Starting phenix.real_space_refine on Wed Feb 4 05:55:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mfd_23813/02_2026/7mfd_23813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mfd_23813/02_2026/7mfd_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mfd_23813/02_2026/7mfd_23813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mfd_23813/02_2026/7mfd_23813.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mfd_23813/02_2026/7mfd_23813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mfd_23813/02_2026/7mfd_23813.map" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'GLN:plan1': 1} 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: 1.98, per 1000 atoms: 0.22 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: 0.55 Conformation dependent library (CDL) restraints added in 213.6 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: 0.28 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: 1.27 Time building geometry restraints manager: 0.72 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: 0.430 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.100 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.910 ------------------------------------------------------------------------------- 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 : 0.007 0.510 9298 Z= 0.260 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.001 ARG C 41 TYR 0.030 0.002 TYR D 125 PHE 0.034 0.002 PHE D 174 TRP 0.009 0.001 TRP A 619 HIS 0.009 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9293) covalent geometry : angle 0.67368 (12529) hydrogen bonds : bond 0.31562 ( 392) hydrogen bonds : angle 10.22586 ( 1128) metal coordination : bond 0.25297 ( 5) *********************** 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 : 0.293 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: 0.6376 (m-30) outliers start: 2 outliers final: 1 residues processed: 151 average time/residue: 0.0787 time to fit residues: 17.2779 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 : 0.311 ------------------------------------------------------------------------------- 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 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.163152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.134944 restraints weight = 14402.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.138867 restraints weight = 10612.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.140524 restraints weight = 6710.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.141030 restraints weight = 4776.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.142203 restraints weight = 4539.530| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9298 Z= 0.154 Angle : 0.692 8.350 12529 Z= 0.365 Chirality : 0.044 0.207 1386 Planarity : 0.005 0.060 1599 Dihedral : 6.136 60.673 1260 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.92 % Allowed : 10.94 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.24), residues: 1115 helix: -0.73 (0.21), residues: 584 sheet: -2.32 (0.62), residues: 63 loop : -1.72 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 127 TYR 0.035 0.002 TYR D 126 PHE 0.028 0.002 PHE D 174 TRP 0.006 0.001 TRP C 59 HIS 0.012 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9293) covalent geometry : angle 0.69155 (12529) hydrogen bonds : bond 0.06157 ( 392) hydrogen bonds : angle 6.28225 ( 1128) metal coordination : bond 0.00108 ( 5) *********************** 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 153 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5352 (tt0) cc_final: 0.4674 (pm20) REVERT: A 620 MET cc_start: 0.6846 (mtp) cc_final: 0.6642 (mtm) REVERT: B 68 PHE cc_start: 0.4765 (m-80) cc_final: 0.4550 (m-80) REVERT: B 87 HIS cc_start: 0.3581 (t70) cc_final: 0.3177 (t-170) REVERT: B 178 THR cc_start: 0.6336 (m) cc_final: 0.5927 (p) REVERT: C 216 LEU cc_start: 0.7590 (mp) cc_final: 0.7334 (mp) REVERT: D 96 ASP cc_start: 0.6796 (m-30) cc_final: 0.6408 (m-30) outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.0774 time to fit residues: 17.3739 Evaluate side-chains 128 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 150 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.164091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.135692 restraints weight = 14197.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.139198 restraints weight = 10614.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.141170 restraints weight = 6934.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.141838 restraints weight = 4815.