Starting phenix.real_space_refine on Tue May 27 03:23:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eoi_28376/05_2025/8eoi_28376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eoi_28376/05_2025/8eoi_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_28376/05_2025/8eoi_28376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eoi_28376/05_2025/8eoi_28376.map" model { file = "/net/cci-nas-00/data/ceres_data/8eoi_28376/05_2025/8eoi_28376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eoi_28376/05_2025/8eoi_28376.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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: 17.43, per 1000 atoms: 0.61 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: 7.83 Conformation dependent library (CDL) restraints added in 3.7 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: 3.20 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: 11.64 Time building geometry restraints manager: 9.06 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: 16881 21.85 - 43.70: 685 43.70 - 65.54: 89 65.54 - 87.39: 20 87.39 - 109.24: 4 Dihedral angle restraints: 17679 sinusoidal: 7288 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 17676 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: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.290 Check model and map are aligned: 0.220 Set scattering table: 0.310 Process input model: 66.250 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 11.715 109.238 10941 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (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 TRP 0.010 0.001 TRP J 103 HIS 0.002 0.000 HIS G 74 PHE 0.009 0.001 PHE K 185 TYR 0.010 0.001 TYR B 214 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 4) link_NAG-ASN : angle 2.15216 ( 12) link_BETA1-4 : bond 0.00371 ( 3) link_BETA1-4 : angle 2.61721 ( 9) hydrogen bonds : bond 0.15957 ( 1430) hydrogen bonds : angle 5.62631 ( 4152) SS BOND : bond 0.00290 ( 4) SS BOND : angle 1.07785 ( 8) covalent geometry : bond 0.00234 (29381) covalent geometry : angle 0.50560 (39827) *********************** 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 : 3.197 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: 0.7355 (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: 0.9208 (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: 0.3784 time to fit residues: 146.3460 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 : 3.150 ------------------------------------------------------------------------------- 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 297 optimal weight: 0.0020 chunk 266 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 275 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 319 optimal weight: 50.0000 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3902 r_free = 0.3902 target = 0.092902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055942 restraints weight = 103467.851| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.69 r_work: 0.2780 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0881 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= 0.119 Angle : 0.550 10.420 39856 Z= 0.283 Chirality : 0.041 0.284 4514 Planarity : 0.004 0.054 5010 Dihedral : 7.133 92.031 4183 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 2.57 % Allowed : 8.41 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3510 helix: 1.58 (0.14), residues: 1551 sheet: 0.69 (0.23), residues: 539 loop : -1.78 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K1331 HIS 0.005 0.001 HIS J 314 PHE 0.017 0.001 PHE J 62 TYR 0.016 0.001 TYR E 58 ARG 0.005 0.000 ARG K1377 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 4) link_NAG-ASN : angle 1.84389 ( 12) link_BETA1-4 : bond 0.00353 ( 3) link_BETA1-4 : angle 1.98287 ( 9) hydrogen bonds : bond 0.04715 ( 1430) hydrogen bonds : angle 4.72821 ( 4152) SS BOND : bond 0.00191 ( 4) SS BOND : angle 0.67392 ( 8) covalent geometry : bond 0.00249 (29381) covalent geometry : angle 0.54813 (39827) *********************** 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 219 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 139 time to evaluate : 3.104 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: 0.8388 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: A 442 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9188 (tt) REVERT: A 892 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7907 (pp20) REVERT: A 894 ASN cc_start: 0.9145 (t0) cc_final: 0.8882 (t0) REVERT: C 75 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8892 (m) REVERT: C 135 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8095 (p90) REVERT: C 242 MET cc_start: 0.9115 (mmt) cc_final: 0.8771 (mmm) REVERT: E 31 MET cc_start: 0.8565 (tmm) cc_final: 0.8193 (tmm) REVERT: G 72 