011' Processing helix chain 'A' and resid 1024 through 1042 Processing helix chain 'A' and resid 1046 through 1051 removed outlier: 3.919A pdb=" N GLU A1050 " --> pdb=" O PRO A1046 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1051' Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1072 through 1085 removed outlier: 3.707A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1116 removed outlier: 5.373A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 5.346A 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 1175 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 1218 through 1225 Processing helix chain 'A' and resid 1251 through 1272 removed outlier: 3.538A pdb=" N ASN A1268 " --> pdb=" O GLU A1265 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A1269 " --> pdb=" O CYS A1266 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A1271 " --> pdb=" O ASN A1268 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY A1272 " --> pdb=" O THR A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1299 removed outlier: 4.068A pdb=" N GLU A1299 " --> pdb=" O ALA A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1350 removed outlier: 4.274A pdb=" N GLU A1328 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A1332 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1358 Processing helix chain 'A' and resid 1365 through 1382 removed outlier: 4.453A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Proline residue: A1379 - end of helix removed outlier: 4.697A 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: 3.813A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1420 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 1485 removed outlier: 3.786A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1491 No H-bonds generated for 'chain 'A' and resid 1489 through 1491' Processing helix chain 'A' and resid 1507 through 1520 Processing helix chain 'A' and resid 1525 through 1532 removed outlier: 3.656A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1573 removed outlier: 6.342A pdb=" N GLU A1565 " --> pdb=" O SER A1561 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR A1566 " --> pdb=" O LEU A1562 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1585 removed outlier: 3.686A 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 1632 removed outlier: 5.364A pdb=" N LYS A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS A1628 " --> pdb=" O GLN A1624 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N CYS A1629 " --> pdb=" O HIS A1625 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP A1630 " --> pdb=" O TRP A1626 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SER A1631 " --> pdb=" O LYS A1627 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TRP A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1655 Processing helix chain 'A' and resid 1668 through 1680 Processing helix chain 'A' and resid 1686 through 1699 removed outlier: 3.558A pdb=" N THR A1694 " --> pdb=" O GLY A1690 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A1695 " --> pdb=" O GLN A1691 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A1696 " --> pdb=" O ALA A1692 " (cutoff:3.500A) Proline residue: A1697 - end of helix 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 1766 Processing helix chain 'A' and resid 1775 through 1787 removed outlier: 3.584A 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 1813 through 1822 removed outlier: 3.835A pdb=" N SER A1818 " --> pdb=" O PHE A1814 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1828 Processing helix chain 'A' and resid 1835 through 1844 Processing helix chain 'A' and resid 1847 through 1852 removed outlier: 3.665A pdb=" N LEU A1851 " --> pdb=" O ALA A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1881 Processing helix chain 'A' and resid 1912 through 1923 removed outlier: 3.913A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1955 Processing helix chain 'A' and resid 2094 through 2104 Processing helix chain 'A' and resid 2124 through 2134 removed outlier: 3.826A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2140 through 2152 Processing helix chain 'A' and resid 2154 through 2171 removed outlier: 3.600A pdb=" N ARG A2158 " --> pdb=" O GLU A2154 " (cutoff:3.500A) Proline residue: A2159 - end of helix removed outlier: 5.420A pdb=" N LYS A2162 " --> pdb=" O ARG A2158 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N HIS A2163 " --> pdb=" O PRO A2159 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (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 2222 Processing helix chain 'A' and resid 2228 through 2244 Processing helix chain 'A' and resid 2246 through 2248 No H-bonds generated for 'chain 'A' and resid 2246 through 2248' Processing helix chain 'A' and resid 2255 through 2260 Processing helix chain 'A' and resid 2268 through 2282 removed outlier: 3.517A pdb=" N SER A2271 " --> pdb=" O LYS A2268 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2308 removed outlier: 3.603A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N MET A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2330 