Starting phenix.real_space_refine on Sat Dec 28 21:21:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mfd_23813/12_2024/7mfd_23813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mfd_23813/12_2024/7mfd_23813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mfd_23813/12_2024/7mfd_23813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mfd_23813/12_2024/7mfd_23813.map" model { file = "/net/cci-nas-00/data/ceres_data/7mfd_23813/12_2024/7mfd_23813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mfd_23813/12_2024/7mfd_23813.cif" } resolution = 3.66 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= 0.004 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 57 5.16 5 C 5795 2.51 5 N 1574 2.21 5 O 1696 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9127 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3297 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2291 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 16, 'TRANS': 276} Chain breaks: 1 Chain: "C" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1738 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1766 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'CHU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 673 SG CYS A 248 63.720 26.552 51.589 1.00 80.27 S ATOM 698 SG CYS A 251 64.077 23.314 53.654 1.00 66.34 S ATOM 880 SG CYS A 272 62.080 23.273 50.310 1.00 90.13 S ATOM 786 SG CYS A 261 57.199 35.051 42.449 1.00 69.90 S ATOM 808 SG CYS A 264 56.805 35.956 45.817 1.00 69.91 S Time building chain proxies: 5.31, per 1000 atoms: 0.58 Number of scatterers: 9127 At special positions: 0 Unit cell: (113.206, 89.93, 119.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 57 16.00 P 2 15.00 F 1 9.00 O 1696 8.00 N 1574 7.00 C 5795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 248 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 251 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 272 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 261 " 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 56.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.639A pdb=" N LYS A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.750A pdb=" N TRP A 216 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.528A pdb=" N GLN A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY A 503 " --> pdb=" O LYS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.527A pdb=" N HIS A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 570 removed outlier: 3.888A pdb=" N ASP A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS A 568 " --> pdb=" O MET A 564 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 570 " --> pdb=" O TYR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.823A pdb=" N ILE A 644 " --> pdb=" O TYR A 640 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 649 " --> pdb=" O VAL A 645 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 651 " --> pdb=" O TYR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 Processing helix chain 'A' and resid 677 through 681 removed outlier: 3.905A pdb=" N LYS A 680 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 681 " --> pdb=" O LEU A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 681' Processing helix chain 'A' and resid 686 through 697 removed outlier: 3.803A pdb=" N LYS A 690 " --> pdb=" O PRO A 686 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 691 " --> pdb=" O LYS A 687 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU A 695 " --> pdb=" O ARG A 691 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 697 " --> pdb=" O MET A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.528A pdb=" N ILE A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'B' and resid 52 through 58 removed outlier: 10.364A pdb=" N GLN B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N LYS B 57 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N GLN B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 52 through 58' Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.584A pdb=" N ARG B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.501A pdb=" N LEU B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.797A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 185 removed outlier: 3.558A pdb=" N LEU B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 Processing helix chain 'B' and resid 212 through 219 removed outlier: 3.641A pdb=" N ASP B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 240 through 258 removed outlier: 3.526A pdb=" N SER B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 318 removed outlier: 3.509A pdb=" N ASP B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 removed outlier: 3.751A pdb=" N PHE B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.565A pdb=" N HIS B 358 " --> pdb=" O GLN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 365 removed outlier: 