Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 13:25:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otm_13062/08_2023/7otm_13062_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otm_13062/08_2023/7otm_13062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otm_13062/08_2023/7otm_13062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otm_13062/08_2023/7otm_13062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otm_13062/08_2023/7otm_13062_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otm_13062/08_2023/7otm_13062_updated.pdb" } resolution = 3.33 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= 0.003 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 30 atoms to isotropic. 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 192 5.16 5 C 18634 2.51 5 N 4904 2.21 5 O 5310 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 176": "OE1" <-> "OE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "A GLU 1102": "OE1" <-> "OE2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A GLU 1215": "OE1" <-> "OE2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "A ARG 1321": "NH1" <-> "NH2" Residue "A GLU 1378": "OE1" <-> "OE2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A ARG 1497": "NH1" <-> "NH2" Residue "A GLU 1516": "OE1" <-> "OE2" Residue "A PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1565": "OE1" <-> "OE2" Residue "A GLU 1570": "OE1" <-> "OE2" Residue "A ARG 1608": "NH1" <-> "NH2" Residue "A GLU 1708": "OE1" <-> "OE2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1837": "NH1" <-> "NH2" Residue "A PHE 1840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1854": "NH1" <-> "NH2" Residue "A GLU 1935": "OE1" <-> "OE2" 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 GLU 2188": "OE1" <-> "OE2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A GLU 2236": "OE1" <-> "OE2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A GLU 2488": "OE1" <-> "OE2" Residue "A GLU 2513": "OE1" <-> "OE2" Residue "A GLU 2551": "OE1" <-> "OE2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2922": "NH1" <-> "NH2" Residue "A GLU 2925": "OE1" <-> "OE2" Residue "A GLU 2946": "OE1" <-> "OE2" Residue "A GLU 2988": "OE1" <-> "OE2" Residue "A GLU 2990": "OE1" <-> "OE2" Residue "A GLU 3007": "OE1" <-> "OE2" Residue "A GLU 3137": "OE1" <-> "OE2" Residue "A ARG 3282": "NH1" <-> "NH2" Residue "A GLU 3295": "OE1" <-> "OE2" Residue "A GLU 3309": "OE1" <-> "OE2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3350": "OE1" <-> "OE2" Residue "A ARG 3357": "NH1" <-> "NH2" Residue "A ARG 3358": "NH1" <-> "NH2" Residue "A ARG 3380": "NH1" <-> "NH2" Residue "A GLU 3393": "OE1" <-> "OE2" Residue "A ARG 3425": "NH1" <-> "NH2" Residue "A GLU 3607": "OE1" <-> "OE2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A GLU 3698": "OE1" <-> "OE2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A ARG 3725": "NH1" <-> "NH2" Residue "A ARG 3737": "NH1" <-> "NH2" Residue "A ARG 3741": "NH1" <-> "NH2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A GLU 3756": "OE1" <-> "OE2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A GLU 3807": "OE1" <-> "OE2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A TYR 3981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4008": "OE1" <-> "OE2" Residue "A GLU 4030": "OE1" <-> "OE2" Residue "A ARG 4082": "NH1" <-> "NH2" Residue "A ARG 4119": "NH1" <-> "NH2" Residue "A GLU 4125": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 29040 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 29040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3657, 29040 Unusual residues: {'2R4': 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="2R4 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: 14.18, per 1000 atoms: 0.49 Number of scatterers: 29040 At special positions: 0 Unit cell: (125.184, 152.568, 185.168, 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 192 16.00 O 5310 8.00 N 4904 7.00 C 18634 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: 11.77 Conformation dependent library (CDL) restraints added in 4.6 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: 187 helices and 4 sheets defined 63.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.05 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 4.745A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.681A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 71 removed outlier: 3.517A pdb=" N GLN A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 96 removed outlier: 3.696A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.630A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 145 removed outlier: 5.185A pdb=" N ARG A 142 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU A 143 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET A 144 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 192 through 206 removed outlier: 4.021A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.040A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 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 Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 309 through 329 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 359 through 368 Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'A' and resid 407 through 421 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 430 through 446 Proline residue: A 433 - end of helix removed outlier: 3.558A pdb=" N MET A 441 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 4.222A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 4.202A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.334A pdb=" N ASP A 529 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 534 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.741A 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: 3.713A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 659 removed outlier: 3.877A pdb=" N VAL A 646 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 648 " --> pdb=" O TRP A 645 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 650 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 658 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.600A pdb=" N LYS A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 720 removed outlier: 3.566A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLN A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 735 removed outlier: 3.713A pdb=" N SER A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 removed outlier: 4.265A 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: 4.322A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 779 removed outlier: 3.518A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 801 Proline residue: A 787 - end of helix removed outlier: 4.688A pdb=" N LYS A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASP A 791 " --> pdb=" O PRO A 787 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 3.940A pdb=" N ASP A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLY A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TYR A 799 " --> pdb=" O CYS A 795 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 861 Processing helix chain 'A' and resid 867 through 876 removed outlier: 4.977A pdb=" N VAL A 873 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 3.614A 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 907 through 920 Proline residue: A 912 - end of helix removed outlier: 4.481A pdb=" N THR A 915 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 920 " --> pdb=" O LEU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 946 removed outlier: 3.817A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 973 removed outlier: 4.076A pdb=" N LYS A 963 " --> pdb=" O GLN A 960 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE A 966 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 978 through 995 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1008 through 1015 removed outlier: 3.643A pdb=" N ILE A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1043 removed outlier: 3.512A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1073 through 1085 removed outlier: 3.715A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1116 removed outlier: 3.767A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1145 removed outlier: 6.297A pdb=" N VAL A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER A1144 " --> pdb=" O LYS A1140 " (cutoff:3.500A) 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 1217 through 1225 Processing helix chain 'A' and resid 1234 through 1237 No H-bonds generated for 'chain 'A' and resid 1234 through 1237' Processing helix chain 'A' and resid 1251 through 1272 removed outlier: 3.793A pdb=" N ASN A1268 " --> pdb=" O GLU A1265 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A1272 " --> pdb=" O THR A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1281 No H-bonds generated for 'chain 'A' and resid 1278 through 1281' Processing helix chain 'A' and resid 1289 through 1299 removed outlier: 3.831A pdb=" N GLU A1299 " --> pdb=" O ALA A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1350 removed outlier: 4.564A pdb=" N GLU A1328 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A1332 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.887A pdb=" N LEU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A1360 " --> pdb=" O TRP A1356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1355 through 1360' Processing helix chain 'A' and resid 1365 through 1382 removed outlier: 4.203A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Proline residue: A1379 - end of helix removed outlier: 4.277A 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: 3.550A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1420 removed outlier: 4.119A pdb=" N ASP A1413 " --> pdb=" O PRO A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1434 removed outlier: 4.225A pdb=" N VAL A1434 " --> pdb=" O GLU A1430 " (cutoff:3.500A) 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 1486 removed outlier: 3.723A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1520 Processing helix chain 'A' and resid 