Starting phenix.real_space_refine on Thu Jul 31 03:23:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o9w_12765/07_2025/7o9w_12765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o9w_12765/07_2025/7o9w_12765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o9w_12765/07_2025/7o9w_12765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o9w_12765/07_2025/7o9w_12765.map" model { file = "/net/cci-nas-00/data/ceres_data/7o9w_12765/07_2025/7o9w_12765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o9w_12765/07_2025/7o9w_12765.cif" } resolution = 3.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 526 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 8101 2.51 5 N 2118 2.21 5 O 2347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12618 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9089 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 27, 'TRANS': 1141} Chain breaks: 2 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 207} Chain: "C" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'V5Q': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.01, per 1000 atoms: 0.71 Number of scatterers: 12618 At special positions: 0 Unit cell: (147.84, 139.92, 162.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2347 8.00 N 2118 7.00 C 8101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 200 " distance=2.47 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.7 seconds 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2978 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 13 sheets defined 52.5% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 removed outlier: 3.802A pdb=" N MET A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 35 through 40' Processing helix chain 'A' and resid 44 through 89 removed outlier: 3.508A pdb=" N LYS A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 105 through 157 removed outlier: 4.147A pdb=" N GLU A 109 " --> pdb=" O MET A 105 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.580A pdb=" N VAL A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 removed outlier: 3.833A pdb=" N LEU A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 211 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.609A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 4.061A pdb=" N SER A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 260 removed outlier: 4.436A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 268 removed outlier: 4.374A pdb=" N ALA A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 323 Processing helix chain 'A' and resid 327 through 348 Processing helix chain 'A' and resid 348 through 371 removed outlier: 4.215A pdb=" N ILE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.687A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.874A pdb=" N THR A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.835A pdb=" N ILE A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.735A pdb=" N GLY A 528 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 546 Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.526A pdb=" N GLU A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.762A pdb=" N LYS A 702 " --> pdb=" O ARG A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 707 through 741 removed outlier: 4.778A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 4.026A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 741 " --> pdb=" O GLY A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 798 Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.643A pdb=" N PHE A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 854 removed outlier: 3.999A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ARG A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 863 Processing helix chain 'A' and resid 864 through 880 removed outlier: 3.785A pdb=" N SER A 880 " --> pdb=" O MET A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 893 Processing helix chain 'A' and resid 894 through 903 removed outlier: 3.506A pdb=" N THR A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 911 removed outlier: 3.723A pdb=" N VAL A 907 " --> pdb=" O ASN A 903 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 911 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 966 removed outlier: 3.523A pdb=" N PHE A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 4.375A pdb=" N TYR A 953 " --> pdb=" O MET A 949 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 954 " --> pdb=" O TYR A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 995 removed outlier: 4.311A pdb=" N PHE A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1014 Processing helix chain 'A' and