4.199A pdb=" N ASP B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.886A pdb=" N CYS B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 removed outlier: 4.277A pdb=" N GLN C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.871A pdb=" N LYS C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C 30 " --> pdb=" O MET C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 67 removed outlier: 3.591A pdb=" N ARG C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 102 removed outlier: 3.959A pdb=" N ARG C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 81 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 87 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 111 through 133 removed outlier: 3.531A pdb=" N LYS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 160 removed outlier: 4.137A pdb=" N LYS C 139 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 157 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 180 removed outlier: 3.981A pdb=" N LEU C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR C 178 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 202 removed outlier: 3.804A pdb=" N LEU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 229 removed outlier: 3.564A pdb=" N ILE C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 12 removed outlier: 3.693A pdb=" N ALA D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 31 removed outlier: 3.533A pdb=" N MET D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 68 removed outlier: 3.520A pdb=" N ASN D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 50 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 104 removed outlier: 3.901A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 82 " --> pdb=" O MET D 78 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 97 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 133 Processing helix chain 'D' and resid 138 through 157 removed outlier: 3.531A pdb=" N VAL D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 181 removed outlier: 3.623A pdb=" N ILE D 181 " --> pdb=" O PHE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 203 removed outlier: 3.804A pdb=" N ALA D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.084A pdb=" N LYS D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR D 215 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 160 removed outlier: 3.730A pdb=" N VAL A 169 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 removed outlier: 3.545A pdb=" N LYS A 206 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 197 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 198 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS A 223 " --> pdb=" O TYR A 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 241 removed outlier: 3.514A pdb=" N VAL A 238 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.345A pdb=" N THR A 458 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 475 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 460 " --> pdb=" O LYS A 473 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS A 473 " --> pdb=" O GLY A 460 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 479 through 483 removed outlier: 4.064A pdb=" N GLY A 518 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLN A 530 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N PHE A 516 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 582 through 585 Processing sheet with id=AA7, first strand: chain 'B' and resid 68 through 75 removed outlier: 3.502A pdb=" N ILE B 71 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS B 84 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLU B 73 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL B 82 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL B 81 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 98 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 94 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 135 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 140 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 133 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS B 142 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY B 131 " --> pdb=" O CYS B 142 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1128 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: 2.64 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1845 1.33 - 1.45: 2102 1.45 - 1.57: 5246 1.57 - 1.70: 10 1.70 - 1.82: 90 Bond restraints: 9293 Sorted by residual: bond pdb=" N LYS A 267 " pdb=" CA LYS A 267 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.19e-02 7.06e+03 7.18e+00 bond pdb=" N HIS A 269 " pdb=" CA HIS A 269 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.22e-02 6.72e+03 6.71e+00 bond pdb=" N PHE A 268 " pdb=" CA PHE A 268 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.16e-02 7.43e+03 6.29e+00 bond pdb=" N