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.143257 restraints weight = 4609.757| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9298 Z= 0.130 Angle : 0.628 8.135 12529 Z= 0.327 Chirality : 0.042 0.210 1386 Planarity : 0.004 0.040 1599 Dihedral : 5.698 57.471 1256 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.64 % Allowed : 13.80 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.24), residues: 1115 helix: -0.63 (0.20), residues: 586 sheet: -2.24 (0.62), residues: 63 loop : -1.68 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 127 TYR 0.031 0.002 TYR D 126 PHE 0.020 0.002 PHE C 174 TRP 0.009 0.001 TRP C 59 HIS 0.017 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9293) covalent geometry : angle 0.62798 (12529) hydrogen bonds : bond 0.05006 ( 392) hydrogen bonds : angle 5.54084 ( 1128) metal coordination : bond 0.00158 ( 5) *********************** 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 153 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5671 (tt0) cc_final: 0.5035 (pm20) REVERT: A 668 MET cc_start: 0.4984 (mmt) cc_final: 0.4448 (mmm) REVERT: B 87 HIS cc_start: 0.3642 (t70) cc_final: 0.3226 (t-170) REVERT: B 178 THR cc_start: 0.6180 (m) cc_final: 0.5828 (p) REVERT: B 223 PHE cc_start: 0.5413 (t80) cc_final: 0.4916 (t80) REVERT: C 41 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7374 (ptm-80) REVERT: D 22 MET cc_start: 0.4389 (OUTLIER) cc_final: 0.4122 (ppp) REVERT: D 96 ASP cc_start: 0.6701 (m-30) cc_final: 0.6325 (m-30) outliers start: 16 outliers final: 7 residues processed: 147 average time/residue: 0.0790 time to fit residues: 17.1131 Evaluate side-chains 131 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 12 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 0.0370 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 overall best weight: 1.5062 ------------------------------------------------------------------------------- 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 = 0.4446 r_free = 0.4446 target = 0.163127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.134746 restraints weight = 14247.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.138692 restraints weight = 10219.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.140412 restraints weight = 6480.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.141078 restraints weight = 4654.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.143458 restraints weight = 4458.146| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9298 Z= 0.145 Angle : 0.633 8.723 12529 Z= 0.326 Chirality : 0.043 0.229 1386 Planarity : 0.004 0.040 1599 Dihedral : 5.662 55.875 1256 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.15 % Allowed : 15.85 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.24), residues: 1115 helix: -0.48 (0.21), residues: 579 sheet: -2.30 (0.61), residues: 63 loop : -1.75 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 167 TYR 0.028 0.002 TYR B 179 PHE 0.017 0.002 PHE A 707 TRP 0.008 0.001 TRP C 59 HIS 0.014 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9293) covalent geometry : angle 0.63273 (12529) hydrogen bonds : bond 0.04713 ( 392) hydrogen bonds : angle 5.41544 ( 1128) metal coordination : bond 0.00291 ( 5) *********************** 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 152 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5919 (tt0) cc_final: 0.4823 (pm20) REVERT: B 110 GLN cc_start: 0.6959 (tm-30) cc_final: 0.6593 (tm-30) REVERT: B 178 THR cc_start: 0.6222 (m) cc_final: 0.5842 (p) REVERT: B 223 PHE cc_start: 0.5400 (t80) cc_final: 0.4824 (t80) REVERT: B 249 MET cc_start: 0.7777 (tmm) cc_final: 0.7349 (ppp) REVERT: D 96 ASP cc_start: 0.6623 (m-30) cc_final: 0.6247 (m-30) outliers start: 21 outliers final: 15 residues processed: 142 average time/residue: 0.0739 time to fit residues: 16.0401 Evaluate side-chains 132 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR 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 13 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 59 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS C 15 GLN ** 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 = 0.4454 r_free = 0.4454 target = 0.164010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.135607 restraints weight = 14235.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.139291 restraints weight = 10174.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.141174 restraints weight = 6572.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.141863 restraints weight = 4706.