Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 12:22:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otp_13064/08_2023/7otp_13064_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otp_13064/08_2023/7otp_13064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otp_13064/08_2023/7otp_13064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otp_13064/08_2023/7otp_13064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otp_13064/08_2023/7otp_13064_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otp_13064/08_2023/7otp_13064_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 192 5.16 5 C 18616 2.51 5 N 4907 2.21 5 O 5319 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 ARG 82": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 713": "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 GLU 1002": "OE1" <-> "OE2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "A GLU 1102": "OE1" <-> "OE2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A GLU 1189": "OE1" <-> "OE2" 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 1557": "OE1" <-> "OE2" Residue "A GLU 1581": "OE1" <-> "OE2" Residue "A ARG 1608": "NH1" <-> "NH2" Residue "A GLU 1709": "OE1" <-> "OE2" Residue "A GLU 1715": "OE1" <-> "OE2" Residue "A GLU 1764": "OE1" <-> "OE2" 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 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 2175": "OE1" <-> "OE2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A GLU 2243": "OE1" <-> "OE2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A GLU 2321": "OE1" <-> "OE2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A GLU 2338": "OE1" <-> "OE2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A GLU 2488": "OE1" <-> "OE2" Residue "A GLU 2578": "OE1" <-> "OE2" Residue "A GLU 2828": "OE1" <-> "OE2" Residue "A GLU 2895": "OE1" <-> "OE2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2922": "NH1" <-> "NH2" Residue "A GLU 2925": "OE1" <-> "OE2" Residue "A GLU 2990": "OE1" <-> "OE2" Residue "A GLU 3038": "OE1" <-> "OE2" Residue "A GLU 3137": "OE1" <-> "OE2" Residue "A ARG 3282": "NH1" <-> "NH2" Residue "A GLU 3295": "OE1" <-> "OE2" Residue "A GLU 3309": "OE1" <-> "OE2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3350": "OE1" <-> "OE2" Residue "A GLU 3353": "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 3427": "OE1" <-> "OE2" Residue "A GLU 3460": "OE1" <-> "OE2" Residue "A GLU 3519": "OE1" <-> "OE2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A GLU 3698": "OE1" <-> "OE2" Residue "A ARG 3708": "NH1" <-> "NH2" 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 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 GLU 3933": "OE1" <-> "OE2" Residue "A GLU 4030": "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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 29039 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 29039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3659, 29039 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'peptide': 3656, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 158, 'TRANS': 3497, None: 3} Not linked: pdbres="UNK A6020 " pdbres="AGS A6101 " Not linked: pdbres="AGS A6101 " pdbres=" MG A6102 " Not linked: pdbres=" MG A6102 " pdbres=" MG A6103 " Chain breaks: 17 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 308 Unresolved non-hydrogen dihedrals: 194 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: 14.07, per 1000 atoms: 0.48 Number of scatterers: 29039 At special positions: 0 Unit cell: (126.488, 152.568, 182.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 3 15.00 Mg 2 11.99 O 5319 8.00 N 4907 7.00 C 18616 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: 11.74 Conformation dependent library (CDL) restraints added in 4.5 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: 188 helices and 5 sheets defined 63.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.45 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 removed outlier: 4.146A pdb=" N ARG A 14 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.522A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 70 removed outlier: 5.577A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 removed outlier: 3.830A pdb=" N GLU A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 85 " --> pdb=" O CYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 removed outlier: 4.351A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 145 removed outlier: 3.544A pdb=" N ILE A 132 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ARG A 142 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 143 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET A 144 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 4.197A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.997A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 removed outlier: 4.365A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.587A pdb=" N SER A 228 " --> pdb=" O LEU A 224 " (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 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' 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 357 through 376 removed outlier: 5.224A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 381 through 396 removed outlier: 3.587A pdb=" N CYS A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 422 Proline residue: A 411 - end of helix removed outlier: 3.526A pdb=" N LEU A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 446 Proline residue: A 433 - end of helix removed outlier: 3.556A pdb=" N PHE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 473 through 491 removed outlier: 4.099A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 4.227A pdb=" N ASP A 529 