ARG A 271 " pdb=" CA ARG A 271 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.74e+00 bond pdb=" N GLN A 270 " pdb=" CA GLN A 270 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.46e+00 ... (remaining 9288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 12277 2.12 - 4.23: 224 4.23 - 6.35: 20 6.35 - 8.47: 7 8.47 - 10.59: 1 Bond angle restraints: 12529 Sorted by residual: angle pdb=" N ASN A 163 " pdb=" CA ASN A 163 " pdb=" C ASN A 163 " ideal model delta sigma weight residual 113.40 106.80 6.60 1.47e+00 4.63e-01 2.02e+01 angle pdb=" C ASN A 163 " pdb=" CA ASN A 163 " pdb=" CB ASN A 163 " ideal model delta sigma weight residual 111.06 118.38 -7.32 1.83e+00 2.99e-01 1.60e+01 angle pdb=" N ILE A 554 " pdb=" CA ILE A 554 " pdb=" C ILE A 554 " ideal model delta sigma weight residual 113.42 108.80 4.62 1.17e+00 7.31e-01 1.56e+01 angle pdb=" N LEU A 485 " pdb=" CA LEU A 485 " pdb=" C LEU A 485 " ideal model delta sigma weight residual 108.24 113.08 -4.84 1.32e+00 5.74e-01 1.34e+01 angle pdb=" N PHE A 707 " pdb=" CA PHE A 707 " pdb=" C PHE A 707 " ideal model delta sigma weight residual 109.81 117.31 -7.50 2.21e+00 2.05e-01 1.15e+01 ... (remaining 12524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5008 17.93 - 35.85: 524 35.85 - 53.78: 110 53.78 - 71.71: 17 71.71 - 89.64: 8 Dihedral angle restraints: 5667 sinusoidal: 2320 harmonic: 3347 Sorted by residual: dihedral pdb=" CA ILE B 263 " pdb=" C ILE B 263 " pdb=" N PRO B 264 " pdb=" CA PRO B 264 " ideal model delta harmonic sigma weight residual 180.00 154.63 25.37 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" C ASN A 163 " pdb=" N ASN A 163 " pdb=" CA ASN A 163 " pdb=" CB ASN A 163 " ideal model delta harmonic sigma weight residual -122.60 -134.67 12.07 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" N ASN A 163 " pdb=" C ASN A 163 " pdb=" CA ASN A 163 " pdb=" CB ASN A 163 " ideal model delta harmonic sigma weight residual 122.80 133.56 -10.76 0 2.50e+00 1.60e-01 1.85e+01 ... (remaining 5664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1251 0.073 - 0.146: 130 0.146 - 0.219: 4 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA ASN A 163 " pdb=" N ASN A 163 " pdb=" C ASN A 163 " pdb=" CB ASN A 163 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA PHE A 707 " pdb=" N PHE A 707 " pdb=" C PHE A 707 " pdb=" CB PHE A 707 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CB ILE A 724 " pdb=" CA ILE A 724 " pdb=" CG1 ILE A 724 " pdb=" CG2 ILE A 724 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 1383 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 174 " -0.017 2.00e-02 2.50e+03 1.47e-02 3.79e+00 pdb=" CG PHE D 174 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE D 174 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 174 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 174 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 174 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 174 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 125 " -0.014 2.00e-02 2.50e+03 1.22e-02 2.99e+00 pdb=" CG TYR D 125 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR D 125 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D 125 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 125 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 125 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 125 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 125 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 192 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 193 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 193 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 193 " -0.022 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 193 2.67 - 3.23: 9338 3.23 - 3.78: 13940 3.78 - 4.34: 19781 4.34 - 4.90: 30458 Nonbonded interactions: 73710 Sorted by model distance: nonbonded pdb=" OE1 GLN D 161 " pdb=" OG1 THR D 163 " model vdw 2.112 3.040 nonbonded pdb=" OG SER C 37 " pdb=" OE1 GLU C 40 " model vdw 2.132 3.040 nonbonded pdb=" OD1 ASP C 124 " pdb=" OH TYR C 149 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASP D 124 " pdb=" NH2 ARG D 127 " model vdw 2.167 3.120 nonbonded pdb=" NH2 ARG D 127 " pdb=" OD1 ASN D 173 " model vdw 2.198 3.120 ... (remaining 73705 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 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 102 or (resid 103 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 104 through \ 133 or (resid 137 and (name N or name CA or name C or name O or name CB )) or re \ sid 138 through 156 or (resid 157 through 158 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name CE )) or resid 159 through 211 \ or (resid 212 and (name N or name CA or name C or name O or name CB )) or resid \ 213 through 229 or (resid 230 and (name N or name CA or name C or name O or nam \ e CB )))) selection = (chain 'D' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name CE )) or resid 4 through 67 or (resid 68 \ and (name N or name CA or name C or name O or name CB )) or resid 69 or resid 7 \ 3 through 74 or (resid 75 and (name N or name CA or name C or name O or name CB \ or name CG )) or (resid 76 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 102 or (resid 103 and (name N or name CA or name C or na \ me O or name CB or name CG )) or resid 104 through 138 or (resid 139 and (name N \ or name CA or name C or name O or name CB or name CG )) or resid 140 through 15 \ 7 or (resid 158 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE )) or resid 159 through 203 or resid 210 through 230)) } 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 group one per residue 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.380 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 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 : 0.004 0.038 9293 Z= 0.242 Angle : 0.674 10.587 12529 Z= 0.357 Chirality : 0.045 0.365 1386 Planarity : 0.005 0.054 1599 Dihedral : 15.471 89.636 3495 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.20 % Allowed : 0.92 % Favored : 98.88 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.24), residues: 1115 helix: -1.12 (0.21), residues: 536 sheet: -2.17 (0.63), residues: 57 loop : -1.60 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.009 0.001 HIS A 235 PHE 0.034 0.002 PHE D 174 TYR 0.030 0.002 TYR D 125 ARG 0.005 0.001 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5239 (tt0) cc_final: 0.4758 (pm20) REVERT: B 68 PHE cc_start: 0.4878 (m-80) cc_final: 0.4472 (m-80) REVERT: B 87 HIS cc_start: 0.3528 (t70) cc_final: 0.2954 (t-170) REVERT: B 219 MET cc_start: 0.7079 (ttt) cc_final: 0.6770 (ttp) REVERT: D 96 ASP cc_start: 0.6875 (m-30) cc_final: 0.6375 (m-30) outliers start: 2 outliers final: 1 residues processed: 151 average time/residue: 0.2073 time to fit residues: 45.4253 Evaluate side-chains 123 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9293 Z= 0.213 Angle : 0.686 8.535 12529 Z= 0.363 Chirality : 0.044 0.209 1386 Planarity : 0.005 0.059 1599 Dihedral : 6.101 61.157 1260 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.92 % Allowed : 10.43 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.24), residues: 1115 helix: -0.72 (0.21), residues: 584 sheet: -2.30 (0.62), residues: 63 loop : -1.70 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 59 HIS 0.012 0.001 HIS A 477 PHE 0.028 0.002 PHE D 174 TYR 0.038 0.002 TYR D 126 ARG 0.004 0.001 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5181 (tt0) cc_final: 0.4569 (pm20) REVERT: B 87 HIS cc_start: 0.3577 (t70) cc_final: 0.3158 (t-170) REVERT: B 178 THR cc_start: 0.6479 (m) cc_final: 0.6079 (p) REVERT: C 216 LEU cc_start: 0.7545 (mp) cc_final: 0.7312 (mp) REVERT: D 96 ASP cc_start: 0.6769 (m-30) cc_final: 0.6384 (m-30) outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.1874 time to fit residues: 41.6800 Evaluate side-chains 131 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 28 optimal weight: 0.0030 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 102 optimal weight: 0.0770 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS A 496 GLN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9293 Z= 0.204 Angle : 0.641 8.056 12529 Z= 0.335 Chirality : 0.043 0.213 1386 Planarity : 0.004 0.040 1599 Dihedral : 5.759 57.728 1256 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.64 % Allowed : 14.31 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.24), residues: 1115 helix: -0.64 (0.20), residues: 586 sheet: -2.25 (0.62), residues: 63 loop : -1.69 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 59 HIS 0.016 0.001 HIS A 477 PHE 0.020 0.002 PHE D 174 TYR 0.029 0.002 TYR D 126 ARG 0.003 0.000 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5555 (tt0) cc_final: 0.4934 (pm20) REVERT: A 668 MET cc_start: 0.5047 (mmt) cc_final: 0.4469 (mmm) REVERT: B 68 PHE cc_start: 0.4741 (m-80) cc_final: 0.4441 (m-80) REVERT: B 87 HIS cc_start: 0.3586 (t70) cc_final: 0.3196 (t-170) REVERT: B 178 THR cc_start: 0.6365 (m) cc_final: 0.5992 (p) REVERT: B 223 PHE cc_start: 0.5475 (t80) cc_final: 0.4992 (t80) REVERT: C 41 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7357 (ptm-80) REVERT: D 22 MET cc_start: 0.4419 (OUTLIER) cc_final: 0.4136 (ppp) REVERT: D 96 ASP cc_start: 0.6707 (m-30) cc_final: 0.6369 (m-30) outliers start: 16 outliers final: 7 residues processed: 149 average time/residue: 0.1865 time to fit residues: 40.6674 Evaluate side-chains 132 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9293 Z= 0.260 Angle : 0.666 8.923 12529 Z= 0.345 Chirality : 0.044 0.233 1386 Planarity : 0.004 0.040 1599 Dihedral : 5.841 55.950 1256 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.15 % Allowed : 15.85 