Starting phenix.real_space_refine on Thu Mar 13 19:13:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mfd_23813/03_2025/7mfd_23813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mfd_23813/03_2025/7mfd_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_23813/03_2025/7mfd_23813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mfd_23813/03_2025/7mfd_23813.map" model { file = "/net/cci-nas-00/data/ceres_data/7mfd_23813/03_2025/7mfd_23813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mfd_23813/03_2025/7mfd_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-5624/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: 5.29, 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: 2.37 Conformation dependent library (CDL) restraints added in 988.9 milliseconds 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: 0.77 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: 2.20 Time building geometry restraints manager: 2.76 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 24.230 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- 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 : 1.020 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: 0.1904 time to fit residues: 41.5567 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 : 1.066 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.163506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.135339 restraints weight = 14196.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.139102 restraints weight = 10489.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.140836 restraints weight = 6764.374| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 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 : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5292 (tt0) cc_final: 0.4649 (pm20) REVERT: A 620 MET cc_start: 0.6844 (mtp) cc_final: 0.6642 (mtm) REVERT: B 68 PHE cc_start: 0.4781 (m-80) cc_final: 0.4567 (m-80) REVERT: B 87 HIS cc_start: 0.3585 (t70) cc_final: 0.3170 (t-170) REVERT: B 178 THR cc_start: 0.6455 (m) cc_final: 0.6059 (p) REVERT: C 216 LEU cc_start: 0.7600 (mp) cc_final: 0.7363 (mp) REVERT: D 96 ASP cc_start: 0.6781 (m-30) cc_final: 0.6394 (m-30) outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.1890 time to fit residues: 42.1851 Evaluate side-chains 132 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 8 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.162370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.134131 restraints weight = 14371.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.137870 restraints weight = 10275.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.139579 restraints weight = 6674.269| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9293 Z= 0.223 Angle : 0.652 8.416 12529 Z= 0.340 Chirality : 0.043 0.211 1386 Planarity : 0.004 0.040 1599 Dihedral : 5.822 57.687 1256 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.64 % Allowed : 14.93 % Favored : 83.44 % 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: -1.85 (0.24), residues: 1115 helix: -0.65 (0.20), residues: 586 sheet: -2.27 (0.62), residues: 63 loop : -1.73 (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 0.022 0.002 PHE D 174 TYR 0.028 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 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5718 (tt0) cc_final: 0.4910 (pm20) REVERT: A 668 MET cc_start: 0.5022 (mmt) cc_final: 0.4435 (mmm) REVERT: B 87 HIS cc_start: 0.3626 (t70) cc_final: 0.3197 (t-170) REVERT: B 110 GLN cc_start: 0.6991 (tm-30) cc_final: 0.6612 (tm-30) REVERT: B 178 THR cc_start: 0.6225 (m) cc_final: 0.5843 (p) REVERT: B 223 PHE cc_start: 0.5439 (t80) cc_final: 0.4938 (t80) REVERT: C 41 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7330 (ptm-80) REVERT: D 22 MET cc_start: 0.4466 (OUTLIER) cc_final: 0.4147 (ppp) REVERT: D 92 ASP cc_start: 0.6506 (m-30) cc_final: 0.6302 (m-30) REVERT: D 96 ASP cc_start: 0.6716 (m-30) cc_final: 0.6361 (m-30) outliers start: 16 outliers final: 7 residues processed: 151 average time/residue: 0.2940 time to fit residues: 63.4226 Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.163871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.135636 restraints weight = 14228.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.139271 restraints weight = 10450.