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.834A pdb=" N ALA A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 576 removed outlier: 4.549A pdb=" N ASN A 561 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 633 removed outlier: 3.591A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 657 removed outlier: 3.847A pdb=" N VAL A 646 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 650 " --> pdb=" O TYR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.716A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 720 removed outlier: 3.527A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLN A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 735 removed outlier: 3.894A pdb=" N SER A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 759 removed outlier: 4.466A pdb=" N LEU A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 763 through 779 removed outlier: 3.674A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 804 Proline residue: A 787 - end of helix removed outlier: 4.708A pdb=" N LYS A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP A 791 " --> pdb=" O PRO A 787 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 3.946A pdb=" N ASP A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR A 799 " --> pdb=" O CYS A 795 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER A 803 " --> pdb=" O TYR A 799 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 861 Processing helix chain 'A' and resid 867 through 876 removed outlier: 4.405A pdb=" N VAL A 873 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 874 " --> pdb=" O LEU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 920 Proline residue: A 912 - end of helix removed outlier: 5.100A pdb=" N THR A 915 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 916 " --> pdb=" O ARG A 913 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 920 " --> pdb=" O LEU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 946 removed outlier: 3.830A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 973 removed outlier: 4.407A pdb=" N LYS A 963 " --> pdb=" O GLN A 960 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE A 966 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.617A pdb=" N ALA A 973 " --> pdb=" O LEU A 970 " (cutoff:3.500A) 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 1014 removed outlier: 3.799A pdb=" N ILE A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1042 removed outlier: 3.568A pdb=" N GLY A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1072 through 1079 removed outlier: 3.840A pdb=" N LEU A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1085 No H-bonds generated for 'chain 'A' and resid 1082 through 1085' Processing helix chain 'A' and resid 1093 through 1115 removed outlier: 3.785A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS A1115 " --> pdb=" O LEU A1111 " (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 1174 Processing helix chain 'A' and resid 1181 through 1197 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1204 through 1214 Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.552A pdb=" N GLU A1225 " --> pdb=" O ASN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1271 Processing helix chain 'A' and resid 1278 through 1281 No H-bonds generated for 'chain 'A' and resid 1278 through 1281' Processing helix chain 'A' and resid 1290 through 1299 removed outlier: 4.156A pdb=" N GLU A1299 " --> pdb=" O ALA A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1350 removed outlier: 4.472A pdb=" N GLU A1328 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A1332 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1360 Processing helix chain 'A' and resid 1365 through 1377 removed outlier: 4.134A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1381 No H-bonds generated for 'chain 'A' and resid 1379 through 1381' Processing helix chain 'A' and resid 1391 through 1408 Proline residue: A1396 - end of helix removed outlier: 3.528A pdb=" N ASN A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1422 removed outlier: 3.518A pdb=" N ASP A1413 " --> pdb=" O PRO A1410 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A1421 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1432 Processing helix chain 'A' and resid 1442 through 1461 Processing helix chain 'A' and resid 1464 through 1467 No H-bonds generated for 'chain 'A' and resid 1464 through 1467' Processing helix chain 'A' and resid 1477 through 1486 removed outlier: 3.778A pdb=" N GLU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 3.688A 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: 3.586A 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: 4.090A pdb=" N ASN A1568 " --> pdb=" O SER A1564 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A1570 " --> pdb=" O THR A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1585 removed outlier: 4.585A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) removed outlier: 3.958A 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: 5.164A pdb=" N LYS A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS A1628 " --> pdb=" O GLN A1624 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N CYS A1629 " --> pdb=" O HIS A1625 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A1630 " --> pdb=" O TRP A1626 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER A1631 " --> pdb=" O LYS A1627 " (cutoff:3.500A) removed outlier: 5.473A 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 1700 removed outlier: 3.660A pdb=" N THR A1694 " --> pdb=" O GLY A1690 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU A1695 " --> pdb=" O GLN A1691 " (cutoff:3.500A) removed outlier: 4.409A 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: 4.067A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1805 