resid 1077 through 1084 Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.884A pdb=" N LEU A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A1113 " --> pdb=" O LEU A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1133 Processing helix chain 'A' and resid 1141 through 1152 Processing helix chain 'A' and resid 1154 through 1161 removed outlier: 3.771A pdb=" N LEU A1161 " --> pdb=" O PHE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1174 removed outlier: 3.896A pdb=" N GLY A1173 " --> pdb=" O GLY A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1191 Processing helix chain 'A' and resid 1207 through 1222 removed outlier: 3.945A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 4.235A pdb=" N ASN A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1263 Processing helix chain 'A' and resid 1265 through 1272 Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.901A pdb=" N ARG B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 190 through 195' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.574A pdb=" N ASP C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 91 " --> pdb=" O PHE C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing helix chain 'C' and resid 163 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 417 removed outlier: 3.743A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 450 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 397 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU A 448 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.550A pdb=" N GLY A 471 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP A 555 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 473 " --> pdb=" O ASP A 555 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 423 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1060 removed outlier: 5.227A pdb=" N LEU A1056 " --> pdb=" O GLU A1039 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL A1040 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A1091 " --> pdb=" O VAL A1040 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 4.021A pdb=" N LEU A1198 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1116 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A1200 " --> pdb=" O VAL A1116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A1068 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA A1067 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE A1246 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A1069 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1245 " --> pdb=" O LYS A1252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.969A pdb=" N ALA B 19 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 80 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.620A pdb=" N TRP B 40 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 removed outlier: 4.056A pdb=" N THR B 103 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 123 removed outlier: 3.536A pdb=" N ASN B 143 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 183 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.621A pdb=" N GLU C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 119 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.507A pdb=" N CYS C 149 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 188 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 151 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 186 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR C 184 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU C 179 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR C 185 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA C 177 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER C 187 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE C 175 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 203 through 206 693 hydrogen bonds defined for protein. 1983 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: 4.45 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2038 1.31 - 1.44: 3511 1.44 - 1.57: 7250 1.57 - 1.70: 4 1.70 - 1.83: 86 Bond restraints: 12889 Sorted by residual: bond pdb=" C09 V5Q A1402 " pdb=" N08 V5Q A1402 " ideal model delta sigma weight residual 1.454 1.285 0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" C40 V5Q A1402 " pdb=" O41 V5Q A1402 " ideal model delta sigma weight residual 1.352 1.520 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" C40 V5Q A1401 " pdb=" O41 V5Q A1401 " ideal model delta sigma weight residual 1.352 1.520 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" C09 V5Q A1401 " pdb=" N08 V5Q A1401 " ideal model delta sigma weight