Starting phenix.real_space_refine on Thu Jan 18 17:45:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfd_23813/01_2024/7mfd_23813_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfd_23813/01_2024/7mfd_23813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfd_23813/01_2024/7mfd_23813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfd_23813/01_2024/7mfd_23813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfd_23813/01_2024/7mfd_23813_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfd_23813/01_2024/7mfd_23813_updated.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 57 5.16 5 C 5795 2.51 5 N 1574 2.21 5 O 1696 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9127 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3297 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2291 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 16, 'TRANS': 276} Chain breaks: 1 Chain: "C" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1738 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1766 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'CHU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 673 SG CYS A 248 63.720 26.552 51.589 1.00 80.27 S ATOM 698 SG CYS A 251 64.077 23.314 53.654 1.00 66.34 S ATOM 880 SG CYS A 272 62.080 23.273 50.310 1.00 90.13 S ATOM 786 SG CYS A 261 57.199 35.051 42.449 1.00 69.90 S ATOM 808 SG CYS A 264 56.805 35.956 45.817 1.00 69.91 S Time building chain proxies: 5.34, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 3.70 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 248 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 251 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 272 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 261 " 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 5 sheets defined 49.4% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 177 through 187 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 214 through 217 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 492 through 505 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 537 through 542 Processing helix chain 'A' and resid 550 through 553 No H-bonds generated for 'chain 'A' and resid 550 through 553' Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 640 through 651 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 663 through 671 Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 687 through 691 removed outlier: 4.097A pdb=" N ARG A 691 " --> pdb=" O LYS A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 687 through 691' Processing helix chain 'A' and resid 695 through 697 No H-bonds generated for 'chain 'A' and resid 695 through 697' Processing helix chain 'A' and resid 707 through 719 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) Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 105 through 119 removed outlier: 3.584A pdb=" N ARG B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N HIS B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.790A pdb=" N LEU B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 184 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 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 213 through 218 removed outlier: 3.641A pdb=" N ASP B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 241 through 257 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 312 through 317 Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.751A pdb=" N PHE B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 373 through 376 No H-bonds generated for 'chain 'B' and resid 373 through 376' Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 20 through 30 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 38 through 68 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 104 removed outlier: 4.020A pdb=" N GLU C 81 " --> pdb=" O MET C 78 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR C 88 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG C 91 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS C 94 " --> pdb=" O ARG C 91 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 95 " --> pdb=" O ASP C 92 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 99 " --> pdb=" O ASP C 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 104 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 112 through 132 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 159 removed outlier: 4.255A pdb=" N LYS C 139 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 140 