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.24), residues: 1115 helix: -0.55 (0.21), residues: 582 sheet: -2.37 (0.61), residues: 63 loop : -1.81 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 59 HIS 0.014 0.001 HIS A 477 PHE 0.022 0.002 PHE A 707 TYR 0.027 0.002 TYR B 179 ARG 0.003 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5829 (tt0) cc_final: 0.4539 (pm20) REVERT: A 668 MET cc_start: 0.5074 (mmt) cc_final: 0.4857 (mmt) REVERT: B 178 THR cc_start: 0.6281 (m) cc_final: 0.5886 (p) REVERT: B 223 PHE cc_start: 0.5501 (t80) cc_final: 0.4960 (t80) REVERT: C 41 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7437 (ttt180) REVERT: D 22 MET cc_start: 0.4565 (OUTLIER) cc_final: 0.4187 (ppp) REVERT: D 96 ASP cc_start: 0.6698 (m-30) cc_final: 0.6322 (m-30) outliers start: 21 outliers final: 16 residues processed: 149 average time/residue: 0.1918 time to fit residues: 41.8647 Evaluate side-chains 135 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 213 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9293 Z= 0.423 Angle : 0.802 9.834 12529 Z= 0.413 Chirality : 0.049 0.245 1386 Planarity : 0.006 0.041 1599 Dihedral : 6.550 62.285 1256 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.97 % Allowed : 19.12 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.24), residues: 1115 helix: -0.90 (0.20), residues: 579 sheet: -2.78 (0.56), residues: 73 loop : -2.04 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 59 HIS 0.016 0.002 HIS A 477 PHE 0.036 0.003 PHE A 707 TYR 0.027 0.003 TYR D 125 ARG 0.005 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6529 (OUTLIER) cc_final: 0.5818 (m170) REVERT: A 668 MET cc_start: 0.5146 (mmt) cc_final: 0.4789 (mmt) REVERT: B 98 LEU cc_start: 0.6405 (mt) cc_final: 0.6098 (mt) REVERT: B 204 ILE cc_start: 0.5767 (OUTLIER) cc_final: 0.5528 (pt) REVERT: B 223 PHE cc_start: 0.5510 (t80) cc_final: 0.4955 (t80) REVERT: C 41 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7473 (ttt180) REVERT: D 22 MET cc_start: 0.4675 (OUTLIER) cc_final: 0.4300 (ppp) outliers start: 29 outliers final: 19 residues processed: 145 average time/residue: 0.2063 time to fit residues: 43.1235 Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 213 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS B 87 HIS C 15 GLN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9293 Z= 0.203 Angle : 0.657 9.306 12529 Z= 0.340 Chirality : 0.044 0.269 1386 Planarity : 0.004 0.043 1599 Dihedral : 5.977 53.931 1256 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.07 % Allowed : 19.73 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.24), residues: 1115 helix: -0.56 (0.21), residues: 579 sheet: -2.28 (0.64), residues: 63 loop : -1.97 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 59 HIS 0.014 0.001 HIS A 477 PHE 0.017 0.002 PHE D 174 TYR 0.023 0.002 TYR D 126 ARG 0.004 0.000 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 ARG cc_start: 0.6814 (ptp90) cc_final: 0.6538 (ptp90) REVERT: B 98 LEU cc_start: 0.5946 (mt) cc_final: 0.5674 (mt) REVERT: B 110 GLN cc_start: 0.7003 (tm-30) cc_final: 0.6570 (tm-30) REVERT: B 223 PHE cc_start: 0.5443 (t80) cc_final: 0.4949 (t80) REVERT: B 356 MET cc_start: 0.6543 (mpp) cc_final: 0.6333 (mpp) REVERT: C 41 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7538 (ptm-80) outliers start: 30 outliers final: 18 residues processed: 155 average time/residue: 0.2049 time to fit residues: 45.4367 Evaluate side-chains 147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 213 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 62 optimal weight: 0.0970 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9293 Z= 0.237 Angle : 0.679 9.783 12529 Z= 0.349 Chirality : 0.044 0.282 1386 Planarity : 0.004 0.044 1599 Dihedral : 5.936 52.843 1256 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.07 % Allowed : 20.45 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.24), residues: 1115 helix: -0.49 (0.21), residues: 581 sheet: -2.70 (0.58), residues: 73 loop : -1.90 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 59 HIS 0.006 0.001 HIS A 477 PHE 0.019 0.002 PHE A 595 TYR 0.033 0.002 TYR D 126 ARG 0.008 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6425 (OUTLIER) cc_final: 0.5722 (m170) REVERT: A 668 MET cc_start: 0.5107 (mmt) cc_final: 0.4704 (mmm) REVERT: A 704 ARG cc_start: 0.6855 (ptp90) cc_final: 0.6535 (ptp90) REVERT: B 98 LEU cc_start: 0.6044 (mt) cc_final: 0.5785 (mt) REVERT: B 110 GLN cc_start: 0.7001 (tm-30) cc_final: 0.6572 (tm-30) REVERT: B 223 PHE cc_start: 0.5302 (t80) cc_final: 0.4802 (t80) REVERT: C 41 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7551 (ptm-80) outliers start: 30 outliers final: 22 residues processed: 156 average time/residue: 0.1943 time to fit residues: 44.3264 Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9293 Z= 0.265 Angle : 0.711 13.062 