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8605 (tm-30) REVERT: H 187 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8760 (t0) REVERT: K 358 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: K 712 MET cc_start: 0.9491 (tmm) cc_final: 0.9019 (tmm) REVERT: K 1417 MET cc_start: 0.9444 (ptp) cc_final: 0.9188 (ptm) REVERT: K 1474 MET cc_start: 0.8669 (mmp) cc_final: 0.8297 (mmp) REVERT: K 1524 MET cc_start: 0.9443 (mmm) cc_final: 0.9132 (mmm) REVERT: D 15 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7515 (m-10) outliers start: 80 outliers final: 46 residues processed: 210 average time/residue: 0.3501 time to fit residues: 122.6245 Evaluate side-chains 185 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 3.119 ------------------------------------------------------------------------------- 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 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 495 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 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 263 optimal weight: 4.9990 chunk 343 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 331 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 326 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 142 HIS H 199 ASN K1190 GLN ** 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 = 0.3889 r_free = 0.3889 target = 0.090921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.054146 restraints weight = 104957.095| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.55 r_work: 0.2768 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29392 Z= 0.221 Angle : 0.592 9.694 39856 Z= 0.307 Chirality : 0.043 0.299 4514 Planarity : 0.004 0.056 5010 Dihedral : 7.058 94.327 4172 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.52 % Favored : 93.45 % Rotamer: Outliers : 2.73 % Allowed : 9.27 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3510 helix: 1.47 (0.14), residues: 1563 sheet: 0.58 (0.23), residues: 538 loop : -1.84 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.005 0.001 HIS B 189 PHE 0.017 0.001 PHE B 151 TYR 0.018 0.001 TYR B 200 ARG 0.003 0.000 ARG A 685 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 4) link_NAG-ASN : angle 2.10669 ( 12) link_BETA1-4 : bond 0.00181 ( 3) link_BETA1-4 : angle 1.99746 ( 9) hydrogen bonds : bond 0.05070 ( 1430) hydrogen bonds : angle 4.69690 ( 4152) SS BOND : bond 0.00309 ( 4) SS BOND : angle 1.37075 ( 8) covalent geometry : bond 0.00523 (29381) covalent geometry : angle 0.58959 (39827) *********************** 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 216 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 131 time to evaluate : 3.260 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: 0.8452 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: A 442 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9239 (tt) REVERT: A 892 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7938 (pp20) REVERT: A 894 ASN cc_start: 0.9189 (t0) cc_final: 0.8915 (t0) REVERT: B 280 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.6946 (m-80) REVERT: C 29 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8646 (mpp) REVERT: C 75 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9011 (m) REVERT: C 135 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8135 (p90) REVERT: C 242 MET cc_start: 0.9101 (mmt) cc_final: 0.8726 (mmm) REVERT: E 31 MET cc_start: 0.8590 (tmm) cc_final: 0.8263 (tmm) REVERT: F 73 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8210 (pmt-80) REVERT: G 72 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8717 (tm-30) REVERT: H 187 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8762 (t0) REVERT: K 712 MET cc_start: 0.9501 (tmm) cc_final: 0.9011 (tmm) REVERT: K 1417 MET cc_start: 0.9445 (ptp) cc_final: 0.9196 (ptm) REVERT: K 1474 MET cc_start: 0.8705 (mmp) cc_final: 0.8344 (mmp) REVERT: K 1524 MET cc_start: 0.9445 (mmm) cc_final: 0.9154 (mmm) REVERT: J 218 THR cc_start: 0.9695 (m) cc_final: 0.9481 (p) REVERT: D 15 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7556 (m-10) outliers start: 85 outliers final: 52 residues processed: 204 average time/residue: 0.3633 time to fit residues: 125.9930 Evaluate side-chains 191 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 128 time to evaluate : 3.237 ------------------------------------------------------------------------------- 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 481 LEU Chi-restraints excluded: chain A residue 495 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 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 272 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 171 optimal weight: 0.0270 chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 349 optimal weight: 0.7980 chunk 273 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3909 