1525 through 1532 removed outlier: 3.814A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1562 Processing helix chain 'A' and resid 1564 through 1573 removed outlier: 3.875A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A1570 " --> pdb=" O THR A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1585 removed outlier: 4.503A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1606 Processing helix chain 'A' and resid 1612 through 1632 removed outlier: 4.651A pdb=" N LYS A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS A1628 " --> pdb=" O GLN A1624 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N CYS A1629 " --> pdb=" O HIS A1625 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP A1630 " --> pdb=" O TRP A1626 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER A1631 " --> pdb=" O LYS A1627 " (cutoff:3.500A) removed outlier: 6.045A 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 1679 Processing helix chain 'A' and resid 1686 through 1698 removed outlier: 3.935A pdb=" N THR A1694 " --> pdb=" O GLY A1690 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU A1695 " --> pdb=" O GLN A1691 " (cutoff:3.500A) removed outlier: 4.426A 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 1768 Processing helix chain 'A' and resid 1775 through 1787 removed outlier: 3.849A 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: 4.072A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1828 Processing helix chain 'A' and resid 1835 through 1852 removed outlier: 5.545A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) removed outlier: 3.520A 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 1886 through 1889 No H-bonds generated for 'chain 'A' and resid 1886 through 1889' Processing helix chain 'A' and resid 1911 through 1920 Processing helix chain 'A' and resid 1935 through 1955 Processing helix chain 'A' and resid 2094 through 2106 removed outlier: 3.791A pdb=" N ARG A2106 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2134 removed outlier: 4.211A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A2132 " --> pdb=" O PHE A2128 " (cutoff:3.500A) Processing helix chain 'A' and resid 2140 through 2152 Processing helix chain 'A' and resid 2161 through 2171 removed outlier: 5.521A 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 2221 Processing helix chain 'A' and resid 2228 through 2244 Processing helix chain 'A' and resid 2255 through 2260 Processing helix chain 'A' and resid 2268 through 2283 removed outlier: 4.091A pdb=" N VAL A2272 " --> pdb=" O ASP A2269 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2308 removed outlier: 3.983A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N MET A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2332 removed outlier: 3.571A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) Processing helix chain 'A' and resid 2339 through 2353 removed outlier: 3.670A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2368 Processing helix chain 'A' and resid 2373 through 2377 Processing helix chain 'A' and resid 2379 through 2386 Processing helix chain 'A' and resid 2392 through 2403 Processing helix chain 'A' and resid 2413 through 2417 Processing helix chain 'A' and resid 2420 through 2424 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: 3.637A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2458 through 2461 Processing helix chain 'A' and resid 2470 through 2483 removed outlier: 3.815A pdb=" N ASN A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2511 removed outlier: 4.690A pdb=" N LEU A2510 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 4.554A 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 2541 Processing helix chain 'A' and resid 2543 through 2545 No H-bonds generated for 'chain 'A' and resid 2543 through 2545' Processing helix chain 'A' and resid 2558 through 2568 removed outlier: 4.354A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR A2566 " --> pdb=" O LEU A2562 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A2567 " --> pdb=" O LEU A2563 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N MET A2568 " --> pdb=" O GLU A2564 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2798 removed outlier: 5.221A pdb=" N THR A2792 " --> pdb=" O SER A2789 " (cutoff:3.500A) Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2802 through 2822 removed outlier: 4.021A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS A2822 " --> pdb=" O LYS A2818 " (cutoff:3.500A) Processing helix chain 'A' and resid 2826 through 2845 Processing helix chain 'A' and resid 2852 through 2864 removed outlier: 3.701A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2870 No H-bonds generated for 'chain 'A' and resid 2868 through 2870' Processing helix chain 'A' and resid 2873 through 2882 Processing helix chain 'A' and resid 2886 through 2898 Processing helix chain 'A' and resid 2918 through 2932 removed outlier: 3.639A 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 2951 through 2962 removed outlier: 3.934A pdb=" N SER A2955 " --> pdb=" O ILE A2952 