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP C 143 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN C 147 " --> pdb=" O GLN C 144 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR C 149 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 151 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 153 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 154 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS C 157 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 159 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 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) Processing helix chain 'C' and resid 186 through 201 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) Processing helix chain 'C' and resid 212 through 228 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 11 removed outlier: 3.693A pdb=" N ALA D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 30 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 38 through 67 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 75 through 103 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 112 through 132 Processing helix chain 'D' and resid 138 through 156 removed outlier: 3.531A pdb=" N VAL D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 185 through 202 removed outlier: 3.804A pdb=" N ALA D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 228 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= A, 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= B, first strand: chain 'A' and resid 223 through 226 removed outlier: 3.899A pdb=" N HIS A 223 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 198 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 197 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 206 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 470 through 475 removed outlier: 4.067A pdb=" N THR A 470 " --> pdb=" O MET A 484 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 484 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 480 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 582 through 585 Processing sheet with id= E, first strand: chain 'B' and resid 131 through 135 removed outlier: 4.356A pdb=" N GLY B 131 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS B 142 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 133 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 140 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 135 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 94 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 98 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL B 81 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 72 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N SER B 86 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LYS B 70 " --> pdb=" O SER B 86 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 96.80 - 104.26: 132 104.26 - 111.73: 4231 111.73 - 119.19: 3362 119.19 - 126.65: 4690 126.65 - 134.12: 114 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: 200 2.67 - 3.23: 9387 3.23 - 3.78: 13989 3.78 - 4.34: 19917 4.34 - 4.90: 30485 Nonbonded interactions: 73978 Sorted by model distance: nonbonded pdb=" OE1 GLN D 161 " pdb=" OG1 THR D 163 " model vdw 2.112 2.440 nonbonded pdb=" OG SER C 37 " pdb=" OE1 GLU C 40 " model vdw 2.132 2.440 nonbonded pdb=" OD1 ASP C 124 " pdb=" OH TYR C 149 " model vdw 2.161 2.440 nonbonded pdb=" OD1 ASP D 124 " pdb=" NH2 ARG D 127 " model vdw 2.167 2.520 nonbonded pdb=" NH2 ARG D 127 " pdb=" OD1 ASN D 173 " model vdw 2.198 2.520 ... (remaining 73973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 102 or (resid 103 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 104 through \ 133 or (resid 137 and (name N or name CA or name C or name O or name CB )) or re \ sid 138 through 156 or (resid 157 through 158 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name CE )) or resid 159 through 211 \ or (resid 212 and (name N or name CA or name C or name O or name CB )) or resid \ 213 through 229 or (resid 230 and (name N or name CA or name C or name O or nam \ e CB )))) selection = (chain 'D' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name CE )) or resid 4 through 67 or (resid 68 \ and (name N or name CA or name C or name O or name CB )) or resid 69 or resid 7 \ 3 through 74 or (resid 75 and (name N or name CA or name C or name O or name CB \ or name CG )) or (resid 76 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 102 or (resid 103 and (name