residual 1.454 1.291 0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C20 V5Q A1402 " pdb=" C22 V5Q A1402 " ideal model delta sigma weight residual 1.460 1.580 -0.120 2.00e-02 2.50e+03 3.63e+01 ... (remaining 12884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 17076 2.46 - 4.92: 326 4.92 - 7.39: 42 7.39 - 9.85: 12 9.85 - 12.31: 3 Bond angle restraints: 17459 Sorted by residual: angle pdb=" C PRO B 100 " pdb=" N PRO B 101 " pdb=" CA PRO B 101 " ideal model delta sigma weight residual 119.84 131.34 -11.50 1.25e+00 6.40e-01 8.47e+01 angle pdb=" N ILE B 99 " pdb=" CA ILE B 99 " pdb=" C ILE B 99 " ideal model delta sigma weight residual 108.88 121.19 -12.31 2.16e+00 2.14e-01 3.25e+01 angle pdb=" C LYS B 55 " pdb=" CA LYS B 55 " pdb=" CB LYS B 55 " ideal model delta sigma weight residual 116.63 110.19 6.44 1.16e+00 7.43e-01 3.08e+01 angle pdb=" N LYS B 55 " pdb=" CA LYS B 55 " pdb=" C LYS B 55 " ideal model delta sigma weight residual 108.08 116.69 -8.61 1.69e+00 3.50e-01 2.59e+01 angle pdb=" C ILE B 99 " pdb=" N PRO B 100 " pdb=" CA PRO B 100 " ideal model delta sigma weight residual 120.38 115.14 5.24 1.03e+00 9.43e-01 2.58e+01 ... (remaining 17454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.52: 7156 27.52 - 55.04: 471 55.04 - 82.57: 47 82.57 - 110.09: 5 110.09 - 137.61: 1 Dihedral angle restraints: 7680 sinusoidal: 3037 harmonic: 4643 Sorted by residual: dihedral pdb=" CB CYS C 149 " pdb=" SG CYS C 149 " pdb=" SG CYS C 204 " pdb=" CB CYS C 204 " ideal model delta sinusoidal sigma weight residual 93.00 32.00 61.00 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CA ASN A1163 " pdb=" C ASN A1163 " pdb=" N LYS A1164 " pdb=" CA LYS A1164 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASP A 997 " pdb=" C ASP A 997 " pdb=" N TYR A 998 " pdb=" CA TYR A 998 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 7677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.383: 1978 0.383 - 0.767: 1 0.767 - 1.150: 0 1.150 - 1.533: 1 1.533 - 1.917: 1 Chirality restraints: 1981 Sorted by residual: chirality pdb=" C35 V5Q A1401 " pdb=" C33 V5Q A1401 " pdb=" C36 V5Q A1401 " pdb=" O41 V5Q A1401 " both_signs ideal model delta sigma weight residual False -2.39 -0.47 -1.92 2.00e-01 2.50e+01 9.18e+01 chirality pdb=" C35 V5Q A1402 " pdb=" C33 V5Q A1402 " pdb=" C36 V5Q A1402 " pdb=" O41 V5Q A1402 " both_signs ideal model delta sigma weight residual False -2.39 -1.09 -1.30 2.00e-01 2.50e+01 4.21e+01 chirality pdb=" CB VAL B 56 " pdb=" CA VAL B 56 " pdb=" CG1 VAL B 56 " pdb=" CG2 VAL B 56 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.11e+00 ... (remaining 1978 not shown) Planarity restraints: 2202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 97 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C THR B 97 " -0.061 2.00e-02 2.50e+03 pdb=" O THR B 97 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS B 98 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 174 " 0.213 9.50e-02 1.11e+02 9.53e-02 5.57e+00 pdb=" NE ARG A 174 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 174 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 174 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 174 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 109 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C MET C 109 " 0.040 2.00e-02 2.50e+03 pdb=" O MET C 109 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP C 110 " -0.013 2.00e-02 2.50e+03 ... (remaining 2199 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 398 2.70 - 3.25: 12520 3.25 - 3.80: 20005 3.80 - 4.35: 25200 4.35 - 4.90: 41561 Nonbonded interactions: 99684 Sorted by model distance: nonbonded pdb=" N ASP C 110 " pdb=" OD1 ASP C 110 " model vdw 2.149 3.120 nonbonded pdb=" O GLN A 990 " pdb=" OG SER A 993 " model vdw 2.197 3.040 nonbonded pdb=" O GLY A 854 " pdb=" OG1 THR A 858 " model vdw 2.201 3.040 nonbonded pdb=" O PRO B 8 " pdb=" OG1 THR B 108 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU A 707 " pdb=" NH2 ARG A 787 " model vdw 2.246 3.120 ... (remaining 99679 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.100 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 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 : 0.008 0.441 12894 Z= 0.418 Angle : 0.885 15.402 17469 Z= 0.513 Chirality : 0.072 1.917 1981 Planarity : 0.005 0.095 2202 Dihedral : 16.948 137.612 4687 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.74 % Favored : 95.20 % Rotamer: Outliers : 4.42 % Allowed : 18.76 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: -3.00 (0.18), residues: 1604 helix: -1.45 (0.16), residues: 753 sheet: -1.62 (0.31), residues: 263 loop : -2.71 (0.21), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.009 0.001 HIS A 145 PHE 0.023 0.002 PHE C 50 TYR 0.016 0.002 TYR C 33 ARG 0.006 0.001 ARG A1183 Details of bonding type rmsd hydrogen bonds : bond 0.14431 ( 690) hydrogen bonds : angle 6.34392 ( 1983) SS BOND : bond 0.19732 ( 5) SS BOND : angle 6.52894 ( 10) covalent geometry : bond 0.00693 (12889) covalent geometry : angle 0.87140 (17459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 130 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7400 (tp) REVERT: A 258 LEU cc_start: 0.6295 (mt) cc_final: 0.5911 (tt) REVERT: A 332 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 440 MET cc_start: 0.2756 (tpt) cc_final: 0.2356 (mtt) REVERT: A 514 MET cc_start: 0.3342 (mtm) cc_final: 0.2660 (ttm) REVERT: A 616 MET cc_start: 0.2662 (mmp) cc_final: 0.0905 (mtp) REVERT: A 703 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5828 (mp) REVERT: A 824 GLN cc_start: 0.5937 (OUTLIER) cc_final: 0.5374 (tt0) REVERT: A 875 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6808 (tm-30) REVERT: A 1027 MET cc_start: 0.1858 (tpp) cc_final: 0.1400 (ttp) REVERT: B 18 GLN cc_start: 0.6907 (mm110) cc_final: 0.4806 (pt0) REVERT: B 146 TYR cc_start: 0.4866 (t80) cc_final: 0.4641 (t80) outliers start: 60 outliers final: 39 residues processed: 188 average time/residue: 0.2355 time to fit residues: 65.3875 Evaluate side-chains 145 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 143 GLN A 145 HIS A 158 GLN A 387 ASN A 398 HIS A 438 GLN A 537 GLN A 725 GLN A 750 GLN A 820 ASN A 946 GLN A 966 HIS A1054 GLN A1105 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1232 HIS ** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 167 ASN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 216 ASN C 5 GLN C 102 GLN C 105 ASN C 164 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.231441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.190092 restraints weight = 16843.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.185775 restraints weight = 34707.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.182088 restraints weight = 30044.129| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12894 Z= 0.167 Angle : 0.608 9.020 17469 Z= 0.318 Chirality : 0.043 0.329 1981 Planarity : 0.004 0.044 2202 Dihedral : 10.868 132.525 1865 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.15 % Allowed : 20.01 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -1.43 (0.20), residues: 1604 helix: -0.01 (0.18), residues: 780 sheet: -0.97 (0.32), residues: 269 loop : -2.19 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 232 HIS 0.008 0.001 HIS A 145 PHE 0.021 0.002 PHE C 50 TYR 0.016 0.002 TYR C 33 ARG 0.004 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.05823 ( 690) hydrogen bonds : angle 4.82417 ( 1983) SS BOND : bond 0.00711 ( 5) SS BOND : angle 1.14547 ( 10) covalent geometry : bond 0.00372 (12889) covalent geometry : angle 0.60753 (17459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 100 time to evaluate : 1.755 Fit side-chains REVERT: A 144 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7783 (tp) REVERT: A 258 LEU cc_start: 0.6499 (mt) cc_final: 0.6153 (tt) REVERT: A 332 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8200 (mp) REVERT: A 450 MET cc_start: 0.4407 (ttp) cc_final: 0.4013 (mtp) REVERT: A 628 MET cc_start: 0.1420 (ptt) cc_final: -0.0518 (pmm) REVERT: B 18 GLN cc_start: 0.6589 (mm110) cc_final: 0.4964 (pt0) REVERT: B 99 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7916 (pp) REVERT: B 146 TYR cc_start: 0.4623 (t80) cc_final: 0.4347 (t80) outliers start: 70 outliers final: 43 residues processed: 159 average time/residue: 0.2532 time to fit residues: 62.3929 Evaluate side-chains 143 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 HIS A 799 GLN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.231660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.191682 restraints weight = 17051.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.187833 restraints weight = 33989.