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A2956 " --> pdb=" O THR A2953 " (cutoff:3.500A) Processing helix chain 'A' and resid 2965 through 2976 Processing helix chain 'A' and resid 2988 through 3004 removed outlier: 3.887A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (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: 3.570A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3075 through 3080 Processing helix chain 'A' and resid 3083 through 3093 removed outlier: 3.756A 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 3145 removed outlier: 3.676A pdb=" N THR A3127 " --> pdb=" O GLN A3123 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A3128 " --> pdb=" O SER A3124 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL A3132 " --> pdb=" O LYS A3128 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLN A3133 " --> pdb=" O LEU A3129 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA A3134 " --> pdb=" O GLN A3130 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A3135 " --> pdb=" O SER A3131 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3166 removed outlier: 3.637A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3176 through 3196 removed outlier: 4.270A pdb=" N GLU A3195 " --> pdb=" O SER A3191 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A3196 " --> pdb=" O LYS A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3231 through 3248 removed outlier: 3.955A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) Processing helix chain 'A' and resid 3254 through 3261 Processing helix chain 'A' and resid 3272 through 3286 removed outlier: 3.641A pdb=" N ARG A3282 " --> pdb=" O GLN A3278 " (cutoff:3.500A) Processing helix chain 'A' and resid 3291 through 3306 removed outlier: 4.377A pdb=" N GLU A3295 " --> pdb=" O GLN A3291 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN A3296 " --> pdb=" O GLY A3292 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) Processing helix chain 'A' and resid 3323 through 3343 Processing helix chain 'A' and resid 3346 through 3351 removed outlier: 3.915A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) Processing helix chain 'A' and resid 3354 through 3356 No H-bonds generated for 'chain 'A' and resid 3354 through 3356' Processing helix chain 'A' and resid 3358 through 3363 Processing helix chain 'A' and resid 3370 through 3393 Processing helix chain 'A' and resid 3407 through 3428 Processing helix chain 'A' and resid 3442 through 3454 Processing helix chain 'A' and resid 3459 through 3471 removed outlier: 3.951A pdb=" N LYS A3464 " --> pdb=" O GLU A3460 " (cutoff:3.500A) Proline residue: A3466 - end of helix removed outlier: 3.715A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A3470 " --> pdb=" O PRO A3466 " (cutoff:3.500A) Processing helix chain 'A' and resid 3476 through 3478 No H-bonds generated for 'chain 'A' and resid 3476 through 3478' Processing helix chain 'A' and resid 3481 through 3489 removed outlier: 4.024A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3499 through 3502 No H-bonds generated for 'chain 'A' and resid 3499 through 3502' Processing helix chain 'A' and resid 3515 through 3524 Processing helix chain 'A' and resid 3530 through 3537 Processing helix chain 'A' and resid 3548 through 3562 removed outlier: 3.782A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N PHE A3554 " --> pdb=" O LYS A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3577 removed outlier: 4.005A pdb=" N GLN A3577 " --> pdb=" O ASN A3573 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3593 Processing helix chain 'A' and resid 3606 through 3614 removed outlier: 3.766A pdb=" N MET A3609 " --> pdb=" O ILE A3606 " (cutoff:3.500A) Processing helix chain 'A' and resid 3627 through 3635 removed outlier: 3.837A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 No H-bonds generated for 'chain 'A' and resid 3640 through 3643' Processing helix chain 'A' and resid 3658 through 3670 removed outlier: 4.518A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3681 through 3684 No H-bonds generated for 'chain 'A' and resid 3681 through 3684' Processing helix chain 'A' and resid 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 3819 removed outlier: 4.052A pdb=" N THR A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3822 through 3829 Processing helix chain 'A' and resid 3835 through 3846 removed outlier: 3.989A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3861 removed outlier: 3.833A pdb=" N TYR A3855 " --> pdb=" O VAL A3852 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A3856 " --> pdb=" O GLY A3853 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A3859 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3877 removed outlier: 3.625A pdb=" N SER A3876 " --> pdb=" O ARG A3872 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) Processing helix chain 'A' and resid 3883 through 3889 Processing helix chain 'A' and resid 3894 through 3918 removed outlier: 3.699A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) Processing helix chain 