N or name CA or name C or na \ me O or name CB or name CG )) or resid 104 through 138 or (resid 139 and (name N \ or name CA or name C or name O or name CB or name CG )) or resid 140 through 15 \ 7 or (resid 158 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE )) or resid 159 through 203 or resid 210 through 230)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.760 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 29.130 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9293 Z= 0.243 Angle : 0.674 10.587 12529 Z= 0.357 Chirality : 0.045 0.365 1386 Planarity : 0.005 0.054 1599 Dihedral : 15.471 89.636 3495 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.20 % Allowed : 0.92 % Favored : 98.88 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.24), residues: 1115 helix: -1.12 (0.21), residues: 536 sheet: -2.17 (0.63), residues: 57 loop : -1.60 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.009 0.001 HIS A 235 PHE 0.034 0.002 PHE D 174 TYR 0.030 0.002 TYR D 125 ARG 0.005 0.001 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5239 (tt0) cc_final: 0.4758 (pm20) REVERT: B 68 PHE cc_start: 0.4878 (m-80) cc_final: 0.4472 (m-80) REVERT: B 87 HIS cc_start: 0.3528 (t70) cc_final: 0.2954 (t-170) REVERT: B 219 MET cc_start: 0.7079 (ttt) cc_final: 0.6770 (ttp) REVERT: D 96 ASP cc_start: 0.6875 (m-30) cc_final: 0.6375 (m-30) outliers start: 2 outliers final: 1 residues processed: 151 average time/residue: 0.1948 time to fit residues: 42.1844 Evaluate side-chains 123 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN D 147 GLN ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9293 Z= 0.227 Angle : 0.666 8.101 12529 Z= 0.347 Chirality : 0.044 0.208 1386 Planarity : 0.005 0.042 1599 Dihedral : 6.264 68.371 1260 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.33 % Allowed : 11.04 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.24), residues: 1115 helix: -0.86 (0.20), residues: 576 sheet: -2.40 (0.57), residues: 63 loop : -1.65 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 59 HIS 0.013 0.001 HIS A 477 PHE 0.030 0.002 PHE D 174 TYR 0.038 0.002 TYR D 126 ARG 0.004 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5589 (tt0) cc_final: 0.4957 (pm20) REVERT: B 68 PHE cc_start: 0.4750 (m-80) cc_final: 0.4462 (m-80) REVERT: B 87 HIS cc_start: 0.3571 (t70) cc_final: 0.3108 (t-170) REVERT: B 178 THR cc_start: 0.6393 (m) cc_final: 0.6055 (p) REVERT: D 96 ASP cc_start: 0.6804 (m-30) cc_final: 0.6301 (m-30) outliers start: 13 outliers final: 9 residues processed: 148 average time/residue: 0.1919 time to fit residues: 41.2684 Evaluate side-chains 137 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 57 SER 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 214 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.0370 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.0464 ------------------------------------------------------------------------------- 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 219 GLN C 224 ASN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9293 Z= 0.181 Angle : 0.601 8.327 12529 Z= 0.312 Chirality : 0.042 0.206 1386 Planarity : 0.004 0.039 1599 Dihedral : 5.794 63.575 1256 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.45 % Allowed : 13.60 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.24), residues: 1115 helix: -0.63 (0.21), residues: 568 sheet: -2.15 (0.61), residues: 63 loop : -1.66 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 59 HIS 0.016 0.001 HIS A 477 PHE 0.022 0.002 PHE D 174 TYR 0.030 0.002 TYR D 126 ARG 0.003 0.000 ARG A 252 *********************** 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 163 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.5967 (tt0) cc_final: 0.4643 (pm20) REVERT: A 668 MET cc_start: 0.4845 (mmt) cc_final: 0.4282 (mmm) REVERT: B 87 HIS cc_start: 0.3650 (t70) cc_final: 0.3237 (t-170) REVERT: B 178 THR cc_start: 0.6373 (m) cc_final: 0.5999 (p) REVERT: B 356 MET cc_start: 0.7009 (mpp) cc_final: 0.6691 (mpp) REVERT: D 96 ASP cc_start: 0.6733 (m-30) cc_final: 0.6212 (m-30) REVERT: D 179 TYR cc_start: 0.5571 (t80) cc_final: 0.5325 (t80) outliers start: 24 outliers final: 16 residues processed: 154 average time/residue: 0.1817 time to fit residues: 41.1483 Evaluate side-chains 135 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP 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 180 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 219 GLN 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 147 GLN Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 214 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN C 164 HIS ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 9293 Z= 0.379 Angle : 0.752 9.431 12529 Z= 0.387 Chirality : 0.047 0.218 1386 Planarity : 0.006 0.043 1599 Dihedral : 6.433 64.666 1256 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.52 % Favored : 91.39 % Rotamer: Outliers : 2.76 % Allowed : 19.