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.141122 restraints weight = 6750.595| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9293 Z= 0.194 Angle : 0.623 8.684 12529 Z= 0.322 Chirality : 0.043 0.225 1386 Planarity : 0.004 0.041 1599 Dihedral : 5.623 55.765 1256 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.04 % Allowed : 15.44 % Favored : 82.52 % 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: -1.71 (0.24), residues: 1115 helix: -0.47 (0.21), residues: 582 sheet: -2.28 (0.61), residues: 63 loop : -1.73 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 59 HIS 0.007 0.001 HIS A 477 PHE 0.017 0.002 PHE D 174 TYR 0.025 0.002 TYR B 179 ARG 0.003 0.000 ARG A 704 *********************** 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: 20 poor density : 138 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5912 (tt0) cc_final: 0.4804 (pm20) REVERT: B 110 GLN cc_start: 0.6916 (tm-30) cc_final: 0.6563 (tm-30) REVERT: B 178 THR cc_start: 0.6208 (m) cc_final: 0.5842 (p) REVERT: B 223 PHE cc_start: 0.5462 (t80) cc_final: 0.4889 (t80) REVERT: B 249 MET cc_start: 0.7794 (tmm) cc_final: 0.7397 (ppp) REVERT: D 96 ASP cc_start: 0.6595 (m-30) cc_final: 0.6245 (m-30) outliers start: 20 outliers final: 14 residues processed: 149 average time/residue: 0.2015 time to fit residues: 44.3211 Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 C residue 116 VAL 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 19 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS B 122 ASN C 15 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.160415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.132247 restraints weight = 14280.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.135029 restraints weight = 10715.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.136711 restraints weight = 7690.563| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.2184 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= 0.287 Angle : 0.682 9.209 12529 Z= 0.351 Chirality : 0.045 0.244 1386 Planarity : 0.005 0.050 1599 Dihedral : 5.892 55.009 1256 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.45 % Allowed : 18.40 % Favored : 79.14 % 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: -1.86 (0.24), residues: 1115 helix: -0.49 (0.21), residues: 577 sheet: -2.66 (0.56), residues: 73 loop : -1.86 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 59 HIS 0.009 0.001 HIS A 477 PHE 0.027 0.002 PHE A 707 TYR 0.023 0.002 TYR B 179 ARG 0.006 0.000 ARG C 41 *********************** 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 152 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7464 (mpp) cc_final: 0.6844 (mpp) REVERT: A 270 GLN cc_start: 0.6036 (tt0) cc_final: 0.4896 (pm20) REVERT: A 668 MET cc_start: 0.5004 (mmt) cc_final: 0.4536 (mmm) REVERT: B 110 GLN cc_start: 0.6997 (tm-30) cc_final: 0.6584 (tm-30) REVERT: B 223 PHE cc_start: 0.5423 (t80) cc_final: 0.4878 (t80) REVERT: D 96 ASP cc_start: 0.6690 (m-30) cc_final: 0.6344 (m-30) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 0.1871 time to fit residues: 40.4826 Evaluate side-chains 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 C residue 116 VAL Chi-restraints excluded: chain C residue 153 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.161032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.133050 restraints weight = 14087.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.136471 restraints weight = 10457.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.138227 restraints weight = 6802.661| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9293 Z= 0.235 Angle : 0.658 9.092 12529 Z= 0.339 Chirality : 0.044 0.263 1386 Planarity : 0.004 0.043 1599 Dihedral : 5.816 54.029 1256 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.45 % Allowed : 20.04 % Favored : 77.51 % 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: -1.79 (0.24), residues: 1115 helix: -0.41 (0.21), residues: 578 sheet: -2.63 (0.57), residues: 73 loop : -1.87 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 59 HIS 0.008 0.001 HIS A 477 PHE 0.020 0.002 PHE A 707 TYR 0.024 0.002 TYR D 126 ARG 0.002 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 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6388 (OUTLIER) cc_final: 0.5735 (m170) REVERT: A 521 THR cc_start: 0.6322 (t) cc_final: 0.6030 (t) REVERT: A 704 ARG cc_start: 0.6768 (ptp90) cc_final: 0.6471 (ptp90) REVERT: B 110 GLN cc_start: 0.6991 (tm-30) cc_final: 0.6572 (tm-30) REVERT: B 204 ILE cc_start: 0.5713 (OUTLIER) cc_final: 0.5498 (pt) REVERT: B 223 PHE cc_start: 0.5389 (t80) cc_final: 0.4862 (t80) REVERT: B 249 MET cc_start: 0.7909 (tmm) cc_final: 0.7606 (ppp) outliers start: 24 outliers final: 18 residues processed: 148 average time/residue: 0.1717 time to fit residues: 37.8340 Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 122 ASN 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 315 ASP 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 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 45 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 94 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.160922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.132966 restraints weight = 14179.