'A' and resid 3925 through 3927 No H-bonds generated for 'chain 'A' and resid 3925 through 3927' Processing helix chain 'A' and resid 3948 through 3951 No H-bonds generated for 'chain 'A' and resid 3948 through 3951' Processing helix chain 'A' and resid 3965 through 3970 Processing helix chain 'A' and resid 3979 through 3993 removed outlier: 3.538A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4006 Processing helix chain 'A' and resid 4013 through 4021 Processing helix chain 'A' and resid 4041 through 4052 removed outlier: 4.244A pdb=" N TYR A4046 " --> pdb=" O GLN A4042 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A4051 " --> pdb=" O ALA A4047 " (cutoff:3.500A) Processing helix chain 'A' and resid 4056 through 4067 removed outlier: 4.049A pdb=" N LEU A4064 " --> pdb=" O THR A4060 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4082 Processing helix chain 'A' and resid 4100 through 4112 Processing helix chain 'A' and resid 4114 through 4119 removed outlier: 4.534A pdb=" N ARG A4119 " --> pdb=" O ASN A4115 " (cutoff:3.500A) 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 6015 removed outlier: 3.559A pdb=" N UNK A6008 " --> pdb=" O UNK A6004 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N UNK A6011 " --> pdb=" O UNK A6007 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N UNK A6014 " --> pdb=" O UNK A6010 " (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 893 through 895 Processing sheet with id= C, first strand: chain 'A' and resid 3736 through 3742 removed outlier: 3.925A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 3809 through 3811 removed outlier: 3.518A pdb=" N VAL A3810 " --> pdb=" O VAL A3930 " (cutoff:3.500A) 1366 hydrogen bonds defined for protein. 3633 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: 12.92 Time building geometry restraints manager: 12.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8384 1.33 - 1.45: 4575 1.45 - 1.57: 16377 1.57 - 1.69: 0 1.69 - 1.81: 300 Bond restraints: 29636 Sorted by residual: bond pdb=" CA PHE A3252 " pdb=" C PHE A3252 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.80e-02 3.09e+03 1.83e+01 bond pdb=" CA ARG A3287 " pdb=" C ARG A3287 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.72e-02 3.38e+03 1.75e+01 bond pdb=" CA THR A3479 " pdb=" C THR A3479 " ideal model delta sigma weight residual 1.523 1.466 0.058 1.80e-02 3.09e+03 1.03e+01 bond pdb=" C02 2R4 A6101 " pdb=" C03 2R4 A6101 " ideal model delta sigma weight residual 1.479 1.418 0.061 2.00e-02 2.50e+03 9.20e+00 bond pdb=" CA VAL A3728 " pdb=" CB VAL A3728 " ideal model delta sigma weight residual 1.540 1.504 0.036 1.36e-02 5.41e+03 7.14e+00 ... (remaining 29631 not shown) Histogram of bond angle deviations from ideal: 92.82 - 101.11: 85 101.11 - 109.41: 2855 109.41 - 117.70: 19011 117.70 - 126.00: 17719 126.00 - 134.29: 411 Bond angle restraints: 40081 Sorted by residual: angle pdb=" C PRO A3735 " pdb=" CA PRO A3735 " pdb=" CB PRO A3735 " ideal model delta sigma weight residual 111.23 123.75 -12.52 1.28e+00 6.10e-01 9.56e+01 angle pdb=" N LEU A2337 " pdb=" CA LEU A2337 " pdb=" C LEU A2337 " ideal model delta sigma weight residual 112.03 120.82 -8.79 1.31e+00 5.83e-01 4.50e+01 angle pdb=" N PRO A3735 " pdb=" CA PRO A3735 " pdb=" C PRO A3735 " ideal model delta sigma weight residual 111.21 101.07 10.14 1.59e+00 3.96e-01 4.07e+01 angle pdb=" N GLY A4024 " pdb=" CA GLY A4024 " pdb=" C GLY A4024 " ideal model delta sigma weight residual 112.50 106.16 6.34 1.16e+00 7.43e-01 2.99e+01 angle pdb=" N ILE A1386 " pdb=" CA ILE A1386 " pdb=" C ILE A1386 " ideal model delta sigma weight residual 112.12 107.55 4.57 8.40e-01 1.42e+00 2.96e+01 ... (remaining 40076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16131 17.98 - 35.96: 1627 35.96 - 53.94: 250 53.94 - 71.93: 45 71.93 - 89.91: 24 Dihedral angle restraints: 18077 sinusoidal: 7320 harmonic: 10757 Sorted by residual: dihedral pdb=" CA GLU A3693 " pdb=" C GLU A3693 " pdb=" N PHE A3694 " pdb=" CA PHE A3694 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA THR A1006 " pdb=" C THR A1006 " pdb=" N VAL A1007 " pdb=" CA VAL A1007 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLN A3037 " pdb=" C GLN A3037 " pdb=" N GLU A3038 " pdb=" CA GLU A3038 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 18074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3621 0.063 - 0.125: 858 0.125 - 0.188: 72 0.188 - 0.251: 10 0.251 - 0.314: 3 Chirality restraints: 4564 Sorted by residual: chirality pdb=" CA LEU A2337 " pdb=" N LEU A2337 " pdb=" C LEU A2337 " pdb=" CB LEU A2337 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ALA A3730 " pdb=" N ALA A3730 " pdb=" C ALA A3730 " pdb=" CB ALA A3730 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ALA A3406 " pdb=" N ALA A3406 " pdb=" C ALA A3406 " pdb=" CB ALA A3406 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 4561 not shown) Planarity restraints: 5087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 2R4 A6101 " -0.043 2.00e-02 2.50e+03 2.45e-02 2.10e+01 pdb=" C06 2R4 A6101 " -0.008 