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.181452 restraints weight = 25284.573| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12894 Z= 0.144 Angle : 0.566 7.834 17469 Z= 0.296 Chirality : 0.042 0.356 1981 Planarity : 0.004 0.044 2202 Dihedral : 10.438 131.882 1836 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.00 % Allowed : 22.00 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1604 helix: 0.63 (0.18), residues: 780 sheet: -0.75 (0.33), residues: 267 loop : -1.93 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 232 HIS 0.004 0.001 HIS A 145 PHE 0.034 0.002 PHE A 983 TYR 0.014 0.002 TYR C 33 ARG 0.004 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.05419 ( 690) hydrogen bonds : angle 4.54944 ( 1983) SS BOND : bond 0.00883 ( 5) SS BOND : angle 2.12328 ( 10) covalent geometry : bond 0.00314 (12889) covalent geometry : angle 0.56340 (17459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 97 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: A 144 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7822 (tp) REVERT: A 332 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8326 (mp) REVERT: A 450 MET cc_start: 0.4702 (ttp) cc_final: 0.4096 (mtp) REVERT: A 606 ILE cc_start: -0.0231 (OUTLIER) cc_final: -0.0704 (pt) REVERT: A 628 MET cc_start: 0.1399 (ptt) cc_final: -0.0412 (pmm) REVERT: A 770 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5406 (t80) REVERT: A 875 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7314 (tt0) REVERT: A 917 GLU cc_start: 0.3996 (OUTLIER) cc_final: 0.3775 (tt0) REVERT: B 18 GLN cc_start: 0.6586 (mm110) cc_final: 0.4859 (pt0) REVERT: B 99 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7827 (pp) REVERT: B 146 TYR cc_start: 0.4687 (t80) cc_final: 0.4263 (t80) outliers start: 68 outliers final: 43 residues processed: 153 average time/residue: 0.2248 time to fit residues: 52.4881 Evaluate side-chains 144 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 95 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 200 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 68 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 63 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.230564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.190683 restraints weight = 16838.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.185606 restraints weight = 34753.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.183272 restraints weight = 26025.849| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12894 Z= 0.160 Angle : 0.573 8.006 17469 Z= 0.300 Chirality : 0.043 0.365 1981 Planarity : 0.004 0.045 2202 Dihedral : 10.278 134.203 1833 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.81 % Allowed : 22.00 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1604 helix: 0.82 (0.18), residues: 775 sheet: -0.69 (0.33), residues: 271 loop : -1.73 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 232 HIS 0.005 0.001 HIS A 145 PHE 0.027 0.002 PHE A 983 TYR 0.014 0.002 TYR C 33 ARG 0.003 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.05540 ( 690) hydrogen bonds : angle 4.49636 ( 1983) SS BOND : bond 0.00699 ( 5) SS BOND : angle 1.42629 ( 10) covalent geometry : bond 0.00358 (12889) covalent geometry : angle 0.57213 (17459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 101 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8287 (mp) REVERT: A 450 MET cc_start: 0.4604 (ttp) cc_final: 0.4088 (mtp) REVERT: A 606 ILE cc_start: -0.0040 (OUTLIER) cc_final: -0.0493 (pt) REVERT: A 628 MET cc_start: 0.1627 (ptt) cc_final: -0.0278 (pmm) REVERT: A 770 PHE cc_start: 0.5759 (OUTLIER) cc_final: 0.5499 (t80) REVERT: A 803 TRP cc_start: 0.6230 (t60) cc_final: 0.5949 (t60) REVERT: A 875 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7271 (tt0) REVERT: A 884 LEU cc_start: 0.4436 (OUTLIER) cc_final: 0.4186 (mp) REVERT: B 18 GLN cc_start: 0.6683 (mm110) cc_final: 0.4962 (pt0) REVERT: B 99 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7996 (pp) REVERT: B 146 TYR cc_start: 0.4509 (t80) cc_final: 0.4093 (t80) outliers start: 79 outliers final: 58 residues processed: 167 average time/residue: 0.2247 time to fit residues: 58.0780 Evaluate side-chains 153 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 90 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 200 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 147 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 104 optimal weight: 0.2980 chunk 103 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN A1153 ASN ** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.228486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.187576 restraints weight = 16727.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.183166 restraints weight = 33754.