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.144190 restraints weight = 4496.450| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9298 Z= 0.129 Angle : 0.615 8.888 12529 Z= 0.317 Chirality : 0.043 0.290 1386 Planarity : 0.004 0.041 1599 Dihedral : 5.568 54.381 1256 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.15 % Allowed : 18.20 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.24), residues: 1115 helix: -0.27 (0.21), residues: 577 sheet: -2.27 (0.61), residues: 63 loop : -1.78 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 41 TYR 0.019 0.002 TYR B 179 PHE 0.020 0.002 PHE B 68 TRP 0.013 0.001 TRP C 59 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9293) covalent geometry : angle 0.61516 (12529) hydrogen bonds : bond 0.04373 ( 392) hydrogen bonds : angle 5.21411 ( 1128) metal coordination : bond 0.00216 ( 5) *********************** 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 148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5892 (tt0) cc_final: 0.4616 (pm20) REVERT: A 668 MET cc_start: 0.4851 (mmt) cc_final: 0.4370 (mmm) REVERT: B 110 GLN cc_start: 0.6895 (tm-30) cc_final: 0.6543 (tm-30) REVERT: B 178 THR cc_start: 0.6263 (m) cc_final: 0.5952 (p) REVERT: B 223 PHE cc_start: 0.5325 (t80) cc_final: 0.4748 (t80) REVERT: B 249 MET cc_start: 0.7818 (tmm) cc_final: 0.7361 (ppp) REVERT: D 96 ASP cc_start: 0.6412 (m-30) cc_final: 0.6105 (m-30) outliers start: 21 outliers final: 15 residues processed: 142 average time/residue: 0.0709 time to fit residues: 15.5357 Evaluate side-chains 130 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain 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 98 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 109 optimal weight: 0.0470 chunk 95 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.162883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.134788 restraints weight = 14298.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.138412 restraints weight = 10549.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.140150 restraints weight = 6845.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.140791 restraints weight = 4856.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.142813 restraints weight = 4628.528| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 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 : 0.003 0.033 9298 Z= 0.144 Angle : 0.632 9.061 12529 Z= 0.324 Chirality : 0.043 0.248 1386 Planarity : 0.004 0.042 1599 Dihedral : 5.588 53.602 1256 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.15 % Allowed : 19.02 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.24), residues: 1115 helix: -0.17 (0.21), residues: 576 sheet: -2.23 (0.62), residues: 63 loop : -1.83 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 189 TYR 0.025 0.002 TYR D 126 PHE 0.018 0.002 PHE A 707 TRP 0.015 0.001 TRP C 59 HIS 0.007 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9293) covalent geometry : angle 0.63195 (12529) hydrogen bonds : bond 0.04360 ( 392) hydrogen bonds : angle 5.14173 ( 1128) metal coordination : bond 0.00322 ( 5) *********************** 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 153 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7457 (mpp) cc_final: 0.7020 (mpp) REVERT: A 235 HIS cc_start: 0.6407 (OUTLIER) cc_final: 0.5667 (m170) REVERT: A 270 GLN cc_start: 0.6149 (tt0) cc_final: 0.4790 (pm20) REVERT: A 668 MET cc_start: 0.4854 (mmt) cc_final: 0.4274 (mmm) REVERT: B 178 THR cc_start: 0.6333 (m) cc_final: 0.6002 (p) REVERT: B 223 PHE cc_start: 0.5362 (t80) cc_final: 0.4767 (t80) REVERT: B 249 MET cc_start: 0.7865 (tmm) cc_final: 0.7560 (ppp) REVERT: D 96 ASP cc_start: 0.6402 (m-30) cc_final: 0.6107 (m-30) outliers start: 21 outliers final: 15 residues processed: 145 average time/residue: 0.0780 time to fit residues: 17.0240 Evaluate side-chains 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 695 GLU 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 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 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 50 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 = 0.4463 r_free = 0.4463 target = 0.164783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.136945 restraints weight = 14203.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.140767 restraints weight = 10013.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.142674 restraints weight = 6313.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.143252 restraints weight = 4486.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.146476 restraints weight = 4307.040| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9298 Z= 0.116 Angle : 0.604 9.104 12529 Z= 0.311 Chirality : 0.042 0.275 1386 Planarity : 0.004 0.075 1599 Dihedral : 5.379 51.584 1256 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.25 % Allowed : 19.53 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 1115 helix: 0.02 (0.22), residues: 578 sheet: -2.17 (0.63), residues: 63 loop : -1.78 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 127 TYR 0.019 0.001 TYR B 179 PHE 0.021 0.002 PHE D 174 TRP 0.016 0.001 TRP C 59 HIS 0.009 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9293) covalent geometry : angle 0.60417 (12529) hydrogen bonds : bond 0.04066 ( 392) hydrogen bonds : angle 4.95860 ( 1128) metal coordination : bond 0.00205 ( 5) *********************** 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 160 