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.24), residues: 1115 helix: -0.91 (0.20), residues: 560 sheet: -1.88 (0.61), residues: 65 loop : -1.93 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 59 HIS 0.016 0.001 HIS A 477 PHE 0.026 0.003 PHE A 707 TYR 0.026 0.002 TYR D 125 ARG 0.004 0.001 ARG C 41 *********************** 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 160 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 668 MET cc_start: 0.5069 (mmt) cc_final: 0.4812 (mmt) REVERT: B 87 HIS cc_start: 0.3635 (t70) cc_final: 0.3146 (t-170) REVERT: B 98 LEU cc_start: 0.6475 (mt) cc_final: 0.6164 (mt) REVERT: B 110 GLN cc_start: 0.6976 (tm-30) cc_final: 0.6559 (tm-30) REVERT: D 96 ASP cc_start: 0.6739 (m-30) cc_final: 0.6340 (m-30) outliers start: 27 outliers final: 22 residues processed: 149 average time/residue: 0.1784 time to fit residues: 39.2306 Evaluate side-chains 144 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 267 LYS 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 209 PHE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain 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 214 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.0270 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.0010 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 overall best weight: 0.9648 ------------------------------------------------------------------------------- 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 ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9293 Z= 0.187 Angle : 0.627 8.908 12529 Z= 0.322 Chirality : 0.043 0.237 1386 Planarity : 0.004 0.039 1599 Dihedral : 5.915 60.313 1256 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.76 % Allowed : 19.94 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.24), residues: 1115 helix: -0.70 (0.21), residues: 575 sheet: -1.69 (0.62), residues: 65 loop : -1.75 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 59 HIS 0.008 0.001 HIS A 477 PHE 0.015 0.001 PHE D 174 TYR 0.038 0.002 TYR D 126 ARG 0.003 0.000 ARG D 127 *********************** 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 160 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6402 (OUTLIER) cc_final: 0.5691 (m170) REVERT: A 555 ASP cc_start: 0.5515 (t70) cc_final: 0.5065 (t70) REVERT: A 704 ARG cc_start: 0.6825 (ptp90) cc_final: 0.6362 (ptp90) REVERT: B 68 PHE cc_start: 0.4800 (m-80) cc_final: 0.4435 (m-80) REVERT: B 87 HIS cc_start: 0.3644 (t70) cc_final: 0.3184 (t-170) REVERT: B 98 LEU cc_start: 0.6330 (mt) cc_final: 0.6044 (mt) REVERT: B 110 GLN cc_start: 0.6999 (tm-30) cc_final: 0.6628 (tm-30) REVERT: B 178 THR cc_start: 0.6443 (m) cc_final: 0.6049 (p) REVERT: B 356 MET cc_start: 0.7673 (mpp) cc_final: 0.7442 (mpp) REVERT: D 26 MET cc_start: 0.4576 (mmm) cc_final: 0.4180 (mmm) REVERT: D 96 ASP cc_start: 0.6575 (m-30) cc_final: 0.6275 (m-30) outliers start: 27 outliers final: 19 residues processed: 148 average time/residue: 0.1906 time to fit residues: 41.5633 Evaluate side-chains 142 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 57 SER 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 147 GLN Chi-restraints excluded: chain D residue 151 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 64 optimal weight: 0.0970 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9293 Z= 0.235 Angle : 0.634 9.058 12529 Z= 0.325 Chirality : 0.044 0.245 1386 Planarity : 0.004 0.038 1599 Dihedral : 5.930 59.504 1256 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.00 % Favored : 92.91 % Rotamer: Outliers : 3.17 % Allowed : 20.