removed outlier: 3.508A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2356 removed outlier: 4.022A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR A2355 " --> pdb=" O GLN A2351 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A2356 " --> pdb=" O HIS A2352 " (cutoff:3.500A) Processing helix chain 'A' and resid 2359 through 2370 removed outlier: 4.067A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2388 removed outlier: 3.683A pdb=" N PHE A2378 " --> pdb=" O ALA A2375 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET A2379 " --> pdb=" O ASP A2376 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASN A2380 " --> pdb=" O ARG A2377 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A2386 " --> pdb=" O PHE A2383 " (cutoff:3.500A) 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 2425 Processing helix chain 'A' and resid 2429 through 2445 Proline residue: A2444 - end of helix Processing helix chain 'A' and resid 2448 through 2456 removed outlier: 3.767A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Processing helix chain 'A' and resid 2470 through 2483 Processing helix chain 'A' and resid 2497 through 2511 removed outlier: 3.895A pdb=" N LEU A2510 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 4.642A 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: 3.889A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2558 through 2565 removed outlier: 4.436A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2798 removed outlier: 4.945A 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 2823 removed outlier: 4.233A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A2822 " --> pdb=" O LYS A2818 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A2823 " --> pdb=" O GLU A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2826 through 2845 Processing helix chain 'A' and resid 2852 through 2864 removed outlier: 3.710A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) Processing helix chain 'A' and resid 2873 through 2883 Processing helix chain 'A' and resid 2886 through 2899 Processing helix chain 'A' and resid 2918 through 2932 removed outlier: 3.631A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2945 Processing helix chain 'A' and resid 2952 through 2962 removed outlier: 3.567A pdb=" N ALA A2956 " --> pdb=" O ILE A2952 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2965 through 2976 Processing helix chain 'A' and resid 2988 through 3004 removed outlier: 4.049A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A3000 " --> pdb=" O LEU A2996 " (cutoff:3.500A) Processing helix chain 'A' and resid 3008 through 3012 Processing helix chain 'A' and resid 3041 through 3053 Processing helix chain 'A' and resid 3060 through 3070 removed outlier: 3.514A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3075 through 3081 Processing helix chain 'A' and resid 3083 through 3093 removed outlier: 3.637A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3115 Processing helix chain 'A' and resid 3122 through 3131 removed outlier: 3.538A pdb=" N THR A3127 " --> pdb=" O GLN A3123 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A3128 " --> pdb=" O SER A3124 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) Processing helix chain 'A' and resid 3133 through 3145 removed outlier: 3.750A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3166 removed outlier: 3.675A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3176 through 3195 removed outlier: 3.869A pdb=" N GLU A3195 " --> pdb=" O SER A3191 " (cutoff:3.500A) Processing helix chain 'A' and resid 3232 through 3248 removed outlier: 3.858A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A3243 " --> pdb=" O LYS A3239 " (cutoff:3.500A) Processing helix chain 'A' and resid 3254 through 3261 Processing helix chain 'A' and resid 3272 through 3286 removed outlier: 4.112A pdb=" N ARG A3282 " --> pdb=" O GLN A3278 " (cutoff:3.500A) Processing helix chain 'A' and resid 3294 through 3306 Processing helix chain 'A' and resid 3319 through 3343 removed outlier: 6.105A pdb=" N ARG A3324 " --> pdb=" O ILE A3320 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASP A3325 " --> pdb=" O LEU A3321 " (cutoff:3.500A) Processing helix chain 'A' and resid 3346 through 3351 removed outlier: 3.691A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A3351 " --> pdb=" O LEU A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3354 through 3363 removed outlier: 4.374A pdb=" N ILE A3359 " --> pdb=" O LYS A3355 " (cutoff:3.500A) removed outlier: 3.599A 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 3407 through 3429 Processing helix chain 'A' and resid 3442 through 3455 Processing helix chain 'A' and resid 3459 through 3473 Proline residue: A3466 - end of helix removed outlier: 3.896A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN A3470 " --> pdb=" O PRO A3466 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3481 through 3489 removed outlier: 4.119A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3505 removed outlier: 4.026A pdb=" N ILE A3499 " --> pdb=" O ILE A3496 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER A3500 " --> pdb=" O SER A3497 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL A3503 " --> pdb=" O SER A3500 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3524 removed outlier: 3.502A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3530 through 3538 removed outlier: 3.669A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3562 removed outlier: 3.824A pdb=" N PHE A3554 " --> pdb=" O LYS A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3578 removed outlier: 3.928A pdb=" N GLN A3577 " --> pdb=" O ASN A3573 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A3578 " --> pdb=" O ALA A3574 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3593 Processing helix chain 'A' and resid 3605 through 3614 removed outlier: 3.787A pdb=" N LYS A3608 " --> pdb=" O ASN A3605 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A3609 " --> pdb=" O ILE A3606 " (cutoff:3.500A) Processing helix chain 'A' and resid 3627 through 3635 removed outlier: 3.763A 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 3650 through 3652 No H-bonds generated for 'chain 'A' and resid 3650 through 3652' Processing helix chain 'A' and resid 3658 through 3672 removed outlier: 3.579A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A3672 " --> pdb=" O LEU A3668 " (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 3687 through 3689 No H-bonds generated for 'chain 'A' and resid 3687 through 3689' Processing helix chain 'A' and resid 3759 through 3777 Processing helix chain 'A' and resid 3780 through 3783 No H-bonds generated for 'chain 'A' and resid 3780 through 3783' Processing helix chain 'A' and resid 3812 through 3817 Processing helix chain 'A' and resid 3822 through 3829 Processing helix chain 'A' and resid 3835 through 3845 removed outlier: 4.017A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3854 through 3861 Processing helix chain 'A' and resid 3864 through 3874 Processing helix chain 'A' and resid 3882 through 3889 Processing helix chain 'A' and resid 3894 through 3917 removed outlier: 3.744A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) 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 3968 No H-bonds generated for 'chain 'A' and resid 3965 through 3968' Processing helix chain 'A' and resid 3979 through 3993 Processing helix chain 'A' and resid 3995 through 4006 Processing helix chain 'A' and resid 4013 through 4021 Processing helix chain 'A' and resid 4040 through 4052 removed outlier: 3.628A pdb=" N ILE A4044 " --> pdb=" O PRO A4040 " (cutoff:3.500A) removed outlier: 3.508A 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 4072 through 4082 removed outlier: 4.414A pdb=" N ARG A4075 " --> pdb=" O PRO A4072 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A4082 " --> pdb=" O ALA A4079 " (cutoff:3.500A) Processing helix chain 'A' and resid 4100 through 4112 removed outlier: 3.650A pdb=" N LEU A4107 " --> pdb=" O GLN A4103 " (cutoff:3.500A) Processing helix chain 'A' and resid 4114 through 4117 No H-bonds generated for 'chain 'A' and resid 4114 through 4117' Processing helix chain 'A' and resid 4122 through 4124 No H-bonds generated for 'chain 'A' and resid 4122 through 4124' Processing helix chain 'A' and resid 6003 through 6009 removed outlier: 3.700A pdb=" N UNK A6008 " --> pdb=" O UNK A6004 " (cutoff:3.500A) 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 3739 through 3742 removed outlier: 3.677A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 3809 through 3811 1363 hydrogen bonds defined for protein. 3753 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: 14.35 Time building geometry restraints manager: 12.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5577 1.32 - 1.45: 6866 1.45 - 1.57: 16891 1.57 - 1.69: 1 1.69 - 1.81: 298 Bond restraints: 29633 Sorted by residual: bond pdb=" C14 MBW A6101 " pdb=" C9 MBW A6101 " ideal model delta sigma weight residual 1.355 1.476 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C7 MBW A6101 " pdb=" N1 MBW A6101 " ideal model delta sigma weight residual 1.483 1.388 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" N MBW A6101 " pdb=" C17 MBW A6101 " ideal model delta sigma weight residual 1.483 1.395 0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C9 MBW A6101 " pdb=" N3 MBW A6101 " ideal model delta sigma weight residual 1.454 1.369 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C8 MBW A6101 " pdb=" N3 MBW A6101 " ideal model delta sigma weight residual 1.453 1.386 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 29628 not shown) Histogram of bond angle deviations from ideal: 96.99 - 105.15: 574 105.15 - 113.31: 16581 113.31 - 121.48: 16652 121.48 - 129.64: 6068 129.64 - 137.80: 202 Bond angle restraints: 40077 Sorted by residual: angle pdb=" N LYS A3455 " pdb=" CA LYS A3455 " pdb=" C LYS A3455 " ideal model delta sigma weight residual 111.36 103.46 7.90 1.09e+00 8.42e-01 5.25e+01 angle pdb=" N ILE A4028 " pdb=" CA ILE A4028 " pdb=" C ILE A4028 " ideal model delta sigma weight residual 113.71 