2.00e-02 2.50e+03 pdb=" C07 2R4 A6101 " -0.017 2.00e-02 2.50e+03 pdb=" C08 2R4 A6101 " -0.002 2.00e-02 2.50e+03 pdb=" C09 2R4 A6101 " 0.018 2.00e-02 2.50e+03 pdb=" C10 2R4 A6101 " 0.025 2.00e-02 2.50e+03 pdb=" C11 2R4 A6101 " 0.012 2.00e-02 2.50e+03 pdb=" C13 2R4 A6101 " 0.004 2.00e-02 2.50e+03 pdb=" C14 2R4 A6101 " 0.014 2.00e-02 2.50e+03 pdb=" C15 2R4 A6101 " -0.015 2.00e-02 2.50e+03 pdb=" C16 2R4 A6101 " -0.007 2.00e-02 2.50e+03 pdb=" C17 2R4 A6101 " -0.024 2.00e-02 2.50e+03 pdb=" C18 2R4 A6101 " -0.018 2.00e-02 2.50e+03 pdb=" S12 2R4 A6101 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A4008 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A4009 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A4009 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A4009 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A2851 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A2852 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A2852 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A2852 " 0.034 5.00e-02 4.00e+02 ... (remaining 5084 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 467 2.64 - 3.20: 30086 3.20 - 3.77: 45630 3.77 - 4.33: 62969 4.33 - 4.90: 99807 Nonbonded interactions: 238959 Sorted by model distance: nonbonded pdb=" O SER A 280 " pdb=" OG SER A 283 " model vdw 2.071 2.440 nonbonded pdb=" O GLU A3361 " pdb=" OG SER A3367 " model vdw 2.086 2.440 nonbonded pdb=" O LYS A3355 " pdb=" NH1 ARG A3358 " model vdw 2.097 2.520 nonbonded pdb=" O GLU A3804 " pdb=" CG GLU A3804 " model vdw 2.099 3.440 nonbonded pdb=" OH TYR A3855 " pdb=" OE1 GLU A4122 " model vdw 2.101 2.440 ... (remaining 238954 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 9.490 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 74.330 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.008 0.077 29636 Z= 0.542 Angle : 0.928 12.518 40081 Z= 0.498 Chirality : 0.052 0.314 4564 Planarity : 0.005 0.100 5087 Dihedral : 14.505 89.907 11065 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.22 % Favored : 90.56 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3602 helix: -0.50 (0.10), residues: 2298 sheet: -2.39 (0.84), residues: 39 loop : -2.34 (0.17), residues: 1265 *********************** 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 365 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 356 time to evaluate : 3.390 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 outliers start: 9 outliers final: 1 residues processed: 361 average time/residue: 0.4376 time to fit residues: 253.8305 Evaluate side-chains 251 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 3.342 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2695 time to fit residues: 5.2308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 0.9990 chunk 276 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 286 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 331 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2283 ASN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2518 GLN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS A4018 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 29636 Z= 0.230 Angle : 0.687 9.851 40081 Z= 0.349 Chirality : 0.042 0.175 4564 Planarity : 0.005 0.080 5087 Dihedral : 5.422 27.098 3927 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.11 % Favored : 92.81 % Rotamer Outliers : 0.91 % 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: -1.33 (0.14), residues: 3602 helix: -0.11 (0.11), residues: 2333 sheet: -2.29 (0.72), residues: 50 loop : -2.25 (0.18), residues: 1219 *********************** 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 324 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 295 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 306 average time/residue: 0.4193 time to fit residues: 207.3899 Evaluate side-chains 263 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 245 time to evaluate : 3.956 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2754 time to fit residues: 13.7253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 30.0000 chunk 102 optimal weight: 0.9990 chunk 275 optimal weight: 4.9990 chunk 225 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 332 optimal weight: 3.9990 chunk 358 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 329 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 266 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 29636 Z= 0.190 Angle : 0.630 8.456 40081 Z= 0.318 Chirality : 0.040 0.242 4564 Planarity : 0.005 0.068 5087 Dihedral : 5.060 25.726 3927 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.75 % Favored : 93.17 % Rotamer Outliers : 0.88 % 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: -1.08 (0.14), residues: 3602 helix: 0.08 (0.11), residues: 2344 sheet: -2.03 (0.71), residues: 50 loop : -2.18 (0.18), residues: 1208 *********************** 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 297 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 269 time to evaluate : 3.414 