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.179655 restraints weight = 32116.396| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12894 Z= 0.189 Angle : 0.619 8.175 17469 Z= 0.324 Chirality : 0.044 0.383 1981 Planarity : 0.004 0.047 2202 Dihedral : 10.513 136.378 1833 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.11 % Allowed : 23.18 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1604 helix: 0.67 (0.18), residues: 783 sheet: -0.64 (0.33), residues: 275 loop : -1.67 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 232 HIS 0.006 0.001 HIS A 145 PHE 0.030 0.002 PHE A 983 TYR 0.023 0.002 TYR A 510 ARG 0.006 0.001 ARG A1188 Details of bonding type rmsd hydrogen bonds : bond 0.06017 ( 690) hydrogen bonds : angle 4.62211 ( 1983) SS BOND : bond 0.00845 ( 5) SS BOND : angle 1.50777 ( 10) covalent geometry : bond 0.00432 (12889) covalent geometry : angle 0.61776 (17459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 96 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8335 (mp) REVERT: A 450 MET cc_start: 0.4676 (ttp) cc_final: 0.4070 (mtp) REVERT: A 475 GLN cc_start: 0.2635 (OUTLIER) cc_final: 0.2055 (tt0) REVERT: A 606 ILE cc_start: 0.0120 (OUTLIER) cc_final: -0.0350 (pt) REVERT: A 628 MET cc_start: 0.1723 (ptt) cc_final: -0.0194 (pmm) REVERT: A 770 PHE cc_start: 0.5963 (OUTLIER) cc_final: 0.5615 (t80) REVERT: A 777 PHE cc_start: 0.6772 (m-80) cc_final: 0.6437 (m-80) REVERT: A 803 TRP cc_start: 0.6203 (t60) cc_final: 0.5962 (t60) REVERT: A 875 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7226 (tt0) REVERT: A 884 LEU cc_start: 0.4459 (OUTLIER) cc_final: 0.4211 (mp) REVERT: B 18 GLN cc_start: 0.6922 (mm110) cc_final: 0.5174 (pt0) REVERT: B 99 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8060 (pp) REVERT: B 146 TYR cc_start: 0.4688 (t80) cc_final: 0.4090 (t80) outliers start: 83 outliers final: 66 residues processed: 165 average time/residue: 0.2679 time to fit residues: 70.7493 Evaluate side-chains 163 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 91 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 200 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1238 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.230046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.191360 restraints weight = 16902.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.184842 restraints weight = 33939.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.181039 restraints weight = 30269.916| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12894 Z= 0.143 Angle : 0.557 7.997 17469 Z= 0.290 Chirality : 0.041 0.291 1981 Planarity : 0.004 0.047 2202 Dihedral : 10.054 134.624 1832 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.96 % Allowed : 23.99 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1604 helix: 1.00 (0.18), residues: 783 sheet: -0.71 (0.33), residues: 289 loop : -1.51 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 232 HIS 0.004 0.001 HIS A 145 PHE 0.025 0.002 PHE A 983 TYR 0.013 0.002 TYR C 33 ARG 0.002 0.000 ARG B 59 Details of bonding type rmsd hydrogen bonds : bond 0.05374 ( 690) hydrogen bonds : angle 4.39934 ( 1983) SS BOND : bond 0.00597 ( 5) SS BOND : angle 1.22005 ( 10) covalent geometry : bond 0.00315 (12889) covalent geometry : angle 0.55653 (17459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 96 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 393 GLU cc_start: 0.4634 (tp30) cc_final: 0.3537 (tp30) REVERT: A 450 MET cc_start: 0.4697 (ttp) cc_final: 0.4042 (mtp) REVERT: A 606 ILE cc_start: 0.0134 (OUTLIER) cc_final: -0.0328 (pt) REVERT: A 628 MET cc_start: 0.1639 (ptt) cc_final: -0.0233 (pmm) REVERT: A 770 PHE cc_start: 0.5831 (OUTLIER) cc_final: 0.5481 (t80) REVERT: A 875 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7214 (tt0) REVERT: A 884 LEU cc_start: 0.4289 (OUTLIER) cc_final: 0.4060 (mp) REVERT: A 1010 MET cc_start: 0.4465 (OUTLIER) cc_final: 0.4176 (ttm) REVERT: B 18 GLN cc_start: 0.6743 (mm110) cc_final: 0.4951 (pt0) REVERT: B 99 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8106 (pp) outliers start: 81 outliers final: 55 residues processed: 163 average time/residue: 0.2029 time to fit residues: 52.7454 Evaluate side-chains 152 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 91 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 200 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 156 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 34 optimal weight: 0.0370 chunk 158 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.232655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.194482 restraints weight = 16794.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.190481 restraints weight = 31899.