r_free = 0.3909 target = 0.091339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055886 restraints weight = 106247.507| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.75 r_work: 0.2788 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1293 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= 0.117 Angle : 0.529 10.781 39856 Z= 0.272 Chirality : 0.041 0.292 4514 Planarity : 0.004 0.055 5010 Dihedral : 6.742 91.228 4168 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 2.66 % Allowed : 9.88 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3510 helix: 1.58 (0.14), residues: 1564 sheet: 0.66 (0.23), residues: 539 loop : -1.79 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.003 0.001 HIS C 32 PHE 0.013 0.001 PHE K1175 TYR 0.012 0.001 TYR B 214 ARG 0.002 0.000 ARG K 685 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 4) link_NAG-ASN : angle 1.79107 ( 12) link_BETA1-4 : bond 0.00209 ( 3) link_BETA1-4 : angle 2.01673 ( 9) hydrogen bonds : bond 0.03992 ( 1430) hydrogen bonds : angle 4.48416 ( 4152) SS BOND : bond 0.00190 ( 4) SS BOND : angle 1.07430 ( 8) covalent geometry : bond 0.00256 (29381) covalent geometry : angle 0.52687 (39827) *********************** 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 211 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 128 time to evaluate : 3.508 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: 0.8443 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: A 442 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9220 (tt) REVERT: A 892 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7926 (pp20) REVERT: A 894 ASN cc_start: 0.9258 (t0) cc_final: 0.8996 (t0) REVERT: C 29 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8910 (mpp) REVERT: C 75 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8909 (m) REVERT: C 135 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8234 (p90) REVERT: C 242 MET cc_start: 0.9077 (mmt) cc_final: 0.8756 (mmm) REVERT: E 31 MET cc_start: 0.8625 (tmm) cc_final: 0.8306 (tmm) REVERT: E 61 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9135 (p) REVERT: F 73 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8184 (pmt-80) REVERT: G 72 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8657 (tm-30) REVERT: H 187 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8734 (t0) REVERT: K 575 MET cc_start: 0.9281 (mmm) cc_final: 0.8984 (mmm) REVERT: K 712 MET cc_start: 0.9504 (tmm) cc_final: 0.8993 (tmm) REVERT: K 1417 MET cc_start: 0.9450 (ptp) cc_final: 0.9192 (ptm) REVERT: K 1474 MET cc_start: 0.8698 (mmp) cc_final: 0.8340 (mmp) REVERT: K 1524 MET cc_start: 0.9451 (mmm) cc_final: 0.9153 (mmm) REVERT: K 1527 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: J 218 THR cc_start: 0.9692 (m) cc_final: 0.9484 (p) REVERT: D 15 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7567 (m-10) outliers start: 83 outliers final: 53 residues processed: 202 average time/residue: 0.3759 time to fit residues: 127.9344 Evaluate side-chains 193 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 128 time to evaluate : 3.408 ------------------------------------------------------------------------------- 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 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 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 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 135 PHE Chi-restraints excluded: chain C residue 140 VAL 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 150 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 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 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 50 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 95 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 chunk 293 optimal weight: 9.9990 chunk 301 optimal weight: 20.0000 chunk 273 optimal weight: 5.9990 chunk 290 optimal weight: 30.0000 chunk 345 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.091306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.055125 restraints weight = 103737.666| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.64 r_work: 0.2741 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 29392 Z= 0.216 Angle : 0.590 11.170 39856 Z= 0.304 Chirality : 0.043 0.306 4514 Planarity : 0.004 0.056 5010 Dihedral : 6.762 92.345 4164 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.52 % Favored : 93.45 % Rotamer: Outliers : 2.82 % Allowed : 10.59 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3510 helix: 1.53 (0.13), residues: 1573 sheet: 0.49 (0.23), residues: 539 loop : -1.89 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.005 0.001 HIS B 189 PHE 0.016 0.001 PHE B 151 TYR 0.018 0.001 TYR B 200 ARG 0.003 0.000 ARG A 827 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 