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 outliers start: 28 outliers final: 14 residues processed: 289 average time/residue: 0.4188 time to fit residues: 197.6574 Evaluate side-chains 255 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 241 time to evaluate : 3.167 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2761 time to fit residues: 11.6061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 328 optimal weight: 0.9980 chunk 249 optimal weight: 0.6980 chunk 172 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 333 optimal weight: 0.9990 chunk 352 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 315 optimal weight: 5.9990 chunk 95 optimal weight: 0.0770 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2225 HIS ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2787 HIS ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3527 GLN A4018 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 29636 Z= 0.191 Angle : 0.621 8.745 40081 Z= 0.311 Chirality : 0.040 0.280 4564 Planarity : 0.005 0.062 5087 Dihedral : 4.865 26.411 3927 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.58 % Favored : 93.34 % Rotamer Outliers : 1.35 % 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: -0.91 (0.14), residues: 3602 helix: 0.20 (0.11), residues: 2352 sheet: -1.93 (0.71), residues: 50 loop : -2.11 (0.18), residues: 1200 *********************** 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 315 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 272 time to evaluate : 4.299 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 outliers start: 43 outliers final: 22 residues processed: 299 average time/residue: 0.4096 time to fit residues: 201.3382 Evaluate side-chains 267 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 3.310 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3153 time to fit residues: 17.0411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 243 optimal weight: 0.0470 chunk 0 optimal weight: 40.0000 chunk 180 optimal weight: 20.0000 chunk 316 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1737 ASN ** A2217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3166 ASN ** A4018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 29636 Z= 0.344 Angle : 0.693 9.428 40081 Z= 0.347 Chirality : 0.043 0.242 4564 Planarity : 0.005 0.058 5087 Dihedral : 5.021 25.524 3927 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.42 % Rotamer Outliers : 1.60 % 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: -1.03 (0.14), residues: 3602 helix: 0.14 (0.11), residues: 2335 sheet: -1.98 (0.72), residues: 50 loop : -2.19 (0.18), residues: 1217 *********************** 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 298 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 3.728 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 outliers start: 51 outliers final: 28 residues processed: 284 average time/residue: 0.4296 time to fit residues: 200.1794 Evaluate side-chains 264 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 3.319 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2998 time to fit residues: 19.9552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 6.9990 chunk 317 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 353 optimal weight: 0.0770 chunk 293 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3177 ASN ** A4018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 29636 Z= 0.177 Angle : 0.632 11.809 40081 Z= 0.312 Chirality : 0.040 0.283 4564 Planarity : 0.005 0.060 5087 Dihedral : 4.782 24.319 3927 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.56 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3602 helix: 0.25 (0.11), residues: 2355 sheet: -1.55 (0.80), residues: 41 loop : -2.11 (0.18), residues: 1206 *********************** 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 289 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 3.196 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 outliers start: 33 outliers final: 12 residues processed: 279 average time/residue: 0.4121 time to fit residues: 190.3476 Evaluate side-chains 252 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 240 time to evaluate : 3.390 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3498 time to fit residues: 12.3266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 257 optimal weight: 0.0170 chunk 199 optimal weight: 2.9990 chunk 297 optimal weight: 0.6980 chunk 197 optimal weight: 20.0000 chunk 351 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 214 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1654 GLN ** A2217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3166 ASN A3716 HIS A4018 GLN A4115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 29636 Z= 0.168 Angle : 0.639 14.272 40081 Z= 0.313 Chirality : 0.040 0.305 4564 Planarity : 0.005 0.062 5087 Dihedral : 4.637 24.203 3927 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.55 % Favored : 93.42 % Rotamer Outliers : 0.91 % 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: -0.75 (0.14), residues: 