Starting phenix.real_space_refine on Sun Jul 5 16:06:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eoi_28376/07_2026/8eoi_28376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eoi_28376/07_2026/8eoi_28376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eoi_28376/07_2026/8eoi_28376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eoi_28376/07_2026/8eoi_28376.map" model { file = "/net/cci-nas-00/data/ceres_data/8eoi_28376/07_2026/8eoi_28376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eoi_28376/07_2026/8eoi_28376.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8eoi_28376/07_2026/8eoi_28376.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eoi_28376/07_2026/8eoi_28376.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 139 5.16 5 C 18562 2.51 5 N 4861 2.21 5 O 5159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28721 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7444 Classifications: {'peptide': 936} Link IDs: {'PCIS': 3, 'PTRANS': 40, 'TRANS': 892} Chain breaks: 2 Chain: "B" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2403 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 4, 'TRANS': 286} Chain: "C" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1777 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain breaks: 2 Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 806 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "F" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "G" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 929 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 106} Chain: "H" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "I" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1150 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain breaks: 1 Chain: "K" Number of atoms: 9024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 9024 Classifications: {'peptide': 1116} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1077} Chain breaks: 6 Chain: "J" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2364 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 280} Chain breaks: 1 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 363 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain breaks: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'9Z9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.23, per 1000 atoms: 0.22 Number of scatterers: 28721 At special positions: 0 Unit cell: (115.138, 163.394, 233.662, 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 139 16.00 O 5159 8.00 N 4861 7.00 C 18562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS K 316 " - pdb=" SG CYS K 332 " distance=2.03 Simple disulfide: pdb=" SG CYS K1479 " - pdb=" SG CYS K1495 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1001 " - " ASN A 370 " " NAG L 1 " - " ASN A 818 " " NAG M 1 " - " ASN A 913 " " NAG N 1 " - " ASN I 182 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6726 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 26 sheets defined 47.6% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 82 through 85 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 468 through 473 removed outlier: 3.693A pdb=" N GLU A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 504 removed outlier: 3.913A pdb=" N MET A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.776A pdb=" N LEU A 525 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 887 through 894 Processing helix chain 'A' and resid 905 through 909 Processing helix chain 'A' and resid 961 through 992 removed outlier: 3.556A pdb=" N ILE A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.722A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 66 removed outlier: 3.872A pdb=" N ILE B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 83 removed outlier: 3.984A pdb=" N ALA B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 100 removed outlier: 3.863A pdb=" N LYS B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.821A pdb=" N ALA B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 removed outlier: 3.661A pdb=" N GLN B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 Processing helix chain 'B' and resid 154 through 168 Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.787A pdb=" N ALA B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.901A pdb=" N CYS B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 222 Processing helix chain 'B' and resid 225 through 241 Processing helix chain 'B' and resid 246 through 275 removed outlier: 3.730A pdb=" N SER B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 removed outlier: 4.000A pdb=" N VAL B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 38 removed outlier: 3.706A pdb=" N ARG C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Proline residue: C 19 - end of helix Processing helix chain 'C' and resid 45 through 65 Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 114 through 133 Proline residue: C 120 - end of helix Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.547A pdb=" N GLN C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 Processing helix chain 'C' and resid 179 through 187 Processing helix chain 'C' and resid 213 through 227 removed outlier: 4.228A pdb=" N LEU C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'E' and resid 4 through 35 removed outlier: 3.793A pdb=" N GLY E 8 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 61 removed outlier: 3.679A pdb=" N VAL E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 85 removed outlier: 3.594A pdb=" N LEU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.684A pdb=" N TYR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 Processing helix chain 'F' and resid 15 through 45 removed outlier: 3.733A pdb=" N VAL F 19 " --> pdb=" O SER F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 71 removed outlier: 3.600A pdb=" N PHE F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'F' and resid 81 through 86 Processing helix chain 'F' and resid 90 through 108 Processing helix chain 'G' and resid 57 through 65 removed outlier: 4.792A pdb=" N ILE G 62 " --> pdb=" O GLN G 59 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER G 63 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA G 65 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.764A pdb=" N TYR H 11 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR H 21 " --> pdb=" O HIS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 85 removed outlier: 4.218A pdb=" N LEU H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 117 removed outlier: 3.545A pdb=" N GLU H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 177 Processing helix chain 'H' and resid 178 through 182 removed outlier: 3.977A pdb=" N GLU H 181 " --> pdb=" O ARG H 178 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 182 " --> pdb=" O SER H 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 178 through 182' Processing helix chain 'H' and resid 185 through 192 Processing helix chain 'H' and resid 199 through 209 Processing helix chain 'I' and resid 91 through 104 Processing helix chain 'I' and resid 134 through 139 Processing helix chain 'I' and resid 174 through 178 removed outlier: 3.672A pdb=" N ASP I 177 " --> pdb=" O GLU I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 206 Processing helix chain 'K' and resid 113 through 119 Processing helix chain 'K' and resid 123 through 144 removed outlier: 3.830A pdb=" N ILE K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR K 144 " --> pdb=" O ALA K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 182 removed outlier: 3.542A pdb=" N ARG K 161 " --> pdb=" O SER K 157 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR K 164 " --> pdb=" O GLU K 160 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 211 Processing helix chain 'K' and resid 235 through 250 removed outlier: 3.558A pdb=" N ALA K 238 " --> pdb=" O ALA K 235 " (cutoff:3.500A) Proline residue: K 244 - end of helix removed outlier: 3.627A pdb=" N GLY K 250 " --> pdb=" O LEU K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 266 removed outlier: 3.513A pdb=" N MET K 265 " --> pdb=" O ILE K 261 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL K 266 " --> pdb=" O ILE K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 290 removed outlier: 3.528A pdb=" N LEU K 274 " --> pdb=" O HIS K 270 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL K 275 " --> pdb=" O ILE K 271 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU K 276 " --> pdb=" O ALA K 272 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA K 283 " --> pdb=" O ILE K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 348 through 361 removed outlier: 3.672A pdb=" N ALA K 352 " --> pdb=" O ASN K 348 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR K 361 " --> pdb=" O PHE K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 377 removed outlier: 3.724A pdb=" N VAL K 368 " --> pdb=" O GLY K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 412 removed outlier: 3.903A pdb=" N PHE K 385 " --> pdb=" O PRO K 381 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS K 410 " --> pdb=" O GLY K 406 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG K 412 " --> pdb=" O PHE K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 419 through 447 Processing helix chain 'K' and resid 507 through 522 removed outlier: 3.627A pdb=" N LYS K 516 " --> pdb=" O PHE K 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 521 " --> pdb=" O CYS K 517 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS K 522 " --> pdb=" O ARG K 518 " (cutoff:3.500A) Processing helix chain 'K' and resid 523 through 542 Processing helix chain 'K' and resid 552 through 567 removed outlier: 3.775A pdb=" N THR K 558 " --> pdb=" O GLU K 554 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA K 559 " --> pdb=" O VAL K 555 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN K 560 " --> pdb=" O GLN K 556 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS K 561 " --> pdb=" O ASP K 557 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA K 565 " --> pdb=" O LYS K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 568 through 577 Processing helix chain 'K' and resid 579 through 584 removed outlier: 3.819A pdb=" N PHE K 584 " --> pdb=" O LEU K 580 " (cutoff:3.500A) Processing helix chain 'K' and resid 588 through 607 Processing helix chain 'K' and resid 614 through 625 Processing helix chain 'K' and resid 626 through 633 removed outlier: 3.619A pdb=" N ILE K 630 " --> pdb=" O ARG K 626 " (cutoff:3.500A) Processing helix chain 'K' and resid 637 through 674 removed outlier: 3.624A pdb=" N VAL K 648 " --> pdb=" O LEU K 644 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG K 649 " --> pdb=" O LEU K 645 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER K 650 " --> pdb=" O ASN K 646 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER K 653 " --> pdb=" O ARG K 649 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU K 654 " --> pdb=" O SER K 650 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 705 Processing helix chain 'K' and resid 707 through 719 removed outlier: 3.536A pdb=" N VAL K 711 " --> pdb=" O ASP K 707 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR K 719 " --> pdb=" O GLY K 715 " (cutoff:3.500A) Processing helix chain 'K' and resid 724 through 726 No H-bonds generated for 'chain 'K' and resid 724 through 726' Processing helix chain 'K' and resid 727 through 759 removed outlier: 3.638A pdb=" N ILE K 731 " --> pdb=" O MET K 727 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR K 732 " --> pdb=" O LEU K 728 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE K 733 " --> pdb=" O VAL K 729 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY K 740 " --> pdb=" O LEU K 736 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE K 743 " --> pdb=" O CYS K 739 " (cutoff:3.500A) Processing helix chain 'K' and resid 1023 through 1029 removed outlier: 3.631A pdb=" N ARG K1027 " --> pdb=" O LEU K1023 " (cutoff:3.500A) Processing helix chain 'K' and resid 1035 through 1071 removed outlier: 5.060A pdb=" N ARG K1047 " --> pdb=" O PHE K1043 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR K1048 " --> pdb=" O VAL K1044 " (cutoff:3.500A) Processing helix chain 'K' and resid 1123 through 1130 Processing helix chain 'K' and resid 1136 through 1145 Processing helix chain 'K' and resid 1160 through 1192 removed outlier: 3.763A pdb=" N ILE K1164 " --> pdb=" O VAL K1160 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE K1170 " --> pdb=" O PHE K1166 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET K1178 " --> pdb=" O ALA K1174 " (cutoff:3.500A) Processing helix chain 'K' and resid 1205 through 1214 Processing helix chain 'K' and resid 1227 through 1236 Processing helix chain 'K' and resid 1238 through 1257 Processing helix chain 'K' and resid 1264 through 1291 Processing helix chain 'K' and resid 1294 through 1327 removed outlier: 4.082A pdb=" N PHE K1327 " --> pdb=" O PRO K1295 " (cutoff:3.500A) Processing helix chain 'K' and resid 1329 through 1347 Processing helix chain 'K' and resid 1374 through 1391 removed outlier: 3.836A pdb=" N LEU K1378 " --> pdb=" O THR K1374 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU K1384 " --> pdb=" O ARG K1380 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL K1385 " --> pdb=" O VAL K1381 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU K1387 " --> pdb=" O ARG K1383 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU K1388 " --> pdb=" O LEU K1384 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER K1389 " --> pdb=" O VAL K1385 " (cutoff:3.500A) Processing helix chain 'K' and resid 1391 through 1402 removed outlier: 4.973A pdb=" N LEU K1397 " --> pdb=" O GLY K1393 " (cutoff:3.500A) Processing helix chain 'K' and resid 1403 through 1405 No H-bonds generated for 'chain 'K' and resid 1403 through 1405' Processing helix chain 'K' and resid 1407 through 1430 removed outlier: 3.835A pdb=" N VAL K1411 " --> pdb=" O ALA K1407 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE K1425 " --> pdb=" O ILE K1421 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY K1426 " --> pdb=" O TYR K1422 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET K1427 " --> pdb=" O ALA K1423 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLN K1428 " --> pdb=" O VAL K1424 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL K1429 " --> pdb=" O ILE K1425 " (cutoff:3.500A) Processing helix chain 'K' and resid 1449 through 1462 Processing helix chain 'K' and resid 1465 through 1472 removed outlier: 3.904A pdb=" N ILE K1469 " --> pdb=" O ALA K1465 " (cutoff:3.500A) Processing helix chain 'K' and resid 1499 through 1526 removed outlier: 3.573A pdb=" N TYR K1503 " --> pdb=" O PHE K1499 " (cutoff:3.500A) Processing helix chain 'K' and resid 1538 through 1553 removed outlier: 3.843A pdb=" N ASP K1553 " --> pdb=" O TRP K1549 " (cutoff:3.500A) Processing helix chain 'K' and resid 1561 through 1566 removed outlier: 3.564A pdb=" N VAL K1566 " --> pdb=" O HIS K1562 " (cutoff:3.500A) Processing helix chain 'K' and resid 1586 through 1593 Processing helix chain 'K' and resid 1605 through 1618 Processing helix chain 'K' and resid 1625 through 1635 Processing helix chain 'K' and resid 1648 through 1653 Processing helix chain 'J' and resid 39 through 55 Processing helix chain 'J' and resid 120 through 135 Processing helix chain 'J' and resid 190 through 208 removed outlier: 3.549A pdb=" N LEU J 200 " --> pdb=" O MET J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 263 removed outlier: 3.593A pdb=" N SER J 263 " --> pdb=" O GLU J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 281 removed outlier: 4.035A pdb=" N ALA J 281 " --> pdb=" O ALA J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 308 removed outlier: 3.903A pdb=" N GLY J 308 " --> pdb=" O ILE J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 327 Processing helix chain 'J' and resid 329 through 333 Processing helix chain 'J' and resid 341 through 360 removed outlier: 3.545A pdb=" N TYR J 352 " --> pdb=" O HIS J 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 168 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 44 removed outlier: 7.046A pdb=" N ALA A 57 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA A 43 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 