Processing helix chain 'A' and resid 1814 through 1821 removed outlier: 3.644A pdb=" N SER A1818 " --> pdb=" O PHE A1814 " (cutoff:3.500A) removed outlier: 3.559A 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 1853 removed outlier: 5.424A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1864 through 1881 Processing helix chain 'A' and resid 1886 through 1888 No H-bonds generated for 'chain 'A' and resid 1886 through 1888' Processing helix chain 'A' and resid 1911 through 1923 removed outlier: 3.800A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1955 removed outlier: 3.920A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1971 through 1973 No H-bonds generated for 'chain 'A' and resid 1971 through 1973' Processing helix chain 'A' and resid 2094 through 2105 Processing helix chain 'A' and resid 2124 through 2134 removed outlier: 3.868A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) removed outlier: 3.895A 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 2154 through 2171 Proline residue: A2159 - end of helix removed outlier: 5.915A pdb=" N LYS A2162 " --> pdb=" O ARG A2158 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N HIS A2163 " --> pdb=" O PRO A2159 " (cutoff:3.500A) removed outlier: 4.451A 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 removed outlier: 3.745A pdb=" N ARG A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2228 through 2244 Processing helix chain 'A' and resid 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 2271 through 2282 Processing helix chain 'A' and resid 2296 through 2308 removed outlier: 3.629A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2331 removed outlier: 4.491A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2354 removed outlier: 3.791A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2368 Processing helix chain 'A' and resid 2372 through 2377 removed outlier: 4.073A pdb=" N ASP A2376 " --> pdb=" O PRO A2373 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A2377 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2379 through 2388 Proline residue: A2387 - end of helix Processing helix chain 'A' and resid 2392 through 2403 Processing helix chain 'A' and resid 2413 through 2417 Processing helix chain 'A' and resid 2420 through 2425 removed outlier: 3.923A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) No H-bonds generated for '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 2461 removed outlier: 3.908A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix removed outlier: 3.761A pdb=" N GLU A2460 " --> pdb=" O ASN A2456 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A2461 " --> pdb=" O PRO A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2470 through 2483 removed outlier: 3.892A pdb=" N ASN A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2511 removed outlier: 3.715A pdb=" N LEU A2510 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A2511 " --> pdb=" O ILE A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2515 through 2526 Processing helix chain 'A' and resid 2535 through 2545 removed outlier: 3.735A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2548 through 2550 No H-bonds generated for 'chain 'A' and resid 2548 through 2550' Processing helix chain 'A' and resid 2558 through 2566 removed outlier: 4.073A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N THR A2566 " --> pdb=" O LEU A2562 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2798 removed outlier: 4.988A 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: 3.988A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A2822 " --> pdb=" O LYS A2818 " (cutoff:3.500A) Processing helix chain 'A' and resid 2826 through 2846 Processing helix chain 'A' and resid 2852 through 2864 removed outlier: 3.768A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) Processing helix chain 'A' and resid 2866 through 2868 No H-bonds generated for 'chain 'A' and resid 2866 through 2868' 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 2933 Processing helix chain 'A' and resid 2936 through 2945 removed outlier: 3.622A pdb=" N SER A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2951 through 2961 removed outlier: 4.316A pdb=" N SER A2955 " --> pdb=" O ILE A2952 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA A2956 " --> pdb=" O THR A2953 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A2961 " --> 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: 4.000A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (cutoff:3.500A) Processing helix chain 'A' and resid 3008 through 3013 Processing helix chain 'A' and resid 3027 through 3030 No H-bonds generated for 'chain 'A' and resid 3027 through 3030' Processing helix chain 'A' and resid 3041 through 3054 Processing helix chain 'A' and resid 3060 through 3070 Processing helix chain 'A' and resid 3076 through 3081 Processing helix chain 'A' and resid 3083 through 3093 removed outlier: 3.760A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3116 removed outlier: 3.843A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) Processing helix chain 'A' and resid 3122 through 3131 removed outlier: 3.834A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) Processing helix chain 'A' and resid 3133 through 3145 removed outlier: 4.035A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3165 removed outlier: 3.798A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3176 through 3195 removed outlier: 3.760A pdb=" N THR A3184 " --> pdb=" O ASP A3180 " (cutoff:3.500A) Processing helix chain 'A' and resid 3231 through 3248 removed outlier: 3.763A 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: 3.764A pdb=" N ARG A3282 " --> pdb=" O GLN A3278 " (cutoff:3.500A) Processing helix chain 'A' and resid 3291 through 3306 removed outlier: 4.448A pdb=" N GLU A3295 " --> pdb=" O GLN A3291 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLN A3296 " --> pdb=" O GLY A3292 " (cutoff:3.500A) Processing helix chain 'A' and resid 3323 through 3343 Processing helix chain 'A' and resid 3346 through 3351 removed outlier: 3.706A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) Processing helix chain 'A' and resid 3355 through 3363 Processing helix chain 'A' and resid 3370 through 3392 Processing helix chain 'A' and resid 3407 through 3429 Processing helix chain 'A' and resid 3441 through 3455 Processing helix chain 'A' and resid 3459 through 3473 Proline residue: A3466 - end of helix removed outlier: 3.954A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (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: 3.537A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3496 through 3505 removed outlier: 3.509A pdb=" N ILE A3499 " --> pdb=" O ILE A3496 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A3500 " --> pdb=" O SER A3497 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL A3503 " --> pdb=" O SER A3500 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3524 removed outlier: 3.656A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3530 through 3537 Processing helix chain 'A' and resid 3552 through 3562 Processing helix chain 'A' and resid 3567 through 3577 removed outlier: 3.750A pdb=" N GLN A3577 " --> pdb=" O ASN A3573 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3593 Processing helix chain 'A' and resid 3605 through 3616 removed outlier: 3.656A pdb=" N LYS A3608 " --> pdb=" O ASN A3605 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A3615 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3627 through 3635 removed outlier: 3.760A 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: 3.838A 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 3819 removed outlier: 3.888A 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: 4.464A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3861 removed outlier: 3.851A pdb=" N TYR A3855 " --> pdb=" O VAL A3852 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR A3859 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3866 through 3874 Processing helix chain 'A' and resid 3882 through 3889 Processing helix chain 'A' and resid 3894 through 3917 removed outlier: 4.269A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.746A 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: 3.870A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A3986 " --> pdb=" O SER A3982 " (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 4049 removed outlier: 4.629A pdb=" N TYR A4046 " --> pdb=" O GLN A4042 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4056 through 4067 removed outlier: 3.567A 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 4102 through 4111 Processing helix chain 'A' and resid 4114 through 4119 removed outlier: 3.784A 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: 3.712A pdb=" N UNK A6008 " --> pdb=" O UNK A6004 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N UNK A6011 " --> pdb=" O UNK A6007 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N UNK A6012 " --> pdb=" O UNK A6008 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK A6013 " --> pdb=" O UNK A6009 " (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 3739 through 3742 removed outlier: 4.173A 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 Processing sheet with id= E, first strand: chain 'A' and resid 3793 through 3797 removed outlier: 3.573A pdb=" N MET A3796 " --> pdb=" O LEU A3800 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) 1362 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.19 Time building geometry restraints manager: 12.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.38: 10952 1.38 - 1.56: 18370 1.56 - 1.75: 10 1.75 - 1.94: 297 1.94 - 2.13: 1 Bond restraints: 29630 Sorted by residual: bond pdb=" C3' AGS A6101 " pdb=" C4' AGS A6101 " ideal model delta sigma weight residual 1.526 1.334 0.192 1.10e-02 8.26e+03 3.05e+02 bond pdb=" C4' AGS A6101 " pdb=" O4' AGS A6101 " ideal model delta sigma weight residual 1.444 1.635 -0.191 1.20e-02 6.94e+03 2.53e+02 bond pdb=" C6 AGS A6101 " pdb=" N6 AGS A6101 " ideal model delta sigma weight residual 1.335 1.472 -0.137 1.00e-02 1.00e+04 1.88e+02 bond pdb=" C1' AGS A6101 " pdb=" O4' AGS A6101 " ideal model delta sigma weight residual 1.415 1.295 0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" PG AGS A6101 " pdb=" S1G AGS A6101 " ideal model delta sigma weight residual 1.949 2.126 -0.177 2.00e-02 2.50e+03 7.84e+01 ... (remaining 29625 not shown) Histogram of bond angle deviations from ideal: 95.62 - 103.58: 405 103.58 - 111.54: 13405 111.54 - 119.51: 11863 119.51 - 127.47: 14116 127.47 - 135.43: 289 Bond angle restraints: 40078 Sorted by residual: angle pdb=" C5 AGS A6101 " pdb=" C4 AGS A6101 " pdb=" N3 AGS A6101 " ideal model delta sigma weight residual 126.80 118.10 8.70 7.41e-01 1.82e+00 1.38e+02 angle pdb=" C5 AGS A6101 " pdb=" N7 AGS A6101 " pdb=" C8 AGS A6101 " ideal model delta sigma weight residual 103.67 108.13 -4.46 4.26e-01 5.51e+00 1.10e+02 angle pdb=" N TYR A3715 " pdb=" CA TYR A3715 " pdb=" C TYR A3715 " ideal model delta sigma weight residual 112.88 101.15 11.73 1.29e+00 6.01e-01 8.27e+01 angle pdb=" N1 AGS A6101 " pdb=" C2 AGS A6101 " pdb=" N3 AGS A6101 " ideal model delta sigma weight residual 128.80 121.75 7.05 8.41e-01 1.41e+00 7.02e+01 angle pdb=" N3 AGS A6101 " pdb=" C4 AGS A6101 " pdb=" N9 AGS A6101 " ideal model delta sigma weight residual 127.16 135.43 -8.27 1.06e+00 8.92e-01 6.09e+01 ... (remaining 