4) link_NAG-ASN : angle 2.15328 ( 12) link_BETA1-4 : bond 0.00179 ( 3) link_BETA1-4 : angle 2.02930 ( 9) hydrogen bonds : bond 0.04691 ( 1430) hydrogen bonds : angle 4.55533 ( 4152) SS BOND : bond 0.00181 ( 4) SS BOND : angle 1.13656 ( 8) covalent geometry : bond 0.00513 (29381) covalent geometry : angle 0.58848 (39827) *********************** 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 215 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 127 time to evaluate : 3.430 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: 0.8470 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: A 442 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9219 (tt) REVERT: A 892 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8010 (pp20) REVERT: A 894 ASN cc_start: 0.9208 (t0) cc_final: 0.8933 (t0) REVERT: B 280 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: C 29 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8803 (mpp) REVERT: C 75 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9042 (m) REVERT: C 135 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8048 (p90) REVERT: C 242 MET cc_start: 0.9114 (mmt) cc_final: 0.8794 (mmm) REVERT: E 31 MET cc_start: 0.8631 (tmm) cc_final: 0.8315 (tmm) REVERT: F 73 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8249 (pmt-80) REVERT: G 72 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8790 (tm-30) REVERT: H 187 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8770 (t0) REVERT: K 575 MET cc_start: 0.9382 (mmm) cc_final: 0.9117 (mmm) REVERT: K 712 MET cc_start: 0.9521 (tmm) cc_final: 0.9005 (tmm) REVERT: K 1417 MET cc_start: 0.9449 (ptp) cc_final: 0.9193 (ptm) REVERT: K 1474 MET cc_start: 0.8665 (mmp) cc_final: 0.8424 (mmm) REVERT: K 1524 MET cc_start: 0.9453 (mmm) cc_final: 0.9153 (mmm) REVERT: K 1527 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: D 15 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7542 (m-10) outliers start: 88 outliers final: 61 residues processed: 204 average time/residue: 0.3724 time to fit residues: 127.9489 Evaluate side-chains 198 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 125 time to evaluate : 3.284 ------------------------------------------------------------------------------- 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 495 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 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 75 THR 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 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 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 200 PHE Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 304 ILE 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 168 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 294 optimal weight: 0.1980 chunk 290 optimal weight: 40.0000 chunk 216 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.091364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055599 restraints weight = 104844.883| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.75 r_work: 0.2766 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1562 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= 0.139 Angle : 0.546 10.290 39856 Z= 0.280 Chirality : 0.041 0.303 4514 Planarity : 0.004 0.056 5010 Dihedral : 6.618 88.111 4164 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 3.05 % Allowed : 10.78 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3510 helix: 1.61 (0.14), residues: 1573 sheet: 0.60 (0.23), residues: 535 loop : -1.87 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.003 0.001 HIS C 32 PHE 0.036 0.001 PHE J 62 TYR 0.013 0.001 TYR B 214 ARG 0.002 0.000 ARG K 685 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 4) link_NAG-ASN : angle 1.90865 ( 12) link_BETA1-4 : bond 0.00325 ( 3) link_BETA1-4 : angle 2.16415 ( 9) hydrogen bonds : bond 0.04029 ( 1430) hydrogen bonds : angle 4.42762 ( 4152) SS BOND : bond 0.00168 ( 4) SS BOND : angle 0.91271 ( 8) covalent geometry : bond 0.00321 (29381) covalent geometry : angle 0.54380 (39827) *********************** 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 224 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 129 time to evaluate : 2.735 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: 0.7860 (tm-30) REVERT: A 442 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9212 (tt) REVERT: A 892 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8009 (pp20) REVERT: A 894 ASN cc_start: 0.9234 (t0) cc_final: 0.8969 (t0) REVERT: C 29 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8828 (mpp) REVERT: C 75 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8965 (m) REVERT: C 135 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8085 (p90) REVERT: C 242 MET cc_start: 0.9062 (mmt) cc_final: 0.8795 (mmm) REVERT: E 31 MET