12529 Z= 0.366 Chirality : 0.046 0.297 1386 Planarity : 0.005 0.044 1599 Dihedral : 6.021 52.192 1256 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.37 % Allowed : 21.37 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.24), residues: 1115 helix: -0.52 (0.21), residues: 583 sheet: -2.73 (0.58), residues: 73 loop : -1.93 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 59 HIS 0.005 0.001 HIS A 477 PHE 0.023 0.002 PHE A 707 TYR 0.018 0.002 TYR B 179 ARG 0.004 0.000 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6412 (OUTLIER) cc_final: 0.5740 (m170) REVERT: A 668 MET cc_start: 0.5095 (mmt) cc_final: 0.4575 (mmm) REVERT: A 704 ARG cc_start: 0.6904 (ptp90) cc_final: 0.6577 (ptp90) REVERT: B 98 LEU cc_start: 0.6085 (mt) cc_final: 0.5794 (mt) REVERT: B 110 GLN cc_start: 0.7009 (tm-30) cc_final: 0.6566 (tm-30) REVERT: B 223 PHE cc_start: 0.5298 (t80) cc_final: 0.4778 (t80) REVERT: C 41 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7537 (ptm-80) outliers start: 33 outliers final: 25 residues processed: 152 average time/residue: 0.1986 time to fit residues: 44.7916 Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9293 Z= 0.215 Angle : 0.679 11.661 12529 Z= 0.347 Chirality : 0.045 0.301 1386 Planarity : 0.004 0.045 1599 Dihedral : 5.817 50.318 1256 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.86 % Allowed : 22.09 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.24), residues: 1115 helix: -0.38 (0.21), residues: 584 sheet: -2.69 (0.58), residues: 73 loop : -1.89 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 59 HIS 0.007 0.001 HIS A 477 PHE 0.021 0.002 PHE A 160 TYR 0.017 0.002 TYR B 179 ARG 0.003 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6407 (OUTLIER) cc_final: 0.5712 (m170) REVERT: A 668 MET cc_start: 0.4860 (mmt) cc_final: 0.4315 (mmm) REVERT: A 704 ARG cc_start: 0.6821 (ptp90) cc_final: 0.6499 (ptp90) REVERT: B 98 LEU cc_start: 0.6102 (mt) cc_final: 0.5815 (mt) REVERT: B 110 GLN cc_start: 0.6970 (tm-30) cc_final: 0.6544 (tm-30) REVERT: B 223 PHE cc_start: 0.5317 (t80) cc_final: 0.4764 (t80) REVERT: B 249 MET cc_start: 0.7902 (tmm) cc_final: 0.7534 (ppp) REVERT: C 41 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7510 (ptm-80) outliers start: 28 outliers final: 25 residues processed: 152 average time/residue: 0.1866 time to fit residues: 41.3416 Evaluate side-chains 150 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9293 Z= 0.201 Angle : 0.681 10.716 12529 Z= 0.349 Chirality : 0.045 0.285 1386 Planarity : 0.004 0.045 1599 Dihedral : 5.659 49.209 1256 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.66 % Allowed : 22.29 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.24), residues: 1115 helix: -0.29 (0.21), residues: 583 sheet: -2.75 (0.57), residues: 73 loop : -1.84 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 59 HIS 0.005 0.001 HIS A 477 PHE 0.017 0.002 PHE D 174 TYR 0.017 0.001 TYR B 179 ARG 0.004 0.000 ARG A 506 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6512 (OUTLIER) cc_final: 0.5895 (m170) REVERT: A 270 GLN cc_start: 0.6186 (tt0) cc_final: 0.5872 (mt0) REVERT: A 668 MET cc_start: 0.4786 (mmt) cc_final: 0.4224 (mmm) REVERT: A 704 ARG cc_start: 0.6784 (ptp90) cc_final: 0.6449 (ptp90) REVERT: B 110 GLN cc_start: 0.6955 (tm-30) cc_final: 0.6579 (tm-30) REVERT: B 155 LEU cc_start: 0.8325 (mm) cc_final: 0.7689 (mm) REVERT: B 223 PHE cc_start: 0.5360 (t80) cc_final: 0.4783 (t80) REVERT: B 249 MET cc_start: 0.7890 (tmm) cc_final: 0.7518 (ppp) REVERT: C 41 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7502 (ptm-80) outliers start: 26 outliers final: 23 residues processed: 152 average time/residue: 0.1906 time to fit residues: 42.3796 Evaluate side-chains 151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** 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 = 0.4446 r_free = 0.4446 target = 0.162969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.134585 restraints weight = 14506.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.139034 restraints weight = 9740.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.140033 restraints weight = 6754.732| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9293 Z= 0.195 Angle : 0.674 10.568 12529 Z= 0.348 Chirality : 0.045 0.268 1386 Planarity : 0.004 0.045 1599 Dihedral : 5.553 48.175 1256 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.86 % Allowed : 22.09 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.24), residues: 1115 helix: -0.27 (0.21), residues: 583 sheet: -2.75 (0.56), residues: 73 loop : -1.77 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 59 HIS 0.005 0.001 HIS A 477 PHE 0.018 0.002 PHE B 68 TYR 0.040 0.002 TYR D 125 ARG 0.004 0.000 ARG A 506 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1862.22 seconds wall clock time: 35 minutes 14.53 seconds (2114.53 seconds total)