40073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 16159 18.16 - 36.32: 1632 36.32 - 54.48: 214 54.48 - 72.64: 38 72.64 - 90.80: 30 Dihedral angle restraints: 18073 sinusoidal: 7316 harmonic: 10757 Sorted by residual: dihedral pdb=" CA ILE A2785 " pdb=" C ILE A2785 " pdb=" N LYS A2786 " pdb=" CA LYS A2786 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LYS A2445 " pdb=" C LYS A2445 " pdb=" N LEU A2446 " pdb=" CA LEU A2446 " ideal model delta harmonic sigma weight residual 180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA GLY A4024 " pdb=" C GLY A4024 " pdb=" N GLY A4025 " pdb=" CA GLY A4025 " ideal model delta harmonic sigma weight residual -180.00 -153.75 -26.25 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 18070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3523 0.055 - 0.111: 929 0.111 - 0.166: 103 0.166 - 0.221: 12 0.221 - 0.276: 3 Chirality restraints: 4570 Sorted by residual: chirality pdb=" CB ILE A4089 " pdb=" CA ILE A4089 " pdb=" CG1 ILE A4089 " pdb=" CG2 ILE A4089 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' AGS A6101 " pdb=" C2' AGS A6101 " pdb=" C4' AGS A6101 " pdb=" O3' AGS A6101 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA GLU A3033 " pdb=" N GLU A3033 " pdb=" C GLU A3033 " pdb=" CB GLU A3033 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 4567 not shown) Planarity restraints: 5084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1238 " -0.103 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO A1239 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO A1239 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO A1239 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1802 " 0.028 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR A1802 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A1802 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A1802 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A1802 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A1802 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A1802 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A1802 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 722 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS A 722 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS A 722 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP A 723 " 0.019 2.00e-02 2.50e+03 ... (remaining 5081 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 360 2.59 - 3.17: 27936 3.17 - 3.75: 46141 3.75 - 4.32: 63370 4.32 - 4.90: 101159 Nonbonded interactions: 238966 Sorted by model distance: nonbonded pdb=" O2G AGS A6101 " pdb="MG MG A6102 " model vdw 2.017 2.170 nonbonded pdb=" O TRP A1632 " pdb=" OG SER A1637 " model vdw 2.068 2.440 nonbonded pdb=" O SER A3288 " pdb=" NH1 ARG A3289 " model vdw 2.119 2.520 nonbonded pdb=" O TYR A 265 " pdb=" OG SER A 269 " model vdw 2.131 2.440 nonbonded pdb=" O1B AGS A6101 " pdb="MG MG A6103 " model vdw 2.145 2.170 ... (remaining 238961 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: 3.260 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: 0.000 Extract box with map and model: 6.190 Check model and map are aligned: 0.440 Set scattering table: 0.300 Process input model: 76.070 Find NCS groups from input model: 0.810 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.007 0.192 29630 Z= 0.465 Angle : 0.866 11.731 40078 Z= 0.479 Chirality : 0.048 0.276 4570 Planarity : 0.005 0.152 5084 Dihedral : 14.562 90.804 11061 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.63 % Favored : 91.17 % Rotamer Outliers : 0.16 % 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: -1.62 (0.14), residues: 3602 helix: -0.18 (0.11), residues: 2316 sheet: -3.36 (0.58), residues: 56 loop : -2.65 (0.17), residues: 1230 *********************** 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 343 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 338 time to evaluate : 3.126 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 343 average time/residue: 0.4126 time to fit residues: 235.0418 Evaluate side-chains 273 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 271 time to evaluate : 3.269 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4692 time to fit residues: 5.9739 ------------------------------------------------------------------------------- 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: 0.6980 chunk 276 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 186 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 212 optimal weight: 8.9990 chunk 331 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2426 HIS A2859 GLN ** A3162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS A3664 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29630 Z= 0.188 Angle : 0.669 10.808 40078 Z= 0.335 Chirality : 0.042 0.307 4570 Planarity : 0.005 0.092 5084 Dihedral : 5.716 75.335 3927 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.30 % Favored : 92.62 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3602 helix: 0.09 (0.11), residues: 2322 sheet: -2.52 (0.69), residues: 47 loop : -2.37 (0.18), residues: 1233 *********************** 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 333 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 307 time to evaluate : 3.