55 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG A 76 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA A 65 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 93 removed outlier: 3.634A pdb=" N TRP A 119 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 135 removed outlier: 7.050A pdb=" N LEU A 146 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU A 131 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA A 144 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU A 133 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR A 142 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY A 135 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL A 140 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 180 removed outlier: 6.926A pdb=" N LEU A 189 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL A 178 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TRP A 187 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER A 180 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL A 185 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASN A 203 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 209 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 230 Processing sheet with id=AA7, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.880A pdb=" N HIS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN A 304 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU A 312 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N HIS A 306 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU A 310 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 327 removed outlier: 4.198A pdb=" N ARG A 384 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 321 through 327 Processing sheet with id=AB1, first strand: chain 'A' and resid 404 through 411 removed outlier: 3.542A pdb=" N ARG A 404 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 430 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER A 444 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE A 432 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 459 removed outlier: 6.847A pdb=" N VAL A 539 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 455 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 537 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N MET A 457 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N MET A 535 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A 549 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 555 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 569 through 576 removed outlier: 6.463A pdb=" N GLN A 586 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 623 through 632 removed outlier: 4.231A pdb=" N VAL A 639 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 692 through 699 removed outlier: 6.649A pdb=" N GLY A 683 " --> pdb=" O SER A 695 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU A 697 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 681 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ILE A 669 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY D 178 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 672 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 180 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 705 through 711 removed outlier: 6.877A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE A 756 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP A 763 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 769 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N THR I 191 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N SER A 772 " --> pdb=" O THR I 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 723 through 725 Processing sheet with id=AB8, first strand: chain 'A' and resid 778 through 787 removed outlier: 5.159A pdb=" N TRP A 796 " --> pdb=" O PRO A 781 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS A 783 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN A 803 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AC1, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.970A pdb=" N THR C 138 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 84 through 89 removed outlier: 5.330A pdb=" N VAL G 85 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLY G 49 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS G 87 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE G 47 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N LEU G 138 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLU G 48 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N MET G 140 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG G 50 " --> pdb=" O MET G 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 74 through 76 removed outlier: 4.531A pdb=" N ALA G 120 " --> pdb=" O LEU G 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 54 through 62 removed outlier: 7.576A pdb=" N PHE H 54 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU H 33 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP H 56 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN H 27 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL H 26 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLN H 94 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLY H 28 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR H 92 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU H 30 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N ALA H 123 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA H 90 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE H 125 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR H 92 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL H 127 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLN H 94 " --> pdb=" O VAL H 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 82 through 87 removed outlier: 5.712A pdb=" N LYS I 70 " --> pdb=" O HIS I 58 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS I 58 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU I 55 " --> pdb=" O PRO I 113 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 156 through 163 Processing sheet with id=AC7, first strand: chain 'J' and resid 115 through 118 removed outlier: 7.782A pdb=" N TRP J 103 " --> pdb=" O LYS J 98 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS J 98 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE J 105 " --> pdb=" O LYS J 96 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA J 89 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL J 68 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG J 65 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP J 172 " --> pdb=" O ARG J 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 212 through 217 removed outlier: 6.869A pdb=" N SER J 213 " --> pdb=" O VAL J 268 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASP J 270 " --> pdb=" O SER J 213 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR J 215 " --> pdb=" O ASP J 270 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL J 180 " --> pdb=" O LEU J 269 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA J 271 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU J 182 " --> pdb=" O ALA J 271 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL J 292 " --> pdb=" O VAL J 183 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE J 289 " --> pdb=" O VAL J 335 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU J 337 " --> pdb=" O ILE J 289 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE J 291 " --> pdb=" O LEU J 337 " (cutoff:3.500A) 1444 hydrogen bonds defined for protein. 