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.136381 restraints weight = 10351.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.138144 restraints weight = 6730.929| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.2401 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= 0.241 Angle : 0.665 10.919 12529 Z= 0.340 Chirality : 0.044 0.241 1386 Planarity : 0.004 0.044 1599 Dihedral : 5.834 52.936 1256 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.37 % Allowed : 19.43 % 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: -1.77 (0.24), residues: 1115 helix: -0.37 (0.21), residues: 578 sheet: -2.61 (0.57), residues: 73 loop : -1.88 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 59 HIS 0.005 0.001 HIS A 477 PHE 0.025 0.002 PHE D 174 TYR 0.018 0.002 TYR B 179 ARG 0.002 0.000 ARG B 189 *********************** 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 168 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.5749 (m170) REVERT: A 270 GLN cc_start: 0.5990 (tt0) cc_final: 0.5782 (mt0) REVERT: A 521 THR cc_start: 0.6126 (t) cc_final: 0.5886 (t) REVERT: A 668 MET cc_start: 0.5042 (mmt) cc_final: 0.4592 (mmm) REVERT: A 704 ARG cc_start: 0.6821 (ptp90) cc_final: 0.6506 (ptp90) REVERT: B 98 LEU cc_start: 0.6088 (mt) cc_final: 0.5796 (mt) REVERT: B 223 PHE cc_start: 0.5343 (t80) cc_final: 0.4776 (t80) REVERT: B 249 MET cc_start: 0.7930 (tmm) cc_final: 0.7605 (ppp) outliers start: 33 outliers final: 18 residues processed: 155 average time/residue: 0.2019 time to fit residues: 45.5334 Evaluate side-chains 144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 556 ILE 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 B residue 315 ASP 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 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 219 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN C 164 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.158952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.130859 restraints weight = 14643.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.133869 restraints weight = 11099.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.135159 restraints weight = 8168.308| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9293 Z= 0.326 Angle : 0.743 10.940 12529 Z= 0.382 Chirality : 0.047 0.316 1386 Planarity : 0.005 0.044 1599 Dihedral : 6.166 53.824 1256 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.07 % Allowed : 20.76 % Favored : 76.18 % 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: -2.02 (0.24), residues: 1115 helix: -0.61 (0.21), residues: 583 sheet: -2.70 (0.57), residues: 73 loop : -1.97 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 59 HIS 0.010 0.001 HIS A 477 PHE 0.031 0.002 PHE A 707 TYR 0.023 0.002 TYR D 126 ARG 0.003 0.000 ARG C 167 *********************** 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 161 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6378 (OUTLIER) cc_final: 0.5710 (m170) REVERT: A 521 THR cc_start: 0.6243 (t) cc_final: 0.6005 (t) REVERT: A 668 MET cc_start: 0.5205 (mmt) cc_final: 0.4714 (mmm) REVERT: A 704 ARG cc_start: 0.6974 (ptp90) cc_final: 0.6647 (ptp90) REVERT: B 98 LEU cc_start: 0.6105 (mt) cc_final: 0.5801 (mt) REVERT: B 110 GLN cc_start: 0.6935 (tm-30) cc_final: 0.6489 (tm-30) REVERT: B 223 PHE cc_start: 0.5354 (t80) cc_final: 0.4792 (t80) REVERT: B 322 PRO cc_start: 0.7058 (Cg_endo) cc_final: 0.6655 (Cg_exo) outliers start: 30 outliers final: 21 residues processed: 152 average time/residue: 0.1911 time to fit residues: 42.0336 Evaluate side-chains 143 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 B residue 315 ASP 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 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 94 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 150 GLN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** 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 = 0.163207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.134925 restraints weight = 14232.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.138202 restraints weight = 11107.