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.24), residues: 1115 helix: -0.56 (0.21), residues: 566 sheet: -1.93 (0.61), residues: 63 loop : -1.85 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 59 HIS 0.003 0.001 HIS C 164 PHE 0.015 0.002 PHE A 707 TYR 0.015 0.002 TYR D 126 ARG 0.002 0.000 ARG B 189 *********************** 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 fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6400 (OUTLIER) cc_final: 0.5692 (m170) REVERT: A 551 ILE cc_start: 0.7041 (mm) cc_final: 0.6748 (mt) REVERT: A 555 ASP cc_start: 0.5514 (OUTLIER) cc_final: 0.5032 (t70) REVERT: A 572 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.7103 (pt) REVERT: A 668 MET cc_start: 0.5044 (mmt) cc_final: 0.4593 (mmm) REVERT: A 704 ARG cc_start: 0.6903 (ptp90) cc_final: 0.6416 (ptp90) REVERT: B 110 GLN cc_start: 0.6975 (tm-30) cc_final: 0.6615 (tm-30) REVERT: B 249 MET cc_start: 0.7852 (tmm) cc_final: 0.7521 (ppp) REVERT: B 356 MET cc_start: 0.7431 (mpp) cc_final: 0.7207 (mpp) REVERT: D 96 ASP cc_start: 0.6560 (m-30) cc_final: 0.6239 (m-30) outliers start: 31 outliers final: 23 residues processed: 143 average time/residue: 0.1793 time to fit residues: 37.9810 Evaluate side-chains 144 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 194 THR 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 194 THR Chi-restraints excluded: chain D residue 213 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 80 optimal weight: 0.0770 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 overall best weight: 2.7544 ------------------------------------------------------------------------------- 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** 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9293 Z= 0.305 Angle : 0.700 9.376 12529 Z= 0.359 Chirality : 0.046 0.262 1386 Planarity : 0.005 0.039 1599 Dihedral : 6.245 63.982 1256 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.80 % Favored : 92.11 % Rotamer: Outliers : 3.78 % Allowed : 20.04 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.24), residues: 1115 helix: -0.75 (0.21), residues: 567 sheet: -2.04 (0.61), residues: 64 loop : -2.00 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 59 HIS 0.011 0.001 HIS B 87 PHE 0.021 0.002 PHE A 707 TYR 0.017 0.002 TYR D 125 ARG 0.003 0.000 ARG D 18 *********************** 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 161 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.5775 (m170) REVERT: A 572 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7111 (pt) REVERT: A 668 MET cc_start: 0.5003 (mmt) cc_final: 0.4442 (mmm) REVERT: A 704 ARG cc_start: 0.7043 (ptp90) cc_final: 0.6564 (ptp90) REVERT: B 98 LEU cc_start: 0.6354 (mt) cc_final: 0.6042 (mt) REVERT: B 110 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6646 (tm-30) REVERT: D 26 MET cc_start: 0.4621 (mmm) cc_final: 0.4384 (mmm) REVERT: D 96 ASP cc_start: 0.6674 (m-30) cc_final: 0.6298 (m-30) REVERT: D 104 PHE cc_start: 0.5805 (m-10) cc_final: 0.5543 (m-80) outliers start: 37 outliers final: 29 residues processed: 150 average time/residue: 0.1961 time to fit residues: 42.2607 Evaluate side-chains 150 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 572 ILE 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 209 PHE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain 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 175 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 214 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9293 Z= 0.278 Angle : 0.695 9.223 12529 Z= 0.357 Chirality : 0.045 0.281 1386 Planarity : 0.005 0.039 1599 Dihedral : 6.252 65.183 1256 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 3.27 % Allowed : 20.96 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.24), residues: 1115 helix: -0.72 (0.21), residues: 566 sheet: -2.06 (0.61), residues: 64 loop : -2.03 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 59 HIS 0.010 0.001 HIS B 87 PHE 0.019 0.002 PHE A 707 TYR 0.014 0.002 TYR A 266 ARG 0.002 0.000 ARG B 189 *********************** 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 157 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6394 (OUTLIER) cc_final: 0.5752 (m170) REVERT: A 572 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7086 (pt) REVERT: A 668 MET cc_start: 0.4945 (mmt) cc_final: 0.4403 (mmm) REVERT: A 704 ARG cc_start: 0.6987 (ptp90) cc_final: 0.6694 (ptp90) REVERT: B 98 LEU cc_start: 0.6343 (mt) cc_final: 0.6043 (mt) REVERT: B 110 GLN cc_start: 0.7022 (tm-30) cc_final: 0.6626 (tm-30) REVERT: D 96 ASP cc_start: 0.6534 (m-30) cc_final: 0.6231 (m-30) REVERT: D 104 PHE cc_start: 0.5938 (m-10) cc_final: 0.5653 (m-80) outliers start: 32 outliers final: 26 residues processed: 148 average time/residue: 0.1880 time to fit residues: 40.4911 Evaluate side-chains 147 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain 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 