cc_start: 0.8608 (tmm) cc_final: 0.8274 (tmm) REVERT: F 68 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8391 (tt) REVERT: F 73 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8234 (pmt-80) REVERT: G 57 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9143 (ptmm) REVERT: G 72 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8677 (tm-30) REVERT: H 187 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8744 (t0) REVERT: H 201 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8594 (pm20) REVERT: K 186 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6888 (m90) REVERT: K 575 MET cc_start: 0.9433 (mmm) cc_final: 0.9140 (mmm) REVERT: K 712 MET cc_start: 0.9533 (tmm) cc_final: 0.9019 (tmm) REVERT: K 1417 MET cc_start: 0.9445 (ptp) cc_final: 0.9180 (ptm) REVERT: K 1474 MET cc_start: 0.8660 (mmp) cc_final: 0.8416 (mmm) REVERT: K 1524 MET cc_start: 0.9449 (mmm) cc_final: 0.9146 (mmm) REVERT: K 1527 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: D 15 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7316 (m-10) outliers start: 95 outliers final: 63 residues processed: 213 average time/residue: 0.3896 time to fit residues: 137.7133 Evaluate side-chains 203 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 126 time to evaluate : 3.193 ------------------------------------------------------------------------------- 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 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 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 75 THR 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 C residue 151 MET 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 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 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 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 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 50 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 98 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 289 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 253 optimal weight: 20.0000 chunk 231 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3884 r_free = 0.3884 target = 0.090226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.054572 restraints weight = 105829.029| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.58 r_work: 0.2751 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29392 Z= 0.187 Angle : 0.583 16.060 39856 Z= 0.296 Chirality : 0.042 0.306 4514 Planarity : 0.004 0.056 5010 Dihedral : 6.629 87.635 4163 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.47 % Favored : 93.50 % Rotamer: Outliers : 2.76 % Allowed : 11.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3510 helix: 1.57 (0.13), residues: 1575 sheet: 0.53 (0.23), residues: 534 loop : -1.90 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.004 0.001 HIS B 189 PHE 0.017 0.001 PHE J 62 TYR 0.015 0.001 TYR B 200 ARG 0.002 0.000 ARG A 827 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 4) link_NAG-ASN : angle 2.07274 ( 12) link_BETA1-4 : bond 0.00219 ( 3) link_BETA1-4 : angle 2.14391 ( 9) hydrogen bonds : bond 0.04329 ( 1430) hydrogen bonds : angle 4.46291 ( 4152) SS BOND : bond 0.00178 ( 4) SS BOND : angle 0.98404 ( 8) covalent geometry : bond 0.00441 (29381) covalent geometry : angle 0.58090 (39827) *********************** 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 213 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 127 time to evaluate : 3.261 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: 0.8448 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: A 442 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9210 (tt) REVERT: A 892 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8042 (pp20) REVERT: A 894 ASN cc_start: 0.9195 (t0) cc_final: 0.8920 (t0) REVERT: C 29 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8770 (mpp) REVERT: C 75 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9031 (m) REVERT: C 135 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8053 (p90) REVERT: C 242 MET cc_start: 0.9085 (mmt) cc_final: 0.8822 (mmm) REVERT: E 31 MET cc_start: 0.8640 (tmm) cc_final: 0.8337 (tmm) REVERT: F 68 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8458 (tt) REVERT: F 73 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8232 (pmt-80) REVERT: G 72 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8730 (tm-30) REVERT: H 149 ASN cc_start: 0.9432 (OUTLIER) cc_final: 0.8840 (p0) REVERT: H 187 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8753 (t0) REVERT: H 201 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8590 (pm20) REVERT: I 93 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8419 (pp20) REVERT: K 186 HIS cc_start: 0.7524 (OUTLIER) cc_final: 0.6836 (m90) REVERT: K 575 MET cc_start: 0.9443 (mmm) cc_final: 0.9227 (mmm) REVERT: K 712 MET cc_start: 0.9519 (tmm) cc_final: 0.8972 (tmm) REVERT: K 1142 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8694 (m-80) REVERT: K 1417 MET cc_start: 0.9447 (ptp) cc_final: 0.9181 (ptm) REVERT: K 1427 MET cc_start: 0.8857 (mmm) cc_final: 0.8507 (mpp) REVERT: K 1474 MET cc_start: 0.8657 (mmp) cc_final: 0.8405 (mmm) REVERT: K 1524 MET cc_start: 0.9454 (mmm) cc_final: 0.9137 (mmm) REVERT: K 1527 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: D 15 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7328 (m-10) outliers start: 86 outliers final: 66 residues processed: 201 average time/residue: 0.3781 time to fit residues: 126.2645 Evaluate side-chains 208 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 126 time to evaluate : 3.171 ------------------------------------------------------------------------------- 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 60 MET 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 75 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 151 MET 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 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 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 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 1059 LEU 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 187 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 302 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.090878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055178 restraints weight = 105986.390| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.72 r_work: 0.2758 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29392 Z= 0.156 Angle : 0.563 12.164 39856 Z= 0.287 Chirality : 0.042 0.304 4514 Planarity : 0.004 0.060 5010 Dihedral : 6.547 83.958 4163 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 2.73 % Allowed : 11.87 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3510 helix: 1.62 (0.14), residues: 1575 sheet: 0.54 (0.23), residues: 534 loop : -1.87 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.003 0.001 HIS B 189 PHE 0.037 0.001 PHE J 62 TYR 0.013 0.001 TYR B 214 ARG 0.002 0.000 ARG A 827 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 4) link_NAG-ASN : angle 1.97594 ( 12) link_BETA1-4 : bond 0.00327 ( 3) link_BETA1-4 : angle 2.20617 ( 9) hydrogen bonds : bond 0.04035 ( 1430) hydrogen bonds : angle 4.40156 ( 4152) SS BOND : bond 0.00174 ( 4) SS BOND : angle 0.87556 ( 8) covalent geometry : bond 0.00366 (29381) covalent geometry : angle 0.56061 (39827) *********************** 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 213 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 128 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: A 442 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9202 (tt) REVERT: A 892 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8011 (pp20) REVERT: A 894 ASN cc_start: 0.9286 (t0) cc_final: 0.9036 (t0) REVERT: C 29 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8730 (mpp) REVERT: C 75 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9000 (m) REVERT: C 135 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7994 (p90) REVERT: C 242 MET cc_start: 0.9070 (mmt) cc_final: 0.8818 (mmm) REVERT: E 31 MET cc_start: 0.8687 (tmm) cc_final: 0.8369 (tmm) REVERT: F 68 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8500 (tt) REVERT: F 73 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8224 (pmt-80) REVERT: G 57 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9126 (ptmm) REVERT: G 72 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8681 (tm-30) REVERT: H 149 ASN cc_start: 0.9497 (OUTLIER) cc_final: 0.8892 (p0) REVERT: H 187 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8743 (t0) REVERT: H 201 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8593 (pm20) REVERT: K 186 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.6619 (m90) REVERT: K 575 MET cc_start: 0.9457 (mmm) cc_final: 0.9088 (mmm) REVERT: K 712 MET cc_start: 0.9537 (tmm) cc_final: 0.8994 (tmm) REVERT: K 1142 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: K 1417 MET cc_start: 0.9447 (ptp) cc_final: 0.9182 (ptm) REVERT: K 1474 MET cc_start: 0.8630 (mmp) cc_final: 0.8378 (mmm) REVERT: K 1524 MET cc_start: 0.9439 (mmm) cc_final: 0.9112 (mmm) REVERT: K 1527 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: D 15 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7342 (m-10) outliers start: 85 outliers final: 64 residues processed: 202 average time/residue: 0.3685 time to fit residues: 123.2645 Evaluate side-chains 207 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 127 time to evaluate : 3.179 ------------------------------------------------------------------------------- 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 