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.140097 restraints weight = 7452.671| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9293 Z= 0.183 Angle : 0.655 10.244 12529 Z= 0.339 Chirality : 0.044 0.256 1386 Planarity : 0.004 0.045 1599 Dihedral : 5.651 50.038 1256 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.94 % Allowed : 21.37 % Favored : 76.69 % 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: -1.67 (0.25), residues: 1115 helix: -0.28 (0.21), residues: 586 sheet: -2.59 (0.58), residues: 73 loop : -1.87 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 59 HIS 0.006 0.001 HIS A 477 PHE 0.023 0.002 PHE D 174 TYR 0.021 0.002 TYR D 126 ARG 0.006 0.000 ARG A 252 *********************** 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 162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6337 (OUTLIER) cc_final: 0.5724 (m170) REVERT: A 270 GLN cc_start: 0.6255 (tt0) cc_final: 0.5899 (mt0) REVERT: A 462 ARG cc_start: 0.5434 (tpt170) cc_final: 0.4744 (tpp-160) REVERT: A 521 THR cc_start: 0.6295 (t) cc_final: 0.6092 (t) REVERT: A 668 MET cc_start: 0.4944 (mmt) cc_final: 0.4419 (mmm) REVERT: A 704 ARG cc_start: 0.6727 (ptp90) cc_final: 0.6409 (ptp90) REVERT: B 110 GLN cc_start: 0.6855 (tm-30) cc_final: 0.6440 (tm-30) REVERT: B 155 LEU cc_start: 0.8364 (mm) cc_final: 0.7742 (mm) REVERT: B 223 PHE cc_start: 0.5391 (t80) cc_final: 0.4785 (t80) outliers start: 19 outliers final: 14 residues processed: 156 average time/residue: 0.1884 time to fit residues: 42.6756 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 123 SER 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 116 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 PHE 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 219 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 0.6980 chunk 71 optimal weight: 0.0040 chunk 36 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 580 ASN ** B 87 HIS ** 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 224 ASN ** 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 = 0.4450 r_free = 0.4450 target = 0.163719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.135432 restraints weight = 14612.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.139941 restraints weight = 9948.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.141070 restraints weight = 6331.213| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9293 Z= 0.191 Angle : 0.674 11.969 12529 Z= 0.348 Chirality : 0.044 0.277 1386 Planarity : 0.004 0.045 1599 Dihedral : 5.519 49.089 1256 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.74 % Allowed : 22.39 % Favored : 75.87 % 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: -1.54 (0.25), residues: 1115 helix: -0.19 (0.21), residues: 586 sheet: -2.68 (0.57), residues: 73 loop : -1.77 (0.28), residues: 456 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 0.019 0.002 TYR D 126 ARG 0.010 0.000 ARG C 41 ********************** 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 151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6455 (OUTLIER) cc_final: 0.5881 (m170) REVERT: A 270 GLN cc_start: 0.6278 (tt0) cc_final: 0.5938 (mt0) REVERT: A 462 ARG cc_start: 0.5410 (tpt170) cc_final: 0.4729 (tpp-160) REVERT: A 521 THR cc_start: 0.6256 (t) cc_final: 0.6052 (t) REVERT: A 668 MET cc_start: 0.4888 (mmt) cc_final: 0.4367 (mmm) REVERT: A 704 ARG cc_start: 0.6721 (ptp90) cc_final: 0.6378 (ptp90) REVERT: B 110 GLN cc_start: 0.6894 (tm-30) cc_final: 0.6512 (tm-30) REVERT: B 155 LEU cc_start: 0.8333 (mm) cc_final: 0.7715 (mm) REVERT: B 223 PHE cc_start: 0.5320 (t80) cc_final: 0.4706 (t80) REVERT: D 96 ASP cc_start: 0.6402 (m-30) cc_final: 0.6078 (m-30) outliers start: 17 outliers final: 13 residues processed: 146 average time/residue: 0.1849 time to fit residues: 39.7178 Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 209 PHE 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 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 219 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 62 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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** B 122 ASN C 95 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.160714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.132169 restraints weight = 14661.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.135709 restraints weight = 10838.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.137155 restraints weight = 7523.119| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9293 Z= 0.281 Angle : 0.732 11.487 12529 Z= 0.376 Chirality : 0.047 0.288 1386 Planarity : 0.005 0.051 1599 Dihedral : 5.813 49.908 1256 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.35 % Allowed : 21.88 % Favored : 75.77 % 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: -1.73 (0.24), residues: 1115 helix: -0.35 (0.21), residues: 586 sheet: -2.75 (0.56), residues: 73 loop : -1.85 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 59 HIS 0.006 0.001 HIS A 477 PHE 0.028 0.002 PHE A 707 TYR 0.037 0.002 TYR D 126 ARG 0.005 0.000 ARG A 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3154.15 seconds wall clock time: 57 minutes 41.03 seconds (3461.03 seconds total)