106.90 6.81 9.50e-01 1.11e+00 5.14e+01 angle pdb=" C13 MBW A6101 " pdb=" C14 MBW A6101 " pdb=" C15 MBW A6101 " ideal model delta sigma weight residual 101.94 121.89 -19.95 3.00e+00 1.11e-01 4.42e+01 angle pdb=" N ILE A3231 " pdb=" CA ILE A3231 " pdb=" C ILE A3231 " ideal model delta sigma weight residual 112.96 107.14 5.82 1.00e+00 1.00e+00 3.39e+01 angle pdb=" C15 MBW A6101 " pdb=" C14 MBW A6101 " pdb=" C9 MBW A6101 " ideal model delta sigma weight residual 137.61 120.49 17.12 3.00e+00 1.11e-01 3.26e+01 ... (remaining 40072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.92: 17371 27.92 - 55.85: 649 55.85 - 83.77: 52 83.77 - 111.69: 1 111.69 - 139.62: 2 Dihedral angle restraints: 18075 sinusoidal: 7318 harmonic: 10757 Sorted by residual: dihedral pdb=" CA GLN A3037 " pdb=" C GLN A3037 " pdb=" N GLU A3038 " pdb=" CA GLU A3038 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+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 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLY A1016 " pdb=" C GLY A1016 " pdb=" N ILE A1017 " pdb=" CA ILE A1017 " ideal model delta harmonic sigma weight residual -180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 18072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3876 0.072 - 0.144: 637 0.144 - 0.216: 44 0.216 - 0.287: 6 0.287 - 0.359: 2 Chirality restraints: 4565 Sorted by residual: chirality pdb=" CA PHE A3694 " pdb=" N PHE A3694 " pdb=" C PHE A3694 " pdb=" CB PHE A3694 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 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 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CG LEU A1010 " pdb=" CB LEU A1010 " pdb=" CD1 LEU A1010 " pdb=" CD2 LEU A1010 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4562 not shown) Planarity restraints: 5085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A4008 " -0.059 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO A4009 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A4009 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A4009 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 697 " 0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 698 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 698 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 698 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A3710 " -0.053 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO A3711 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A3711 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A3711 " -0.045 5.00e-02 4.00e+02 ... (remaining 5082 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 59 2.32 - 2.96: 14903 2.96 - 3.61: 45312 3.61 - 4.25: 68517 4.25 - 4.90: 113164 Nonbonded interactions: 241955 Sorted by model distance: nonbonded pdb=" CE2 TYR A 721 " pdb=" SG CYS A 729 " model vdw 1.672 3.700 nonbonded pdb=" O SER A3288 " pdb=" NH1 ARG A3289 " model vdw 2.061 2.520 nonbonded pdb=" O ALA A1078 " pdb=" OH TYR A1107 " model vdw 2.160 2.440 nonbonded pdb=" OE2 GLU A3137 " pdb=" NH2 ARG A3186 " model vdw 2.176 2.520 nonbonded pdb=" OH TYR A 423 " pdb=" O ALA A 549 " model vdw 2.178 2.440 ... (remaining 241950 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: 1.400 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: 5.710 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 80.600 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.009 0.122 29633 Z= 0.587 Angle : 0.965 19.946 40077 Z= 0.512 Chirality : 0.053 0.359 4565 Planarity : 0.006 0.087 5085 Dihedral : 14.262 139.615 11063 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.97 % Favored : 89.87 % Rotamer: Outliers : 0.28 % Allowed : 0.72 % Favored : 99.00 % 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: -2.30 (0.13), residues: 3602 helix: -0.75 (0.10), residues: 2384 sheet: -2.69 (0.84), residues: 37 loop : -2.98 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A4127 HIS 0.011 0.002 HIS A 484 PHE 0.052 0.003 PHE A3571 TYR 0.032 0.003 TYR A3540 ARG 0.020 0.001 ARG A3741 *********************** 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 234 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 225 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3044 MET cc_start: 0.6667 (tmm) cc_final: 0.6285 (ttp) outliers start: 9 outliers final: 3 residues processed: 232 average time/residue: 1.5180 time to fit residues: 411.5741 Evaluate side-chains 168 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1751 GLU Chi-restraints excluded: chain A residue 1757 MET Chi-restraints excluded: chain A residue 3693 GLU 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: 1.9990 chunk 153 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 186 optimal weight: 30.0000 chunk 147 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 173 optimal weight: 30.0000 chunk 212 optimal weight: 0.0770 chunk 331 optimal weight: 0.8980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN ** A1568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 ASN A2305 ASN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3004 HIS ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29633 Z= 0.209 Angle : 0.694 12.040 40077 Z= 0.348 Chirality : 0.042 0.179 4565 Planarity : 0.005 0.059 5085 Dihedral : 6.695 132.813 3934 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 0.78 % Allowed : 8.45 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3602 helix: -0.16 (0.11), residues: 2375 sheet: -2.11 (0.89), residues: 38 loop : -2.50 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A3031 HIS 0.011 0.001 HIS A2105 PHE 0.026 0.002 PHE A3542 TYR 0.040 0.002 TYR A2572 ARG 0.007 0.000 ARG A1938 *********************** 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 197 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2443 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7789 (tmm) REVERT: A 3044 MET cc_start: 0.6524 (tmm) cc_final: 0.6308 (ttp) outliers start: 25 outliers final: 7 residues processed: 182 average time/residue: 1.4880 time to fit residues: 319.8426 Evaluate side-chains 159 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3712 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 225 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 358 optimal weight: 0.0670 chunk 295 optimal weight: 0.9980 chunk 329 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 266 optimal weight: 0.8980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3422 GLN A3564 GLN A3643 HIS A4042 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 0.044 29633 Z= 0.173 Angle : 0.649 12.439 40077 Z= 0.320 Chirality : 0.040 0.175 4565 Planarity : 0.004 0.056 5085 Dihedral : 5.745 131.838 3925 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.59 % Rotamer: Outliers : 1.25 % Allowed : 10.89 % Favored : 87.86 % 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: -0.95 (0.14), residues: 3602 helix: 0.26 (0.11), residues: 2352 sheet: -2.15 (0.86), residues: 40 loop : -2.33 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 300 HIS 0.008 0.001 HIS A2105 PHE 0.025 0.001 PHE A1923 TYR 0.043 0.001 TYR A1881 ARG 0.006 0.000 ARG A1783 *********************** 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 204 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 3.358 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 96 MET cc_start: 0.4593 (mmp) cc_final: 0.3068 (ppp) REVERT: A 238 MET cc_start: 0.3229 (mmp) cc_final: 0.2666 (mtp) outliers start: 40 outliers final: 8 residues processed: 184 average time/residue: 1.5239 time to fit residues: 331.6771 Evaluate side-chains 156 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 1219 PHE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 3454 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 328 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 158 optimal weight: 0.0970 chunk 222 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 315 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN A1568 ASN ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 ASN A2283 ASN ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29633 Z= 0.245 Angle : 0.657 13.317 40077 Z= 0.323 Chirality : 0.041 0.182 4565 Planarity : 0.004 0.051 5085 Dihedral : 5.562 133.908 3925 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.70 % Rotamer: Outliers : 1.72 % Allowed : 13.02 % Favored : 85.26 % 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: -0.76 (0.15), residues: 3602 helix: 0.40 (0.11), residues: 2359 sheet: -2.09 (0.87), residues: 40 loop : -2.25 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP A 300 HIS 0.006 0.001 HIS A2105 PHE 0.033 0.001 PHE A2231 TYR 0.028 0.001 TYR A1881 ARG 0.004 0.000 ARG A 82 *********************** 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 217 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 162 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 875 SER cc_start: 0.6418 (p) cc_final: 0.6173 (t) outliers start: 55 outliers final: 12 residues processed: 200 average time/residue: 1.4293 time to fit residues: 341.7697 Evaluate side-chains 160 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 MET Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3454 LEU 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: 5.9990 chunk 5 optimal weight: 8.9990 chunk 262 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 301 optimal weight: 0.5980 chunk 243 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 180 optimal weight: 30.0000 chunk 316 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1568 ASN ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2481 HIS A3430 ASN A3664 ASN A3969 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29633 Z= 0.307 Angle : 0.691 15.218 40077 Z= 0.338 Chirality : 0.042 0.198 4565 Planarity : 0.004 0.049 5085 Dihedral : 5.506 138.049 3925 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.61 % Favored : 92.34 % Rotamer: Outliers : 1.47 % Allowed : 14.74 % Favored : 83.79 % 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: -0.67 (0.15), residues: 3602 helix: 0.48 (0.11), residues: 2347 sheet: -2.08 (0.87), residues: 40 loop : -2.21 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP A 300 HIS 0.006 0.001 HIS A2105 PHE 0.027 0.001 PHE A2231 TYR 0.027 0.002 TYR A1881 ARG 0.004 0.000 ARG A 82 *********************** 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 198 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 3.475 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 238 MET cc_start: 0.3660 (OUTLIER) cc_final: 0.3154 (mtp) REVERT: A 875 SER cc_start: 0.6446 (p) cc_final: 0.6200 (t) REVERT: A 2443 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7925 (tmm) REVERT: A 3176 MET cc_start: 0.7729 (mmt) cc_final: 0.7347 (mmt) outliers start: 47 outliers final: 17 residues processed: 183 average time/residue: 1.4306 time to fit residues: 312.4491 Evaluate side-chains 164 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1512 SER Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3692 VAL Chi-restraints excluded: chain A residue 3811 THR Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 0.5980 chunk 317 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 353 optimal weight: 7.9990 chunk 293 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2305 ASN ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2787 HIS ** A4088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29633 Z= 0.275 Angle : 0.685 11.177 40077 Z= 0.334 Chirality : 0.041 0.197 4565 Planarity : 0.004 0.049 5085 Dihedral : 5.430 138.697 3925 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.72 % Favored : 92.23 % Rotamer: Outliers : 2.07 % Allowed : 15.08 % Favored : 82.85 % 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: -0.54 (0.15), residues: 3602 helix: 0.58 (0.11), residues: 2331 sheet: -2.02 (0.87), residues: 40 loop : -2.12 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP A 300 HIS 0.007 0.001 HIS A2105 PHE 0.024 0.001 PHE A2231 TYR 0.020 0.002 TYR A2184 ARG 0.004 0.000 ARG A 82 *********************** 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 218 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 152 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.4512 (mmp) cc_final: 0.3259 (pp-130) REVERT: A 238 MET cc_start: 0.3763 (OUTLIER) cc_final: 0.3209 (mtm) outliers start: 66 outliers final: 24 residues processed: 200 average time/residue: 1.3707 time to fit residues: 327.6569 Evaluate side-chains 168 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1512 SER Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 2486 ASP Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3445 LEU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3692 VAL Chi-restraints excluded: chain A residue 4008 GLU Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 201 optimal weight: 10.0000 chunk 257 optimal weight: 0.5980 chunk 199 optimal weight: 6.9990 chunk 297 optimal weight: 0.5980 chunk 197 optimal weight: 20.0000 chunk 351 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29633 Z= 0.171 Angle : 0.675 19.298 40077 Z= 0.323 Chirality : 0.040 0.191 4565 Planarity : 0.004 0.048 5085 Dihedral : 5.288 136.171 3925 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.94 % Favored : 93.00 % Rotamer: Outliers : 1.38 % Allowed : 16.49 % Favored : 82.13 % 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: 0.68 (0.11), residues: 2334 sheet: -1.92 (0.86), residues: 40 loop : -2.09 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A 300 HIS 0.005 0.001 HIS A2105 PHE 0.022 0.001 PHE A1923 TYR 0.025 0.001 TYR A1881 ARG 0.004 0.000 ARG A2377 *********************** 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 195 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 151 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.4170 (mmp) cc_final: 0.3273 (pp-130) REVERT: A 238 MET cc_start: 0.3789 (OUTLIER) cc_final: 0.3258 (mtm) REVERT: A 2443 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7786 (tmm) REVERT: A 3176 MET cc_start: 0.7547 (mmt) cc_final: 0.7224 (mmt) outliers start: 44 outliers final: 21 residues processed: 185 average time/residue: 1.4009 time to fit residues: 309.9646 Evaluate side-chains 169 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 1219 PHE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 2094 MET Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 4008 GLU Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 210 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29633 Z= 0.199 Angle : 0.688 16.291 40077 Z= 0.330 Chirality : 0.041 0.205 4565 Planarity : 0.004 0.049 5085 Dihedral : 5.242 136.507 3925 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.92 % Rotamer: Outliers : 0.97 % Allowed : 17.12 % Favored : 81.91 % 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: 0.69 (0.11), residues: 2338 sheet: -1.92 (0.85), residues: 40 loop : -2.07 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP A 300 HIS 0.005 0.001 HIS A2105 PHE 0.023 0.001 PHE A1819 TYR 0.028 0.001 TYR A2299 ARG 0.004 0.000 ARG A2377 *********************** 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 184 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.4001 (mmp) cc_final: 0.3266 (pp-130) REVERT: A 238 MET cc_start: 0.3820 (OUTLIER) cc_final: 0.3282 (mtm) REVERT: A 2443 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7907 (tmm) outliers start: 31 outliers final: 20 residues processed: 177 average time/residue: 1.5328 time to fit residues: 321.3406 Evaluate side-chains 167 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 1219 PHE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 4008 GLU Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 0.0980 chunk 337 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 chunk 327 optimal weight: 0.9990 chunk 336 optimal weight: 0.9980 chunk 197 optimal weight: 0.0980 chunk 142 optimal weight: 3.9990 chunk 257 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 310 optimal weight: 4.