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 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 75 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 151 MET 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 123 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 231 optimal weight: 0.2980 chunk 117 optimal weight: 0.0030 chunk 214 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 347 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 775 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1541 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.085378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052745 restraints weight = 112985.462| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.07 r_work: 0.2770 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29392 Z= 0.105 Angle : 0.546 13.615 39856 Z= 0.275 Chirality : 0.041 0.302 4514 Planarity : 0.004 0.055 5010 Dihedral : 6.333 80.932 4163 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 2.47 % Allowed : 12.39 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3510 helix: 1.71 (0.14), residues: 1574 sheet: 0.64 (0.23), residues: 535 loop : -1.78 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.004 0.000 HIS I 58 PHE 0.054 0.001 PHE J 62 TYR 0.012 0.001 TYR A 672 ARG 0.002 0.000 ARG J 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 4) link_NAG-ASN : angle 1.83822 ( 12) link_BETA1-4 : bond 0.00300 ( 3) link_BETA1-4 : angle 2.18451 ( 9) hydrogen bonds : bond 0.03447 ( 1430) hydrogen bonds : angle 4.27605 ( 4152) SS BOND : bond 0.00153 ( 4) SS BOND : angle 0.73579 ( 8) covalent geometry : bond 0.00232 (29381) covalent geometry : angle 0.54375 (39827) *********************** 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 204 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 127 time to evaluate : 3.535 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: 0.9535 (OUTLIER) cc_final: 0.9219 (tt) REVERT: A 892 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8058 (pp20) REVERT: A 894 ASN cc_start: 0.9210 (t0) cc_final: 0.8951 (t0) REVERT: C 29 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8840 (mpp) REVERT: C 75 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8931 (m) REVERT: C 135 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8183 (p90) REVERT: C 242 MET cc_start: 0.9057 (mmt) cc_final: 0.8807 (mmm) REVERT: E 31 MET cc_start: 0.8596 (tmm) cc_final: 0.8287 (tmm) REVERT: E 61 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9114 (p) REVERT: F 73 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8205 (pmt-80) REVERT: G 57 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9150 (ptmm) REVERT: G 72 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8732 (tm-30) REVERT: H 149 ASN cc_start: 0.9395 (m-40) cc_final: 0.8796 (p0) REVERT: H 187 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8744 (t0) REVERT: K 712 MET cc_start: 0.9540 (tmm) cc_final: 0.8983 (tmm) REVERT: K 1142 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: K 1417 MET cc_start: 0.9433 (ptp) cc_final: 0.9165 (ptm) REVERT: K 1474 MET cc_start: 0.8582 (mmp) cc_final: 0.8313 (mmm) REVERT: K 1524 MET cc_start: 0.9452 (mmm) cc_final: 0.9137 (mmm) REVERT: K 1527 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: J 196 MET cc_start: 0.9066 (mmm) cc_final: 0.8777 (mmm) REVERT: D 15 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7425 (m-10) outliers start: 77 outliers final: 56 residues processed: 192 average time/residue: 0.3899 time to fit residues: 124.0714 Evaluate side-chains 195 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 126 time to evaluate : 3.544 ------------------------------------------------------------------------------- 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 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 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 75 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 151 MET 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 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 196 ASN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 184 optimal weight: 5.9990 chunk 290 optimal weight: 30.0000 chunk 50 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 145 optimal weight: 5.9990 chunk 346 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 266 optimal weight: 0.0020 chunk 329 optimal weight: 0.0570 overall best weight: 1.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3886 r_free = 0.3886 target = 0.085266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.052618 restraints weight = 112943.290| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.02 r_work: 0.2771 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1862 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= 0.114 Angle : 0.567 16.679 39856 Z= 0.282 Chirality : 0.041 0.306 4514 Planarity : 0.004 0.055 5010 Dihedral : 6.036 80.636 4151 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 2.31 % Allowed : 12.