4152 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: 7.02 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9179 1.34 - 1.46: 6822 1.46 - 1.58: 13156 1.58 - 1.70: 1 1.70 - 1.82: 223 Bond restraints: 29381 Sorted by residual: bond pdb=" C73 9Z9 K1701 " pdb=" O80 9Z9 K1701 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" C48 9Z9 K1701 " pdb=" O49 9Z9 K1701 " ideal model delta sigma weight residual 1.402 1.444 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C24 9Z9 K1701 " pdb=" O25 9Z9 K1701 " ideal model delta sigma weight residual 1.403 1.441 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C06 9Z9 K1701 " pdb=" C07 9Z9 K1701 " ideal model delta sigma weight residual 1.520 1.558 -0.038 2.00e-02 2.50e+03 3.59e+00 ... (remaining 29376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 39182 1.60 - 3.20: 526 3.20 - 4.80: 88 4.80 - 6.40: 24 6.40 - 8.00: 7 Bond angle restraints: 39827 Sorted by residual: angle pdb=" N VAL H 137 " pdb=" CA VAL H 137 " pdb=" C VAL H 137 " ideal model delta sigma weight residual 113.71 108.17 5.54 9.50e-01 1.11e+00 3.40e+01 angle pdb=" N ILE K1373 " pdb=" CA ILE K1373 " pdb=" C ILE K1373 " ideal model delta sigma weight residual 113.20 108.02 5.18 9.60e-01 1.09e+00 2.91e+01 angle pdb=" N VAL H 4 " pdb=" CA VAL H 4 " pdb=" C VAL H 4 " ideal model delta sigma weight residual 113.53 108.84 4.69 9.80e-01 1.04e+00 2.30e+01 angle pdb=" C LYS C 254 " pdb=" CA LYS C 254 " pdb=" CB LYS C 254 " ideal model delta sigma weight residual 115.79 111.42 4.37 1.19e+00 7.06e-01 1.35e+01 angle pdb=" C LYS D 50 " pdb=" N GLN D 51 " pdb=" CA GLN D 51 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 ... (remaining 39822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 16678 21.85 - 43.70: 667 43.70 - 65.54: 83 65.54 - 87.39: 18 87.39 - 109.24: 3 Dihedral angle restraints: 17449 sinusoidal: 7058 harmonic: 10391 Sorted by residual: dihedral pdb=" CA ASP D 49 " pdb=" C ASP D 49 " pdb=" N LYS D 50 " pdb=" CA LYS D 50 " ideal model delta harmonic sigma weight residual 180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" C73 9Z9 K1701 " pdb=" C76 9Z9 K1701 " pdb=" C77 9Z9 K1701 " pdb=" C78 9Z9 K1701 " ideal model delta sinusoidal sigma weight residual 51.88 -57.36 109.24 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C23 9Z9 K1701 " pdb=" C21 9Z9 K1701 " pdb=" C22 9Z9 K1701 " pdb=" O20 9Z9 K1701 " ideal model delta sinusoidal sigma weight residual 177.26 -73.77 -108.97 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 17446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3500 0.045 - 0.090: 777 0.090 - 0.135: 225 0.135 - 0.179: 9 0.179 - 0.224: 3 Chirality restraints: 4514 Sorted by residual: chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 370 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C17 9Z9 K1701 " pdb=" C16 9Z9 K1701 " pdb=" C18 9Z9 K1701 " pdb=" O20 9Z9 K1701 " both_signs ideal model delta sigma weight residual False 2.46 2.68 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C73 9Z9 K1701 " pdb=" C76 9Z9 K1701 " pdb=" O72 9Z9 K1701 " pdb=" O80 9Z9 K1701 " both_signs ideal model delta sigma weight residual False 2.26 2.48 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 4511 not shown) Planarity restraints: 5014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN K1573 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO K1574 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO K1574 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO K1574 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K1654 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO K1655 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO K1655 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K1655 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 132 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO I 133 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO I 133 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 133 " 0.027 5.00e-02 4.00e+02 ... (remaining 5011 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 529 2.69 - 3.24: 28243 3.24 - 3.79: 43816 3.79 - 4.35: 55814 4.35 - 4.90: 92876 Nonbonded interactions: 221278 Sorted by model distance: nonbonded pdb=" O PRO C 141 " pdb=" OG1 THR F 47 " model vdw 2.137 3.040 nonbonded pdb=" O ALA K1127 " pdb=" OG1 THR K1130 " model vdw 2.166 3.040 nonbonded pdb=" O ARG K1370 " pdb=" OG1 THR K1374 " model vdw 2.168 3.040 nonbonded pdb=" O LEU K1613 " pdb=" OG1 THR K1616 " model vdw 2.218 3.040 nonbonded pdb=" NE1 TRP G 155 " pdb=" O TRP G 157 " model vdw 2.234 3.120 ... (remaining 221273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.960 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: 0.040 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 29.310 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.002 0.045 29392 Z= 0.119 Angle : 0.509 7.997 39856 Z= 0.270 Chirality : 0.040 0.224 4514 Planarity : 0.004 0.050 5010 Dihedral : 11.589 109.238 10711 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.62 % Rotamer: Outliers : 2.73 % Allowed : 6.71 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3510 helix: 1.62 (0.14), residues: 1515 sheet: 0.58 (0.23), residues: 557 loop : -1.75 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.010 0.001 TYR B 214 PHE 0.009 0.001 PHE K 185 TRP 0.010 0.001 TRP J 103 HIS 0.002 0.000 HIS G 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (29381) covalent geometry : angle 0.50560 / 0.27 (39827) SS BOND : bond 0.00290 / 0.14 ( 4) SS BOND : angle 1.07785 / 0.61 ( 8) hydrogen bonds : bond 0.15957 / 11.25 ( 1430) hydrogen bonds : angle 5.62631 / 3.88 ( 4152) link_BETA1-4 : bond 0.00371 / 0.17 ( 3) link_BETA1-4 : angle 2.61721 / 1.65 ( 9) link_NAG-ASN : bond 0.00439 / 0.22 ( 4) link_NAG-ASN : angle 2.15216 / 1.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 152 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: A 442 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 894 ASN cc_start: 0.9072 (t0) cc_final: 0.8847 (t0) REVERT: B 280 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: C 75 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8717 (m) REVERT: C 135 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7908 (p90) REVERT: E 31 MET cc_start: 0.8565 (tmm) cc_final: 0.8348 (tmm) REVERT: G 72 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: H 131 LYS cc_start: 0.9391 (mptt) cc_final: 0.9169 (mtpt) REVERT: H 187 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8169 (t0) REVERT: K 712 MET cc_start: 0.9358 (tmm) cc_final: 0.8872 (tmm) REVERT: K 1125 MET cc_start: 0.7651 (pmm) cc_final: 0.7403 (pmm) REVERT: K 1417 MET cc_start: 0.9451 (ptp) cc_final: 0.9209 (ptm) REVERT: K 1474 MET cc_start: 0.8668 (mmp) cc_final: 0.8365 (mmp) REVERT: K 1524 MET cc_start: 0.9349 (mmm) cc_final: 0.9088 (mmm) REVERT: D 15 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7269 (m-10) outliers start: 85 outliers final: 34 residues processed: 232 average time/residue: 0.1893 time to fit residues: 73.5206 Evaluate side-chains 174 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 518 ARG Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain K residue 665 PHE Chi-restraints excluded: chain K residue 755 ASN Chi-restraints excluded: chain K residue 1560 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain D residue 15 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 30.0000 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN A 280 GLN A 705 GLN A 952 GLN C 114 ASN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN E 19 HIS E 48 GLN H 158 HIS I 188 GLN K 325 GLN K 358 GLN K 429 GLN K 581 GLN K 701 GLN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1206 GLN K1259 GLN K1445 ASN ** K1446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1517 ASN K1599 ASN J 50 GLN J 251 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.092893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056258 restraints weight = 104457.617| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.66 r_work: 0.2827 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29392 Z= 0.127 Angle : 0.556 10.542 39856 Z= 0.286 Chirality : 0.041 0.282 4514 Planarity : 0.004 0.054 5010 Dihedral : 6.462 108.452 3953 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 2.76 % Allowed : 8.28 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3510 helix: 1.55 (0.14), residues: 1552 sheet: 0.68 (0.23), residues: 539 loop : -1.78 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K1377 TYR 0.017 0.001 TYR E 58 PHE 0.016 0.001 PHE J 62 TRP 0.009 0.001 TRP K1331 HIS 0.004 0.001 HIS J 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (29381) covalent geometry : angle 