175 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 214 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.0050 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9293 Z= 0.194 Angle : 0.639 9.128 12529 Z= 0.329 Chirality : 0.043 0.284 1386 Planarity : 0.004 0.039 1599 Dihedral : 5.899 60.762 1256 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.97 % Allowed : 21.88 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 1115 helix: -0.43 (0.21), residues: 567 sheet: -2.08 (0.61), residues: 64 loop : -1.83 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 59 HIS 0.010 0.001 HIS B 87 PHE 0.018 0.002 PHE D 174 TYR 0.030 0.002 TYR D 126 ARG 0.002 0.000 ARG B 189 *********************** 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 157 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6375 (OUTLIER) cc_final: 0.5673 (m170) REVERT: A 462 ARG cc_start: 0.5304 (tpt170) cc_final: 0.4533 (tpp-160) REVERT: A 555 ASP cc_start: 0.5465 (t70) cc_final: 0.5019 (t70) REVERT: A 668 MET cc_start: 0.5088 (mmt) cc_final: 0.4568 (mmm) REVERT: A 704 ARG cc_start: 0.6856 (ptp90) cc_final: 0.6559 (ptp90) REVERT: B 98 LEU cc_start: 0.6409 (mt) cc_final: 0.6154 (mt) REVERT: B 110 GLN cc_start: 0.6990 (tm-30) cc_final: 0.6636 (tm-30) REVERT: D 96 ASP cc_start: 0.6447 (m-30) cc_final: 0.6188 (m-30) REVERT: D 104 PHE cc_start: 0.5874 (m-10) cc_final: 0.5634 (m-80) outliers start: 29 outliers final: 22 residues processed: 148 average time/residue: 0.1958 time to fit residues: 41.6872 Evaluate side-chains 145 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 271 ARG 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 B residue 315 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 7 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 175 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 214 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 0.0040 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9293 Z= 0.360 Angle : 0.765 9.314 12529 Z= 0.393 Chirality : 0.048 0.292 1386 Planarity : 0.005 0.042 1599 Dihedral : 6.541 67.548 1256 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.07 % Allowed : 21.57 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.24), residues: 1115 helix: -0.88 (0.21), residues: 568 sheet: -1.89 (0.62), residues: 66 loop : -2.13 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 59 HIS 0.008 0.002 HIS B 87 PHE 0.026 0.003 PHE D 174 TYR 0.024 0.002 TYR D 126 ARG 0.008 0.001 ARG A 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 HIS cc_start: 0.6454 (OUTLIER) cc_final: 0.5893 (m170) REVERT: A 462 ARG cc_start: 0.5609 (tpt170) cc_final: 0.4815 (tpp-160) REVERT: A 668 MET cc_start: 0.4973 (mmt) cc_final: 0.4756 (mmt) REVERT: B 98 LEU cc_start: 0.6443 (mt) cc_final: 0.6135 (mt) REVERT: B 110 GLN cc_start: 0.6957 (tm-30) cc_final: 0.6547 (tm-30) REVERT: D 96 ASP cc_start: 0.6529 (m-30) cc_final: 0.6131 (m-30) outliers start: 30 outliers final: 28 residues processed: 150 average time/residue: 0.1884 time to fit residues: 40.8514 Evaluate side-chains 156 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 452 ILE 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 B residue 315 ASP Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 7 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 172 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 214 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 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 = 0.4385 r_free = 0.4385 target = 0.157786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.129813 restraints weight = 14513.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.133684 restraints weight = 10920.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.134581 restraints weight = 7754.159| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9293 Z= 0.310 Angle : 0.736 9.687 12529 Z= 0.378 Chirality : 0.047 0.298 1386 Planarity : 0.005 0.041 1599 Dihedral : 6.495 68.633 1256 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.97 % Allowed : 22.19 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.24), residues: 1115 helix: -0.91 (0.21), residues: 570 sheet: -1.94 (0.61), residues: 67 loop : -2.18 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 59 HIS 0.008 0.001 HIS B 87 PHE 0.023 0.002 PHE D 174 TYR 0.027 0.002 TYR D 125 ARG 0.008 0.000 ARG A 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1878.17 seconds wall clock time: 35 minutes 10.47 seconds (2110.47 seconds total)