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 ASN ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29633 Z= 0.170 Angle : 0.694 16.214 40077 Z= 0.329 Chirality : 0.040 0.200 4565 Planarity : 0.004 0.047 5085 Dihedral : 5.165 135.407 3925 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.83 % Favored : 93.11 % Rotamer: Outliers : 0.78 % Allowed : 17.71 % Favored : 81.51 % 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: -0.33 (0.15), residues: 3602 helix: 0.75 (0.11), residues: 2333 sheet: -1.78 (0.82), residues: 40 loop : -2.07 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP A 300 HIS 0.004 0.001 HIS A2105 PHE 0.032 0.001 PHE A1219 TYR 0.040 0.001 TYR A2253 ARG 0.018 0.000 ARG A1938 *********************** 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 178 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.3859 (mmp) cc_final: 0.3258 (pp-130) REVERT: A 238 MET cc_start: 0.3849 (OUTLIER) cc_final: 0.3314 (mtm) REVERT: A 2443 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7881 (tmm) outliers start: 25 outliers final: 18 residues processed: 174 average time/residue: 1.5198 time to fit residues: 314.2076 Evaluate side-chains 166 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3155 VAL Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 346 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 164 optimal weight: 0.2980 chunk 240 optimal weight: 0.9990 chunk 363 optimal weight: 5.9990 chunk 334 optimal weight: 0.6980 chunk 289 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 223 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29633 Z= 0.171 Angle : 0.698 15.968 40077 Z= 0.332 Chirality : 0.040 0.188 4565 Planarity : 0.004 0.047 5085 Dihedral : 5.116 134.873 3925 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 0.72 % Allowed : 17.87 % Favored : 81.41 % 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: -0.29 (0.15), residues: 3602 helix: 0.79 (0.11), residues: 2326 sheet: -1.66 (0.82), residues: 40 loop : -2.05 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 300 HIS 0.004 0.001 HIS A3743 PHE 0.020 0.001 PHE A1923 TYR 0.033 0.001 TYR A2253 ARG 0.013 0.000 ARG A1938 ********************** 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 173 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.3717 (mmp) cc_final: 0.3198 (pp-130) REVERT: A 238 MET cc_start: 0.3843 (OUTLIER) cc_final: 0.3298 (mtm) REVERT: A 785 MET cc_start: 0.6227 (mmm) cc_final: 0.5966 (mmm) REVERT: A 2443 MET cc_start: 0.8053 (tmm) cc_final: 0.7792 (tmm) outliers start: 23 outliers final: 17 residues processed: 170 average time/residue: 1.6219 time to fit residues: 326.3735 Evaluate side-chains 165 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1606 ARG Chi-restraints excluded: chain A residue 1654 GLN Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1889 VAL Chi-restraints excluded: chain A residue 3155 VAL Chi-restraints excluded: chain A residue 3361 GLU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 4008 GLU Chi-restraints excluded: chain A residue 4031 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 20.0000 chunk 230 optimal weight: 0.8980 chunk 308 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 266 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 297 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4088 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.095228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.062799 restraints weight = 114265.817| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.38 r_work: 0.3127 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29633 Z= 0.177 Angle : 0.709 15.593 40077 Z= 0.337 Chirality : 0.040 0.194 4565 Planarity : 0.004 0.048 5085 Dihedral : 5.063 134.028 3925 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 0.91 % Allowed : 17.93 % Favored : 81.16 % 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: -0.26 (0.15), residues: 3602 helix: 0.82 (0.11), residues: 2329 sheet: -1.51 (0.82), residues: 40 loop : -2.08 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A3031 HIS 0.005 0.001 HIS A2105 PHE 0.042 0.001 PHE A1605 TYR 0.031 0.001 TYR A2253 ARG 0.012 0.000 ARG A1938 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7682.35 seconds wall clock time: 139 minutes 58.00 seconds (8398.00 seconds total)