0.55503 / 0.29 (39827) SS BOND : bond 0.00183 / 0.09 ( 4) SS BOND : angle 0.69225 / 0.38 ( 8) hydrogen bonds : bond 0.04788 / 3.30 ( 1430) hydrogen bonds : angle 4.74766 / 3.32 ( 4152) link_BETA1-4 : bond 0.00186 / 0.09 ( 3) link_BETA1-4 : angle 1.89726 / 1.20 ( 9) link_NAG-ASN : bond 0.00178 / 0.09 ( 4) link_NAG-ASN : angle 1.73668 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 137 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: A 442 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9194 (tt) REVERT: A 892 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7930 (pp20) REVERT: A 894 ASN cc_start: 0.9157 (t0) cc_final: 0.8890 (t0) REVERT: C 75 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8895 (m) REVERT: C 135 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8165 (p90) REVERT: C 242 MET cc_start: 0.9157 (mmt) cc_final: 0.8833 (mmm) REVERT: E 31 MET cc_start: 0.8535 (tmm) cc_final: 0.8158 (tmm) REVERT: G 72 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8593 (tm-30) REVERT: H 187 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8739 (t0) REVERT: K 358 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8650 (tm-30) REVERT: K 712 MET cc_start: 0.9491 (tmm) cc_final: 0.9019 (tmm) REVERT: K 1417 MET cc_start: 0.9449 (ptp) cc_final: 0.9197 (ptm) REVERT: K 1474 MET cc_start: 0.8681 (mmp) cc_final: 0.8314 (mmp) REVERT: K 1524 MET cc_start: 0.9437 (mmm) cc_final: 0.9107 (mmm) REVERT: D 15 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7529 (m-10) outliers start: 86 outliers final: 47 residues processed: 213 average time/residue: 0.1783 time to fit residues: 64.1978 Evaluate side-chains 186 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 892 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 200 PHE Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 358 GLN Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain K residue 665 PHE Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 755 ASN Chi-restraints excluded: chain K residue 1560 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 50 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 309 optimal weight: 4.9990 chunk 35 optimal weight: 0.0470 chunk 326 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 292 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 284 optimal weight: 0.0670 chunk 258 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 GLN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.091940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.056384 restraints weight = 105184.593| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.87 r_work: 0.2788 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29392 Z= 0.135 Angle : 0.545 12.919 39856 Z= 0.279 Chirality : 0.041 0.294 4514 Planarity : 0.004 0.056 5010 Dihedral : 6.383 108.216 3945 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 2.54 % Allowed : 9.37 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3510 helix: 1.52 (0.14), residues: 1565 sheet: 0.69 (0.23), residues: 539 loop : -1.76 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 514 TYR 0.012 0.001 TYR B 214 PHE 0.014 0.001 PHE K1175 TRP 0.009 0.001 TRP A 163 HIS 0.003 0.001 HIS I 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (29381) covalent geometry : angle 0.54298 / 0.28 (39827) SS BOND : bond 0.00149 / 0.07 ( 4) SS BOND : angle 1.30562 / 0.66 ( 8) hydrogen bonds : bond 0.04397 / 3.03 ( 1430) hydrogen bonds : angle 4.58810 / 3.21 ( 4152) link_BETA1-4 : bond 0.00189 / 0.09 ( 3) link_BETA1-4 : angle 1.92479 / 1.20 ( 9) link_NAG-ASN : bond 0.00132 / 0.07 ( 4) link_NAG-ASN : angle 1.77569 / 1.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 132 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: A 442 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9225 (tt) REVERT: A 892 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7981 (pp20) REVERT: A 894 ASN cc_start: 0.9163 (t0) cc_final: 0.8782 (t0) REVERT: B 280 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: C 29 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8544 (mpp) REVERT: C 75 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8921 (m) REVERT: C 135 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8174 (p90) REVERT: C 242 MET cc_start: 0.9084 (mmt) cc_final: 0.8714 (mmm) REVERT: E 31 MET cc_start: 0.8543 (tmm) cc_final: 0.8188 (tmm) REVERT: F 73 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8196 (pmt-80) REVERT: G 72 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8632 (tm-30) REVERT: H 187 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8743 (t0) REVERT: K 358 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8967 (tm-30) REVERT: K 712 MET cc_start: 0.9494 (tmm) cc_final: 0.9004 (tmm) REVERT: K 1417 MET cc_start: 0.9457 (ptp) cc_final: 0.9205 (ptm) REVERT: K 1474 MET cc_start: 0.8695 (mmp) cc_final: 0.8336 (mmp) REVERT: K 1524 MET cc_start: 0.9455 (mmm) cc_final: 0.9174 (mmm) REVERT: D 15 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7482 (m-10) outliers start: 79 outliers final: 50 residues processed: 201 average time/residue: 0.1682 time to fit residues: 56.3286 Evaluate side-chains 190 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 128 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 892 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 358 GLN Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain K residue 665 PHE Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 755 ASN Chi-restraints excluded: chain K residue 1345 ASP Chi-restraints excluded: chain K residue 1536 ILE Chi-restraints excluded: chain K residue 1560 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 50 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 53 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 287 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 177 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 329 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS H 199 ASN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1325 HIS ** 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 = 0.3878 r_free = 0.3878 target = 0.090981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053845 restraints weight = 103995.073| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.60 r_work: 0.2748 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 29392 Z= 0.264 Angle : 0.617 9.179 39856 Z= 0.321 Chirality : 0.044 0.306 4514 Planarity : 0.004 0.056 5010 Dihedral : 6.645 109.536 3942 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.78 % Favored : 93.19 % Rotamer: Outliers : 3.05 % Allowed : 9.56 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3510 helix: 1.46 (0.14), residues: 1562 sheet: 0.48 (0.23), residues: 539 loop : -1.89 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 827 TYR 0.021 0.002 TYR B 200 PHE 0.019 0.001 PHE B 151 TRP 0.008 0.001 TRP A 163 HIS 0.006 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.26 (29381) covalent geometry : angle 0.61450 / 0.32 (39827) SS BOND : bond 0.00199 / 0.10 ( 4) SS BOND : angle 1.38319 / 0.71 ( 8) hydrogen bonds : bond 0.05152 / 3.50 ( 1430) hydrogen bonds : angle 4.69095 / 3.29 ( 4152) link_BETA1-4 : bond 0.00240 / 0.10 ( 3) link_BETA1-4 : angle 2.04014 / 1.26 ( 9) link_NAG-ASN : bond 0.00228 / 0.11 ( 4) link_NAG-ASN : angle 2.19312 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 125 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: A 442 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9235 (tt) REVERT: A 892 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: A 894 ASN cc_start: 0.9222 (t0) cc_final: 0.8950 (t0) REVERT: B 280 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: C 29 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8733 (mpp) REVERT: C 242 MET cc_start: 0.9105 (mmt) cc_final: 0.8762 (mmm) REVERT: E 31 MET cc_start: 0.8681 (tmm) cc_final: 0.8387 (tmm) REVERT: F 73 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8228 (pmt-80) REVERT: G 72 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8747 (tm-30) REVERT: H 187 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8764 (t0) REVERT: K 575 MET cc_start: 0.9318 (mmm) cc_final: 