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3510 helix: 1.73 (0.14), residues: 1575 sheet: 0.63 (0.23), residues: 536 loop : -1.76 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.003 0.000 HIS I 58 PHE 0.037 0.001 PHE J 62 TYR 0.013 0.001 TYR E 58 ARG 0.002 0.000 ARG E 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 4) link_NAG-ASN : angle 1.90143 ( 12) link_BETA1-4 : bond 0.00313 ( 3) link_BETA1-4 : angle 2.11845 ( 9) hydrogen bonds : bond 0.03531 ( 1430) hydrogen bonds : angle 4.27176 ( 4152) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.73966 ( 8) covalent geometry : bond 0.00259 (29381) covalent geometry : angle 0.56497 (39827) ********************** 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 200 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 128 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: A 442 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9211 (tt) REVERT: A 892 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8065 (pp20) REVERT: A 894 ASN cc_start: 0.9235 (t0) cc_final: 0.8975 (t0) REVERT: C 29 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8835 (mpp) REVERT: C 75 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.8940 (m) REVERT: C 135 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8170 (p90) REVERT: C 242 MET cc_start: 0.9043 (mmt) cc_final: 0.8784 (mmm) REVERT: E 31 MET cc_start: 0.8587 (tmm) cc_final: 0.8277 (tmm) REVERT: E 61 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9105 (p) REVERT: F 73 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8193 (pmt-80) REVERT: G 57 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9110 (ptmm) REVERT: G 72 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8720 (tm-30) REVERT: H 149 ASN cc_start: 0.9424 (m-40) cc_final: 0.8846 (p0) REVERT: H 187 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8741 (t0) REVERT: K 712 MET cc_start: 0.9538 (tmm) cc_final: 0.9002 (tmm) REVERT: K 1142 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: K 1417 MET cc_start: 0.9436 (ptp) cc_final: 0.9171 (ptm) REVERT: K 1474 MET cc_start: 0.8601 (mmp) cc_final: 0.8313 (mmm) REVERT: K 1524 MET cc_start: 0.9449 (mmm) cc_final: 0.9131 (mmm) REVERT: K 1527 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: J 195 MET cc_start: 0.9440 (mmm) cc_final: 0.8981 (mpp) REVERT: J 196 MET cc_start: 0.9110 (mmm) cc_final: 0.8853 (mmm) outliers start: 72 outliers final: 57 residues processed: 192 average time/residue: 0.3816 time to fit residues: 121.9978 Evaluate side-chains 194 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 124 time to evaluate : 3.373 ------------------------------------------------------------------------------- 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 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 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 75 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 151 MET 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 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 196 ASN 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 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 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 186 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1037 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.085322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052700 restraints weight = 113110.434| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.03 r_work: 0.2773 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1939 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= 0.114 Angle : 0.565 14.047 39856 Z= 0.282 Chirality : 0.041 0.304 4514 Planarity : 0.004 0.054 5010 Dihedral : 5.965 79.121 4151 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 2.34 % Allowed : 12.52 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3510 helix: 1.78 (0.14), residues: 1568 sheet: 0.62 (0.23), residues: 546 loop : -1.75 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.003 0.000 HIS I 58 PHE 0.039 0.001 PHE J 62 TYR 0.012 0.001 TYR A 672 ARG 0.002 0.000 ARG E 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 4) link_NAG-ASN : angle 1.87384 ( 12) link_BETA1-4 : bond 0.00298 ( 3) link_BETA1-4 : angle 2.10546 ( 9) hydrogen bonds : bond 0.03482 ( 1430) hydrogen bonds : angle 4.24479 ( 4152) SS BOND : bond 0.00153 ( 4) SS BOND : angle 0.70039 ( 8) covalent geometry : bond 0.00257 (29381) covalent geometry : angle 0.56378 (39827) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17288.56 seconds wall clock time: 298 minutes 47.63 seconds (17927.63 seconds total)