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 319 average time/residue: 0.4106 time to fit residues: 221.0923 Evaluate side-chains 288 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 276 time to evaluate : 3.201 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2738 time to fit residues: 10.7189 ------------------------------------------------------------------------------- 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: 50.0000 chunk 102 optimal weight: 3.9990 chunk 275 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 358 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 266 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 29630 Z= 0.336 Angle : 0.695 11.357 40078 Z= 0.346 Chirality : 0.043 0.181 4570 Planarity : 0.005 0.069 5084 Dihedral : 5.694 71.580 3927 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.25 % Favored : 91.67 % Rotamer Outliers : 0.94 % 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: -1.20 (0.14), residues: 3602 helix: 0.07 (0.11), residues: 2316 sheet: -2.50 (0.68), residues: 47 loop : -2.36 (0.17), residues: 1239 *********************** 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 323 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 293 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 311 average time/residue: 0.3799 time to fit residues: 198.8199 Evaluate side-chains 278 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 266 time to evaluate : 3.345 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2781 time to fit residues: 10.9568 ------------------------------------------------------------------------------- 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: 0.7980 chunk 172 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 333 optimal weight: 3.9990 chunk 352 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 315 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN A 442 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1946 ASN A2234 ASN A2784 GLN ** A3162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 29630 Z= 0.176 Angle : 0.639 12.233 40078 Z= 0.314 Chirality : 0.040 0.233 4570 Planarity : 0.004 0.065 5084 Dihedral : 5.403 67.397 3927 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.17 % Rotamer Outliers : 1.19 % 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: -0.97 (0.14), residues: 3602 helix: 0.25 (0.11), residues: 2315 sheet: -2.16 (0.72), residues: 47 loop : -2.26 (0.17), residues: 1240 *********************** 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 343 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 305 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 333 average time/residue: 0.4009 time to fit residues: 224.2359 Evaluate side-chains 291 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 271 time to evaluate : 3.536 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2709 time to fit residues: 15.1488 ------------------------------------------------------------------------------- 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: 6.9990 chunk 5 optimal weight: 30.0000 chunk 262 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 301 optimal weight: 0.0870 chunk 243 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 0.2980 chunk 316 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN A1817 GLN ** A3104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS A3664 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 29630 Z= 0.171 Angle : 0.639 12.716 40078 Z= 0.312 Chirality : 0.040 0.203 4570 Planarity : 0.004 0.061 5084 Dihedral : 5.253 65.658 3927 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.83 % Favored : 93.11 % Rotamer Outliers : 0.85 % 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: -0.84 (0.14), residues: 3602 helix: 0.35 (0.11), residues: 2313 sheet: -1.85 (0.81), residues: 42 loop : -2.22 (0.17), residues: 1247 *********************** 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 324 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 297 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 315 average time/residue: 0.3971 time to fit residues: 210.0116 Evaluate side-chains 282 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 273 time to evaluate : 3.652 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2917 time to fit residues: 9.7615 ------------------------------------------------------------------------------- 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: 0.0170 chunk 317 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 353 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN ** A3104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 29630 Z= 0.201 Angle : 0.639 11.310 40078 Z= 0.312 Chirality : 0.040 0.255 4570 Planarity : 0.004 0.057 5084 Dihedral : 5.160 63.660 3927 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.80 % Favored : 93.14 % Rotamer Outliers : 0.72 % 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: -0.77 (0.14), residues: 3602 helix: 0.41 (0.11), residues: 2308 sheet: -1.75 (0.82), residues: 42 loop : -2.20 (0.17), residues: 1252 *********************** 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 312 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 289 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 302 average time/residue: 0.4069 time to fit residues: 207.8031 Evaluate side-chains 282 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 269 time to evaluate : 3.667 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2894 time to fit residues: 11.7890 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 257 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 297 optimal weight: 0.1980 chunk 197 optimal weight: 5.9990 chunk 351 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2152 ASN ** A3104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS A3664 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 29630 Z= 0.190 Angle : 0.641 11.965 40078 Z= 0.312 Chirality : 0.041 0.283 4570 Planarity : 0.004 0.056 5084 Dihedral : 5.082 61.460 3927 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.83 % Favored : 93.11 % Rotamer Outliers : 0.53 % 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: -0.71 (0.14), residues: 3602 helix: 0.46 (0.11), residues: 2304 sheet: -1.74 (0.83), residues: 42 loop : -2.17 (0.17), residues: 1256 *********************** 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 303 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 286 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 295 average time/residue: 0.4091 time to fit residues: 202.4286 Evaluate side-chains 282 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 277 time to evaluate : 3.359 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2750 time to fit residues: 7.2674 ------------------------------------------------------------------------------- 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: 2.9990 chunk 140 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1817 GLN A2426 HIS ** A3104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29630 Z= 0.214 Angle : 0.658 11.229 40078 Z= 0.320 Chirality : 0.041 0.330 4570 Planarity : 0.004 0.054 5084 Dihedral : 5.058 61.435 3927 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.17 % Rotamer Outliers : 0.66 % 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: -0.69 (0.14), residues: 3602 helix: 0.46 (0.11), residues: 2302 sheet: -1.72 (0.84), residues: 42 loop : -2.12 (0.17), residues: 1258 *********************** 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 308 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 287 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 297 average time/residue: 0.4068 time to fit residues: 202.0291 Evaluate side-chains 284 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 272 time to evaluate : 3.337 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3109 time to fit residues: 11.5577 ------------------------------------------------------------------------------- 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: 5.9990 chunk 337 optimal weight: 3.9990 chunk 307 optimal weight: 0.2980 chunk 327 optimal weight: 0.7980 chunk 336 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 100 optimal weight: 0.0570 chunk 296 optimal weight: 6.9990 chunk 310 optimal weight: 0.0570 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2305 ASN ** A3104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 29630 Z= 0.164 Angle : 0.655 11.997 40078 Z= 0.317 Chirality : 0.040 0.355 4570 Planarity : 0.004 0.055 5084 Dihedral : 4.962 61.774 3927 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.59 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3602 helix: 0.52 (0.11), residues: 2294 sheet: -1.63 (0.85), residues: 42 loop : -2.09 (0.17), residues: 1266 *********************** 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 309 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 300 time to evaluate : 3.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 305 average time/residue: 0.4126 time to fit residues: 209.0805 Evaluate side-chains 279 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 275 time to evaluate : 3.290 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2980 time to fit residues: 6.6580 ------------------------------------------------------------------------------- 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: 1.9990 chunk 215 optimal weight: 0.9980 chunk 346 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 363 optimal weight: 5.9990 chunk 334 optimal weight: 0.5980 chunk 289 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 223 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2787 HIS ** A3104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29630 Z= 0.178 Angle : 0.666 12.511 40078 Z= 0.323 Chirality : 0.041 0.362 4570 Planarity : 0.004 0.054 5084 Dihedral : 4.923 61.285 3927 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.48 % 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: -0.56 (0.14), residues: 3602 helix: 0.55 (0.11), residues: 2293 sheet: -1.60 (0.85), residues: 42 loop : -2.05 (0.17), residues: 1267 ********************** 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 299 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 289 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 296 average time/residue: 0.4095 time to fit residues: 201.6581 Evaluate side-chains 277 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 273 time to evaluate : 3.082 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3011 time to fit residues: 6.6612 ------------------------------------------------------------------------------- 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: 8.9990 chunk 230 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 290 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 297 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 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 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 ASN A2266 ASN ** A3104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3457 ASN A3643 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.141552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.102848 restraints weight = 61031.320| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.12 r_work: 0.3327 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 29630 Z= 0.180 Angle : 0.658 12.442 40078 Z= 0.319 Chirality : 0.041 0.363 4570 Planarity : 0.004 0.054 5084 Dihedral : 4.897 61.230 3927 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.61 % 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: -0.56 (0.14), residues: 3602 helix: 0.55 (0.11), residues: 2297 sheet: -1.70 (0.82), residues: 44 loop : -2.04 (0.17), residues: 1261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5710.05 seconds wall clock time: 105 minutes 12.79 seconds (6312.79 seconds total)