0.9039 (mmm) REVERT: K 712 MET cc_start: 0.9497 (tmm) cc_final: 0.8996 (tmm) REVERT: K 1382 MET cc_start: 0.9478 (mtt) cc_final: 0.9265 (tmm) REVERT: K 1417 MET cc_start: 0.9446 (ptp) cc_final: 0.9194 (ptm) REVERT: K 1474 MET cc_start: 0.8709 (mmp) cc_final: 0.8347 (mmp) REVERT: K 1524 MET cc_start: 0.9492 (mmm) cc_final: 0.9206 (mmm) REVERT: D 15 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7541 (m-10) outliers start: 95 outliers final: 62 residues processed: 210 average time/residue: 0.1548 time to fit residues: 54.2111 Evaluate side-chains 194 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 123 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 892 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 200 PHE Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 332 CYS Chi-restraints excluded: chain K residue 346 PHE Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain K residue 665 PHE Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 1345 ASP Chi-restraints excluded: chain K residue 1532 ARG Chi-restraints excluded: chain K residue 1536 ILE Chi-restraints excluded: chain K residue 1560 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 157 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 264 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 274 optimal weight: 40.0000 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 338 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 175 ASN K 137 ASN ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1179 ASN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.091191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055739 restraints weight = 105666.994| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.82 r_work: 0.2783 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29392 Z= 0.116 Angle : 0.539 11.269 39856 Z= 0.276 Chirality : 0.041 0.302 4514 Planarity : 0.004 0.056 5010 Dihedral : 6.318 108.222 3934 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 2.57 % Allowed : 10.69 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3510 helix: 1.56 (0.14), residues: 1572 sheet: 0.64 (0.23), residues: 535 loop : -1.85 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K1370 TYR 0.013 0.001 TYR B 214 PHE 0.015 0.001 PHE J 62 TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS K1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (29381) covalent geometry : angle 0.53696 / 0.28 (39827) SS BOND : bond 0.00156 / 0.07 ( 4) SS BOND : angle 0.94387 / 0.49 ( 8) hydrogen bonds : bond 0.03985 / 2.75 ( 1430) hydrogen bonds : angle 4.48211 / 3.14 ( 4152) link_BETA1-4 : bond 0.00365 / 0.17 ( 3) link_BETA1-4 : angle 2.07501 / 1.31 ( 9) link_NAG-ASN : bond 0.00204 / 0.11 ( 4) link_NAG-ASN : angle 1.76795 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 129 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: A 442 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9206 (tt) REVERT: A 892 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8026 (pp20) REVERT: A 894 ASN cc_start: 0.9171 (t0) cc_final: 0.8898 (t0) REVERT: B 280 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: C 29 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8796 (mpp) REVERT: C 135 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8102 (p90) REVERT: C 242 MET cc_start: 0.9076 (mmt) cc_final: 0.8784 (mmm) REVERT: E 31 MET cc_start: 0.8610 (tmm) cc_final: 0.8289 (tmm) REVERT: F 73 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8231 (pmt-80) REVERT: G 72 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: H 187 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8725 (t0) REVERT: K 712 MET cc_start: 0.9528 (tmm) cc_final: 0.9028 (tmm) REVERT: K 1417 MET cc_start: 0.9453 (ptp) cc_final: 0.9195 (ptm) REVERT: K 1470 MET cc_start: 0.7759 (mmp) cc_final: 0.7533 (mmp) REVERT: K 1474 MET cc_start: 0.8667 (mmp) cc_final: 0.8430 (mmm) REVERT: K 1524 MET cc_start: 0.9557 (mmm) cc_final: 0.9229 (mmm) REVERT: D 15 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7426 (m-10) outliers start: 80 outliers final: 51 residues processed: 201 average time/residue: 0.1809 time to fit residues: 60.8271 Evaluate side-chains 187 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 892 GLU Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 332 CYS Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain K residue 665 PHE Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 1345 ASP Chi-restraints excluded: chain K residue 1532 ARG Chi-restraints excluded: chain K residue 1536 ILE Chi-restraints excluded: chain K residue 1560 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 286 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 chunk 250 optimal weight: 40.0000 chunk 41 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 308 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.090573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054954 restraints weight = 105958.975| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.68 r_work: 0.2758 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29392 Z= 0.168 Angle : 0.565 11.457 39856 Z= 0.289 Chirality : 0.042 0.305 4514 Planarity : 0.004 0.055 5010 Dihedral : 6.285 108.604 3932 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.24 % Favored : 93.73 % Rotamer: Outliers : 2.70 % Allowed : 10.91 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3510 helix: 1.57 (0.13), residues: 1574 sheet: 0.59 (0.23), residues: 534 loop : -1.88 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 827 TYR 0.014 0.001 TYR B 214 PHE 0.013 0.001 PHE K 349 TRP 0.009 0.001 TRP A 163 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (29381) covalent geometry : angle 0.56282 / 0.29 (39827) SS BOND : bond 0.00165 / 0.08 ( 4) SS BOND : angle 0.99055 / 0.50 ( 8) hydrogen bonds : bond 0.04223 / 2.89 ( 1430) hydrogen bonds : angle 4.46790 / 3.13 ( 4152) link_BETA1-4 : bond 0.00278 / 0.13 ( 3) link_BETA1-4 : angle 2.06480 / 1.28 ( 9) link_NAG-ASN : bond 0.00094 / 0.05 ( 4) link_NAG-ASN : angle 1.94577 / 1.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 128 time to evaluate : 1.205 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: A 211 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: A 442 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9209 (tt) REVERT: A 892 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8041 (pp20) REVERT: A 894 ASN cc_start: 0.9243 (t0) cc_final: 0.8975 (t0) REVERT: B 280 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: C 29 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8772 (mpp) REVERT: C 135 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8124 (p90) REVERT: C 242 MET cc_start: 0.9095 (mmt) cc_final: 0.8808 (mmm) REVERT: E 31 MET cc_start: 0.8642 (tmm) cc_final: 0.8298 (tmm) REVERT: F 68 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8421 (tt) REVERT: F 73 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8237 (pmt-80) REVERT: G 72 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8713 (tm-30) REVERT: H 187 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8742 (t0) REVERT: K 186 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.6863 (m90) REVERT: K 575 MET cc_start: 0.9344 (mmm) cc_final: 0.9023 (mmm) REVERT: K 712 MET cc_start: 0.9533 (tmm) cc_final: 0.9009 (tmm) REVERT: K 1417 MET cc_start: 0.9443 (ptp) cc_final: 0.9182 (ptm) REVERT: K 1470 MET cc_start: 0.7797 (mmp) cc_final: 0.7591 (mmp) REVERT: K 1474 MET cc_start: 0.8687 (mmp) cc_final: 0.8449 (mmm) REVERT: K 1524 MET cc_start: 0.9543 (mmm) cc_final: 0.9203 (mmm) REVERT: D 15 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7335 (m-10) outliers start: 84 outliers final: 60 residues processed: 205 average time/residue: 0.1859 time to fit residues: 63.6347 Evaluate side-chains 198 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 126 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 892 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 186 HIS Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 332 CYS Chi-restraints excluded: chain K residue 346 PHE Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain K residue 665 