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6328 (OUTLIER) cc_final: 0.5716 (m170) REVERT: A 270 GLN cc_start: 0.6121 (tt0) cc_final: 0.4906 (pm20) REVERT: A 704 ARG cc_start: 0.6619 (ptp90) cc_final: 0.6297 (ptp90) REVERT: B 110 GLN cc_start: 0.6836 (tm-30) cc_final: 0.6462 (tm-30) REVERT: B 178 THR cc_start: 0.6289 (m) cc_final: 0.5983 (p) REVERT: B 223 PHE cc_start: 0.5314 (t80) cc_final: 0.4719 (t80) REVERT: B 249 MET cc_start: 0.7854 (tmm) cc_final: 0.7559 (ppp) REVERT: D 96 ASP cc_start: 0.6304 (m-30) cc_final: 0.5989 (m-30) outliers start: 22 outliers final: 14 residues processed: 153 average time/residue: 0.0811 time to fit residues: 18.4540 Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 548 PHE 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 204 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 153 PHE 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 79 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN C 50 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 = 0.4428 r_free = 0.4428 target = 0.161485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.132897 restraints weight = 14232.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.136353 restraints weight = 10608.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.137627 restraints weight = 7203.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.140310 restraints weight = 5058.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.140566 restraints weight = 4058.737| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9298 Z= 0.172 Angle : 0.685 10.934 12529 Z= 0.355 Chirality : 0.045 0.248 1386 Planarity : 0.005 0.058 1599 Dihedral : 5.664 52.214 1256 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.45 % Allowed : 20.45 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.25), residues: 1115 helix: -0.06 (0.22), residues: 579 sheet: -2.59 (0.57), residues: 73 loop : -1.82 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 719 TYR 0.038 0.002 TYR D 126 PHE 0.025 0.002 PHE A 707 TRP 0.016 0.001 TRP C 59 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9293) covalent geometry : angle 0.68534 (12529) hydrogen bonds : bond 0.04550 ( 392) hydrogen bonds : angle 5.15907 ( 1128) metal coordination : bond 0.00434 ( 5) *********************** 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: 24 poor density : 137 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6363 (OUTLIER) cc_final: 0.5781 (m170) REVERT: A 704 ARG cc_start: 0.6795 (ptp90) cc_final: 0.6457 (ptp90) REVERT: B 110 GLN cc_start: 0.6979 (tm-30) cc_final: 0.6559 (tm-30) REVERT: B 223 PHE cc_start: 0.5300 (t80) cc_final: 0.4705 (t80) REVERT: B 249 MET cc_start: 0.7929 (tmm) cc_final: 0.7584 (ppp) REVERT: D 92 ASP cc_start: 0.6509 (m-30) cc_final: 0.6050 (t0) REVERT: D 96 ASP cc_start: 0.6383 (m-30) cc_final: 0.6014 (m-30) outliers start: 24 outliers final: 19 residues processed: 153 average time/residue: 0.0847 time to fit residues: 18.7362 Evaluate side-chains 147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR 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 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 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 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 64 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 chunk 91 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 62 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN B 122 ASN C 95 ASN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.163334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.135162 restraints weight = 14254.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.138268 restraints weight = 10776.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.140092 restraints weight = 7375.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.141126 restraints weight = 5046.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.142257 restraints weight = 4630.357| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9298 Z= 0.139 Angle : 0.675 11.008 12529 Z= 0.349 Chirality : 0.044 0.227 1386 Planarity : 0.004 0.046 1599 Dihedral : 5.563 50.644 1256 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.15 % Allowed : 21.47 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.25), residues: 1115 helix: -0.05 (0.22), residues: 579 sheet: -2.57 (0.57), residues: 73 loop : -1.71 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 719 TYR 0.021 0.002 TYR D 126 PHE 0.021 0.002 PHE D 174 TRP 0.023 0.001 TRP C 59 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9293) covalent geometry : angle 0.67473 (12529) hydrogen bonds : bond 0.04291 ( 392) hydrogen bonds : angle 5.08961 ( 1128) metal coordination : bond 0.00246 ( 5) *********************** 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 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6301 (OUTLIER) cc_final: 0.5698 (m170) REVERT: A 270 GLN cc_start: 0.5888 (tt0) cc_final: 0.5686 (mt0) REVERT: A 668 MET cc_start: 0.4793 (mmt) cc_final: 0.4313 (mmm) REVERT: A 704 ARG cc_start: 0.6648 (ptp90) cc_final: 0.6310 (ptp90) REVERT: B 110 GLN cc_start: 0.6945 (tm-30) cc_final: 0.6534 (tm-30) REVERT: B 223 PHE cc_start: 0.5341 (t80) cc_final: 0.4697 (t80) REVERT: B 249 MET cc_start: 0.7888 (tmm) cc_final: 0.7574 (ppp) REVERT: D 92 ASP cc_start: 0.6507 (m-30) cc_final: 0.6055 (t0) REVERT: D 96 ASP cc_start: 0.6316 (m-30) cc_final: 0.5976 (m-30) outliers start: 21 outliers final: 15 residues processed: 146 average time/residue: 0.0852 time to fit residues: 18.2821 Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 212 THR 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 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 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 97 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.163185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.134604 restraints weight = 14322.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.137898 restraints weight = 10670.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.139560 restraints weight = 7369.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.140768 restraints weight = 5052.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.141816 restraints weight = 4559.889| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9298 Z= 0.145 Angle : 0.673 10.962 12529 Z= 0.348 Chirality : 0.044 0.294 1386 Planarity : 0.004 0.045 1599 Dihedral : 5.572 50.062 1256 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.04 % Allowed : 21.37 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.25), residues: 1115 helix: -0.09 (0.21), residues: 581 sheet: -2.54 (0.56), residues: 73 loop : -1.72 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 719 TYR 0.020 0.002 TYR D 126 PHE 0.019 0.002 PHE D 104 TRP 0.022 0.001 TRP C 59 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9293) covalent geometry : angle 0.67332 (12529) hydrogen bonds : bond 0.04288 ( 392) hydrogen bonds : angle 5.06064 ( 1128) metal coordination : bond 0.00298 ( 5) ********************** 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 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6329 (OUTLIER) cc_final: 0.5734 (m170) REVERT: A 668 MET cc_start: 0.4795 (mmt) cc_final: 0.4297 (mmm) REVERT: A 704 ARG cc_start: 0.6681 (ptp90) cc_final: 0.6336 (ptp90) REVERT: B 110 GLN cc_start: 0.6954 (tm-30) cc_final: 0.6547 (tm-30) REVERT: B 155 LEU cc_start: 0.8376 (mm) cc_final: 0.7718 (mm) REVERT: B 223 PHE cc_start: 0.5361 (t80) cc_final: 0.4719 (t80) REVERT: B 249 MET cc_start: 0.7946 (tmm) cc_final: 0.7610 (ppp) REVERT: D 92 ASP cc_start: 0.6558 (m-30) cc_final: 0.6082 (t0) REVERT: D 96 ASP cc_start: 0.6376 (m-30) cc_final: 0.6018 (m-30) outliers start: 20 outliers final: 17 residues processed: 143 average time/residue: 0.0768 time to fit residues: 16.6308 Evaluate side-chains 144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR 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 A residue 695 GLU Chi-restraints excluded: chain B residue 169 VAL 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 12 LEU 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 151 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 219 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 29 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.0000 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.165080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.136651 restraints weight = 14250.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.140320 restraints weight = 10558.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.141917 restraints weight = 7116.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.143167 restraints weight = 4912.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.144893 restraints weight = 4424.556| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9298 Z= 0.124 Angle : 0.647 10.991 12529 Z= 0.335 Chirality : 0.043 0.280 1386 Planarity : 0.004 0.044 1599 Dihedral : 5.378 47.758 1256 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.74 % Allowed : 21.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.25), residues: 1115 helix: -0.04 (0.21), residues: 581 sheet: -2.50 (0.57), residues: 73 loop : -1.66 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 719 TYR 0.021 0.001 TYR D 126 PHE 0.019 0.002 PHE D 174 TRP 0.019 0.001 TRP C 59 HIS 0.005 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9293) covalent geometry : angle 0.64719 (12529) hydrogen bonds : bond 0.04024 ( 392) hydrogen bonds : angle 4.94209 ( 1128) metal coordination : bond 0.00175 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1523.84 seconds wall clock time: 27 minutes 17.08 seconds (1637.08 seconds total)