3602 helix: 0.31 (0.11), residues: 2365 sheet: -1.38 (0.78), residues: 41 loop : -2.05 (0.18), residues: 1196 *********************** 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 285 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 256 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 279 average time/residue: 0.4199 time to fit residues: 193.0964 Evaluate side-chains 246 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 235 time to evaluate : 3.212 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2711 time to fit residues: 10.0787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 29636 Z= 0.199 Angle : 0.653 12.921 40081 Z= 0.320 Chirality : 0.041 0.184 4564 Planarity : 0.004 0.057 5087 Dihedral : 4.590 23.964 3927 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.58 % Favored : 93.39 % Rotamer Outliers : 0.59 % 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: -0.70 (0.14), residues: 3602 helix: 0.33 (0.11), residues: 2371 sheet: -1.09 (0.78), residues: 41 loop : -1.99 (0.18), residues: 1190 *********************** 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 262 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 243 time to evaluate : 3.309 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 outliers start: 19 outliers final: 9 residues processed: 256 average time/residue: 0.4287 time to fit residues: 180.1541 Evaluate side-chains 243 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 234 time to evaluate : 3.520 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3948 time to fit residues: 10.9637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 4.9990 chunk 337 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 327 optimal weight: 0.5980 chunk 336 optimal weight: 0.8980 chunk 197 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 296 optimal weight: 10.0000 chunk 310 optimal weight: 0.0170 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2977 ASN ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 29636 Z= 0.176 Angle : 0.651 13.598 40081 Z= 0.317 Chirality : 0.040 0.178 4564 Planarity : 0.005 0.078 5087 Dihedral : 4.522 24.006 3927 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer Outliers : 0.31 % 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: -0.61 (0.14), residues: 3602 helix: 0.43 (0.11), residues: 2355 sheet: -0.95 (0.77), residues: 43 loop : -2.00 (0.18), residues: 1204 *********************** 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 258 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 248 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 256 average time/residue: 0.4217 time to fit residues: 178.3798 Evaluate side-chains 237 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 3.555 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3760 time to fit residues: 7.7963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 346 optimal weight: 0.6980 chunk 211 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 240 optimal weight: 0.0980 chunk 363 optimal weight: 0.6980 chunk 334 optimal weight: 2.9990 chunk 289 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 29636 Z= 0.170 Angle : 0.655 14.214 40081 Z= 0.320 Chirality : 0.041 0.240 4564 Planarity : 0.005 0.066 5087 Dihedral : 4.466 23.787 3927 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.56 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3602 helix: 0.44 (0.11), residues: 2369 sheet: -1.07 (0.76), residues: 43 loop : -2.00 (0.18), residues: 1190 ********************** 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 253 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 245 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 247 average time/residue: 0.4316 time to fit residues: 175.6699 Evaluate side-chains 240 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 3.586 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2937 time to fit residues: 7.3751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 308 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 266 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 290 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 297 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A2152 ASN ** A2301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.121438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.090458 restraints weight = 73763.065| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.61 r_work: 0.3474 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 29636 Z= 0.166 Angle : 0.658 14.251 40081 Z= 0.318 Chirality : 0.040 0.235 4564 Planarity : 0.004 0.058 5087 Dihedral : 4.410 23.852 3927 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.59 % Rotamer Outliers : 0.13 % 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: -0.53 (0.14), residues: 3602 helix: 0.48 (0.11), residues: 2370 sheet: -1.17 (0.74), residues: 43 loop : -1.98 (0.18), residues: 1189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5748.36 seconds wall clock time: 106 minutes 4.98 seconds (6364.98 seconds total)