PHE Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 1345 ASP Chi-restraints excluded: chain K residue 1532 ARG Chi-restraints excluded: chain K residue 1536 ILE Chi-restraints excluded: chain K residue 1560 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1541 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.091464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055826 restraints weight = 104399.829| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.83 r_work: 0.2771 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29392 Z= 0.127 Angle : 0.555 13.341 39856 Z= 0.280 Chirality : 0.041 0.305 4514 Planarity : 0.004 0.056 5010 Dihedral : 6.188 107.748 3932 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 2.57 % Allowed : 11.75 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3510 helix: 1.63 (0.14), residues: 1575 sheet: 0.63 (0.23), residues: 535 loop : -1.84 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 147 TYR 0.013 0.001 TYR B 214 PHE 0.014 0.001 PHE K 349 TRP 0.010 0.001 TRP A 163 HIS 0.003 0.001 HIS K1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (29381) covalent geometry : angle 0.55316 / 0.28 (39827) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 0.84610 / 0.43 ( 8) hydrogen bonds : bond 0.03829 / 2.64 ( 1430) hydrogen bonds : angle 4.38354 / 3.07 ( 4152) link_BETA1-4 : bond 0.00294 / 0.13 ( 3) link_BETA1-4 : angle 2.08340 / 1.29 ( 9) link_NAG-ASN : bond 0.00152 / 0.08 ( 4) link_NAG-ASN : angle 1.82321 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 130 time to evaluate : 1.165 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: A 211 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: A 442 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9218 (tt) REVERT: A 892 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8047 (pp20) REVERT: A 894 ASN cc_start: 0.9167 (t0) cc_final: 0.8889 (t0) REVERT: C 29 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8734 (mpp) REVERT: C 135 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8153 (p90) REVERT: C 242 MET cc_start: 0.9057 (mmt) cc_final: 0.8785 (mmm) REVERT: E 31 MET cc_start: 0.8617 (tmm) cc_final: 0.8315 (tmm) REVERT: E 61 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.9150 (p) REVERT: F 68 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8412 (tt) REVERT: F 73 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8230 (pmt-80) REVERT: G 57 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9140 (ptmm) REVERT: G 72 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: H 187 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8735 (t0) REVERT: H 201 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8611 (pm20) REVERT: K 575 MET cc_start: 0.9379 (mmm) cc_final: 0.9066 (mmm) REVERT: K 712 MET cc_start: 0.9536 (tmm) cc_final: 0.9020 (tmm) REVERT: K 1142 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8697 (m-80) REVERT: K 1417 MET cc_start: 0.9450 (ptp) cc_final: 0.9184 (ptm) REVERT: K 1427 MET cc_start: 0.8873 (mmm) cc_final: 0.8505 (mpp) REVERT: K 1474 MET cc_start: 0.8677 (mmp) cc_final: 0.8428 (mmm) REVERT: K 1524 MET cc_start: 0.9539 (mmm) cc_final: 0.9209 (mmm) REVERT: D 15 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7351 (m-10) outliers start: 80 outliers final: 58 residues processed: 201 average time/residue: 0.1845 time to fit residues: 61.4909 Evaluate side-chains 200 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 129 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 892 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 332 CYS Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain K residue 665 PHE Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 1142 TYR Chi-restraints excluded: chain K residue 1345 ASP Chi-restraints excluded: chain K residue 1527 PHE Chi-restraints excluded: chain K residue 1532 ARG Chi-restraints excluded: chain K residue 1536 ILE Chi-restraints excluded: chain K residue 1560 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 153 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 302 optimal weight: 0.0030 chunk 57 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.085360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053174 restraints weight = 112458.208| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.22 r_work: 0.2771 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29392 Z= 0.109 Angle : 0.543 12.490 39856 Z= 0.274 Chirality : 0.041 0.306 4514 Planarity : 0.004 0.056 5010 Dihedral : 6.041 107.260 3932 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.62 % Rotamer: Outliers : 2.50 % Allowed : 12.03 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3510 helix: 1.68 (0.14), residues: 1575 sheet: 0.66 (0.23), residues: 534 loop : -1.79 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K1532 TYR 0.012 0.001 TYR A 672 PHE 0.013 0.001 PHE K 349 TRP 0.010 0.001 TRP A 163 HIS 0.003 0.000 HIS I 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (29381) covalent geometry : angle 0.54129 / 0.27 (39827) SS BOND : bond 0.00147 / 0.07 ( 4) SS BOND : angle 0.77044 / 0.40 ( 8) hydrogen bonds : bond 0.03511 / 2.42 ( 1430) hydrogen bonds : angle 4.28853 / 3.00 ( 4152) link_BETA1-4 : bond 0.00286 / 0.13 ( 3) link_BETA1-4 : angle 2.06116 / 1.28 ( 9) link_NAG-ASN : bond 0.00201 / 0.10 ( 4) link_NAG-ASN : angle 1.78028 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 129 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9215 (tt) REVERT: A 892 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8048 (pp20) REVERT: A 894 ASN cc_start: 0.9217 (t0) cc_final: 0.8944 (t0) REVERT: C 29 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8769 (mpp) REVERT: C 135 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8196 (p90) REVERT: C 242 MET cc_start: 0.9053 (mmt) cc_final: 0.8794 (mmm) REVERT: E 31 MET cc_start: 0.8620 (tmm) cc_final: 0.8302 (tmm) REVERT: E 61 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9112 (p) REVERT: F 73 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8207 (pmt-80) REVERT: G 57 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9138 (ptmm) REVERT: G 72 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8693 (tm-30) REVERT: H 187 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8748 (t0) REVERT: H 201 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8648 (pm20) REVERT: K 575 MET cc_start: 0.9378 (mmm) cc_final: 0.8913 (mmm) REVERT: K 712 MET cc_start: 0.9554 (tmm) cc_final: 0.9028 (tmm) REVERT: K 1142 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: K 1417 MET cc_start: 0.9444 (ptp) cc_final: 0.9182 (ptm) REVERT: K 1474 MET cc_start: 0.8627 (mmp) cc_final: 0.8370 (mmm) REVERT: K 1524 MET cc_start: 0.9531 (mmm) cc_final: 0.9208 (mmm) REVERT: J 195 MET cc_start: 0.9412 (mmm) cc_final: 0.8985 (mpp) REVERT: D 15 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7396 (m-10) outliers start: 78 outliers final: 56 residues processed: 197 average time/residue: 0.1747 time to fit residues: 57.1279 Evaluate side-chains 195 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 128 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 892 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 332 CYS Chi-restraints excluded: chain K residue 346 PHE Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain K residue 665 PHE Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 1142 TYR Chi-restraints excluded: chain K residue 1345 ASP Chi-restraints excluded: chain K residue 1532 ARG Chi-restraints excluded: chain K residue 1560 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 93 optimal weight: 5.9990 chunk 231 optimal weight: 0.0000 chunk 162 optimal weight: 5.9990 chunk 333 optimal weight: 0.8980 chunk 344 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 271 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 70 optimal weight: 0.0970 chunk 294 optimal weight: 0.0170 overall best weight: 0.