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.186853 restraints weight = 23724.125| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12894 Z= 0.115 Angle : 0.529 12.531 17469 Z= 0.274 Chirality : 0.040 0.259 1981 Planarity : 0.004 0.046 2202 Dihedral : 9.555 132.429 1830 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.27 % Allowed : 25.61 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1604 helix: 1.36 (0.19), residues: 785 sheet: -0.62 (0.33), residues: 294 loop : -1.40 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 803 HIS 0.015 0.001 HIS A1112 PHE 0.023 0.001 PHE C 106 TYR 0.024 0.001 TYR A 510 ARG 0.002 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 690) hydrogen bonds : angle 4.17816 ( 1983) SS BOND : bond 0.00441 ( 5) SS BOND : angle 1.02560 ( 10) covalent geometry : bond 0.00237 (12889) covalent geometry : angle 0.52896 (17459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 100 time to evaluate : 1.330 Fit side-chains REVERT: A 393 GLU cc_start: 0.4664 (tp30) cc_final: 0.3581 (tp30) REVERT: A 450 MET cc_start: 0.4696 (ttp) cc_final: 0.4031 (mtp) REVERT: A 490 TYR cc_start: 0.3258 (OUTLIER) cc_final: 0.3014 (m-10) REVERT: A 628 MET cc_start: 0.1891 (ptt) cc_final: 0.0496 (pmm) REVERT: A 770 PHE cc_start: 0.5783 (OUTLIER) cc_final: 0.5292 (t80) REVERT: A 814 LEU cc_start: 0.6584 (mt) cc_final: 0.6156 (tt) REVERT: A 875 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7153 (tt0) REVERT: A 884 LEU cc_start: 0.4191 (OUTLIER) cc_final: 0.3953 (mp) REVERT: A 1027 MET cc_start: 0.4438 (ttp) cc_final: 0.3477 (tpp) REVERT: B 18 GLN cc_start: 0.6551 (mm110) cc_final: 0.4745 (pt0) REVERT: B 99 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8123 (pp) outliers start: 58 outliers final: 39 residues processed: 146 average time/residue: 0.3159 time to fit residues: 71.8883 Evaluate side-chains 140 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 126 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 40 optimal weight: 0.0060 chunk 52 optimal weight: 8.9990 chunk 142 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.232460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.192695 restraints weight = 16902.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.187225 restraints weight = 30219.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.184274 restraints weight = 28864.279| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12894 Z= 0.114 Angle : 0.514 7.799 17469 Z= 0.268 Chirality : 0.040 0.256 1981 Planarity : 0.004 0.069 2202 Dihedral : 9.150 132.920 1820 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.97 % Allowed : 25.90 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1604 helix: 1.57 (0.19), residues: 779 sheet: -0.52 (0.34), residues: 286 loop : -1.35 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 803 HIS 0.012 0.001 HIS A1112 PHE 0.020 0.001 PHE A 983 TYR 0.018 0.001 TYR A 510 ARG 0.002 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 690) hydrogen bonds : angle 4.09568 ( 1983) SS BOND : bond 0.00433 ( 5) SS BOND : angle 1.00126 ( 10) covalent geometry : bond 0.00239 (12889) covalent geometry : angle 0.51404 (17459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 99 time to evaluate : 1.423 Fit side-chains REVERT: A 244 LEU cc_start: 0.5632 (OUTLIER) cc_final: 0.5145 (tt) REVERT: A 393 GLU cc_start: 0.4649 (tp30) cc_final: 0.3172 (tp30) REVERT: A 450 MET cc_start: 0.4738 (ttp) cc_final: 0.4064 (mtp) REVERT: A 490 TYR cc_start: 0.3226 (OUTLIER) cc_final: 0.3007 (m-10) REVERT: A 628 MET cc_start: 0.1972 (ptt) cc_final: 0.0313 (pmm) REVERT: A 770 PHE cc_start: 0.5735 (OUTLIER) cc_final: 0.5366 (t80) REVERT: A 814 LEU cc_start: 0.6579 (mt) cc_final: 0.6175 (tt) REVERT: A 875 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7202 (tt0) REVERT: A 1010 MET cc_start: 0.4569 (OUTLIER) cc_final: 0.4294 (ttm) REVERT: A 1027 MET cc_start: 0.4413 (ttp) cc_final: 0.3523 (tpp) REVERT: B 18 GLN cc_start: 0.6614 (mm110) cc_final: 0.4782 (pt0) REVERT: B 99 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7963 (pp) outliers start: 54 outliers final: 44 residues processed: 142 average time/residue: 0.2158 time to fit residues: 47.7048 Evaluate side-chains 144 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 95 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 117 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 116 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.229982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.189820 restraints weight = 16750.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.183791 restraints weight = 32667.