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 GLN A 775 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1037 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.086095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.053606 restraints weight = 112597.280| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.05 r_work: 0.2800 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29392 Z= 0.096 Angle : 0.550 15.809 39856 Z= 0.273 Chirality : 0.040 0.305 4514 Planarity : 0.004 0.055 5010 Dihedral : 5.674 106.507 3923 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.19 % Rotamer: Outliers : 2.12 % Allowed : 12.64 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3510 helix: 1.76 (0.14), residues: 1567 sheet: 0.71 (0.23), residues: 552 loop : -1.75 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG K1590 TYR 0.012 0.001 TYR A 672 PHE 0.037 0.001 PHE J 62 TRP 0.011 0.001 TRP A 163 HIS 0.004 0.000 HIS I 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (29381) covalent geometry : angle 0.54858 / 0.27 (39827) SS BOND : bond 0.00135 / 0.06 ( 4) SS BOND : angle 0.65278 / 0.35 ( 8) hydrogen bonds : bond 0.03160 / 2.20 ( 1430) hydrogen bonds : angle 4.22306 / 2.95 ( 4152) link_BETA1-4 : bond 0.00367 / 0.19 ( 3) link_BETA1-4 : angle 2.08278 / 1.31 ( 9) link_NAG-ASN : bond 0.00285 / 0.15 ( 4) link_NAG-ASN : angle 1.67727 / 0.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 132 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9209 (tt) REVERT: A 892 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7711 (pp20) REVERT: A 894 ASN cc_start: 0.9212 (t0) cc_final: 0.8943 (t0) REVERT: C 135 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8109 (p90) REVERT: C 242 MET cc_start: 0.9012 (mmt) cc_final: 0.8772 (mmm) REVERT: E 31 MET cc_start: 0.8600 (tmm) cc_final: 0.8322 (tmm) REVERT: E 61 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.9060 (p) REVERT: F 73 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8229 (pmt-80) REVERT: G 57 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9048 (ptmm) REVERT: H 149 ASN cc_start: 0.9377 (OUTLIER) cc_final: 0.8737 (p0) REVERT: H 187 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8717 (t0) REVERT: K 712 MET cc_start: 0.9544 (tmm) cc_final: 0.9029 (tmm) REVERT: K 1142 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: K 1417 MET cc_start: 0.9433 (ptp) cc_final: 0.9163 (ptm) REVERT: K 1474 MET cc_start: 0.8629 (mmp) cc_final: 0.8360 (mmm) REVERT: K 1524 MET cc_start: 0.9540 (mmm) cc_final: 0.9189 (mmm) REVERT: D 15 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7428 (m-10) outliers start: 66 outliers final: 48 residues processed: 189 average time/residue: 0.1809 time to fit residues: 57.0911 Evaluate side-chains 184 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 126 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 892 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 332 CYS Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain K residue 665 PHE Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 1142 TYR Chi-restraints excluded: chain K residue 1470 MET Chi-restraints excluded: chain K residue 1527 PHE Chi-restraints excluded: chain K residue 1532 ARG Chi-restraints excluded: chain K residue 1560 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 203 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 319 optimal weight: 50.0000 chunk 350 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 225 optimal weight: 0.0970 chunk 106 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.086424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.051056 restraints weight = 113808.249| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.19 r_work: 0.2819 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29392 Z= 0.130 Angle : 0.573 14.352 39856 Z= 0.286 Chirality : 0.041 0.307 4514 Planarity : 0.004 0.055 5010 Dihedral : 5.538 107.267 3917 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 2.09 % Allowed : 12.84 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3510 helix: 1.79 (0.14), residues: 1565 sheet: 0.66 (0.23), residues: 556 loop : -1.75 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 32 TYR 0.014 0.001 TYR B 214 PHE 0.021 0.001 PHE F 102 TRP 0.008 0.001 TRP K1549 HIS 0.003 0.000 HIS K1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (29381) covalent geometry : angle 0.57144 / 0.29 (39827) SS BOND : bond 0.00135 / 0.07 ( 4) SS BOND : angle 0.74217 / 0.38 ( 8) hydrogen bonds : bond 0.03594 / 2.49 ( 1430) hydrogen bonds : angle 4.25318 / 2.97 ( 4152) link_BETA1-4 : bond 0.00305 / 0.14 ( 3) link_BETA1-4 : angle 1.98034 / 1.23 ( 9) link_NAG-ASN : bond 0.00136 / 0.07 ( 4) link_NAG-ASN : angle 1.80840 / 1.02 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 127 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9232 (tt) REVERT: A 892 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8047 (pp20) REVERT: A 894 ASN cc_start: 0.9139 (t0) cc_final: 0.8856 (t0) REVERT: C 135 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8141 (p90) REVERT: C 242 MET cc_start: 0.9007 (mmt) cc_final: 0.8786 (mmm) REVERT: E 31 MET cc_start: 0.8589 (tmm) cc_final: 0.8265 (tmm) REVERT: E 61 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.9133 (p) REVERT: F 73 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8190 (pmt-80) REVERT: G 57 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9098 (ptmm) REVERT: H 149 ASN cc_start: 0.9333 (OUTLIER) cc_final: 0.8702 (p0) REVERT: H 187 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8705 (t0) REVERT: K 186 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6557 (m90) REVERT: K 712 MET cc_start: 0.9542 (tmm) cc_final: 0.9013 (tmm) REVERT: K 1142 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8619 (m-80) REVERT: K 1417 MET cc_start: 0.9407 (ptp) cc_final: 0.9126 (ptm) REVERT: K 1474 MET cc_start: 0.8594 (mmp) cc_final: 0.8296 (mmm) REVERT: K 1524 MET cc_start: 0.9499 (mmm) cc_final: 0.9158 (mmm) REVERT: J 195 MET cc_start: 0.9427 (mmm) cc_final: 0.8959 (mpp) REVERT: J 196 MET cc_start: 0.9106 (mmm) cc_final: 0.8865 (mmm) REVERT: D 15 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7471 (m-10) outliers start: 65 outliers final: 51 residues processed: 183 average time/residue: 0.1743 time to fit residues: 52.7544 Evaluate side-chains 189 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 127 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 892 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 186 HIS Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 332 CYS Chi-restraints excluded: chain K residue 346 PHE Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain K residue 665 PHE Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 1142 TYR Chi-restraints excluded: chain K residue 1345 ASP Chi-restraints excluded: chain K residue 1532 ARG Chi-restraints excluded: chain K residue 1560 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 206 HIS Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 94 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 187 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.091669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056166 restraints weight = 104839.458| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.79 r_work: 0.2779 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29392 Z= 0.127 Angle : 0.576 13.644 39856 Z= 0.289 Chirality : 0.041 0.304 4514 Planarity : 0.004 0.054 5010 Dihedral : 5.488 106.871 3915 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.79 % Rotamer: Outliers : 2.15 % Allowed : 12.90 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3510 helix: 1.78 (0.14), residues: 1566 sheet: 0.64 (0.23), residues: 547 loop : -1.72 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.012 0.001 TYR A 672 PHE 0.031 0.001 PHE J 62 TRP 0.009 0.001 TRP A 163 HIS 0.003 0.001 HIS G 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (29381) covalent geometry : angle 0.57461 / 0.29 (39827) SS BOND : bond 0.00140 / 0.07 ( 4) SS BOND : angle 0.70479 / 0.36 ( 8) hydrogen bonds : bond 0.03600 / 2.51 ( 1430) hydrogen bonds : angle 4.25115 / 2.97 ( 4152) link_BETA1-4 : bond 0.00277 / 0.12 ( 3) link_BETA1-4 : angle 1.99619 / 1.23 ( 9) link_NAG-ASN : bond 0.00137 / 0.07 ( 4) link_NAG-ASN : angle 1.77156 / 1.00 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8850.21 seconds wall clock time: 151 minutes 50.91 seconds (9110.91 seconds total)