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.178162 restraints weight = 31494.897| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12894 Z= 0.152 Angle : 0.564 8.187 17469 Z= 0.295 Chirality : 0.042 0.281 1981 Planarity : 0.004 0.062 2202 Dihedral : 9.555 136.232 1820 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.27 % Allowed : 25.24 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1604 helix: 1.37 (0.19), residues: 779 sheet: -0.47 (0.34), residues: 281 loop : -1.41 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 803 HIS 0.011 0.001 HIS A1112 PHE 0.020 0.002 PHE C 50 TYR 0.013 0.002 TYR C 33 ARG 0.003 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.05290 ( 690) hydrogen bonds : angle 4.28512 ( 1983) SS BOND : bond 0.00556 ( 5) SS BOND : angle 1.49660 ( 10) covalent geometry : bond 0.00339 (12889) covalent geometry : angle 0.56342 (17459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 91 time to evaluate : 1.460 Fit side-chains REVERT: A 244 LEU cc_start: 0.5691 (OUTLIER) cc_final: 0.5027 (tt) REVERT: A 393 GLU cc_start: 0.4745 (tp30) cc_final: 0.3311 (tp30) REVERT: A 450 MET cc_start: 0.4813 (ttp) cc_final: 0.4086 (mtp) REVERT: A 490 TYR cc_start: 0.3249 (OUTLIER) cc_final: 0.3029 (m-10) REVERT: A 514 MET cc_start: 0.2011 (mpp) cc_final: 0.0026 (ptp) REVERT: A 628 MET cc_start: 0.1960 (ptt) cc_final: 0.0321 (pmm) REVERT: A 770 PHE cc_start: 0.5881 (OUTLIER) cc_final: 0.5485 (t80) REVERT: A 875 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7216 (tt0) REVERT: A 1010 MET cc_start: 0.4459 (OUTLIER) cc_final: 0.4203 (ttm) REVERT: A 1027 MET cc_start: 0.4483 (ttp) cc_final: 0.3652 (tpp) REVERT: B 18 GLN cc_start: 0.6847 (mm110) cc_final: 0.5020 (pt0) REVERT: B 99 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8116 (pp) outliers start: 58 outliers final: 46 residues processed: 137 average time/residue: 0.2193 time to fit residues: 46.8334 Evaluate side-chains 140 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 89 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 21 optimal weight: 0.0010 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.231248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.191351 restraints weight = 16575.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.185490 restraints weight = 31815.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.183044 restraints weight = 29790.919| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12894 Z= 0.124 Angle : 0.532 8.766 17469 Z= 0.276 Chirality : 0.041 0.247 1981 Planarity : 0.004 0.057 2202 Dihedral : 9.302 134.443 1820 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.97 % Allowed : 25.68 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1604 helix: 1.47 (0.19), residues: 785 sheet: -0.42 (0.34), residues: 279 loop : -1.43 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 803 HIS 0.011 0.001 HIS A1112 PHE 0.020 0.001 PHE A 983 TYR 0.013 0.001 TYR C 33 ARG 0.003 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 690) hydrogen bonds : angle 4.17499 ( 1983) SS BOND : bond 0.00505 ( 5) SS BOND : angle 1.72192 ( 10) covalent geometry : bond 0.00266 (12889) covalent geometry : angle 0.53017 (17459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 95 time to evaluate : 1.403 Fit side-chains REVERT: A 244 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.4994 (tt) REVERT: A 393 GLU cc_start: 0.4697 (tp30) cc_final: 0.3247 (tp30) REVERT: A 440 MET cc_start: 0.3029 (mtt) cc_final: 0.2768 (mtp) REVERT: A 450 MET cc_start: 0.4798 (ttp) cc_final: 0.4069 (mtp) REVERT: A 514 MET cc_start: 0.1954 (mpp) cc_final: 0.0267 (ptp) REVERT: A 628 MET cc_start: 0.1989 (ptt) cc_final: 0.0365 (pmm) REVERT: A 770 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5440 (t80) REVERT: A 777 PHE cc_start: 0.6760 (m-80) cc_final: 0.6440 (m-80) REVERT: A 875 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7176 (tt0) REVERT: A 1010 MET cc_start: 0.4590 (OUTLIER) cc_final: 0.4351 (ttm) REVERT: A 1027 MET cc_start: 0.4561 (ttp) cc_final: 0.3817 (tpp) REVERT: B 18 GLN cc_start: 0.6759 (mm110) cc_final: 0.4869 (pt0) REVERT: B 99 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8025 (pp) outliers start: 54 outliers final: 45 residues processed: 137 average time/residue: 0.2345 time to fit residues: 49.5008 Evaluate side-chains 141 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.228486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.186451 restraints weight = 16818.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.182848 restraints weight = 34060.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.178906 restraints weight = 31985.094| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12894 Z= 0.185 Angle : 0.603 9.701 17469 Z= 0.316 Chirality : 0.044 0.323 1981 Planarity : 0.004 0.058 2202 Dihedral : 9.854 137.671 1820 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.49 % Allowed : 25.09 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1604 helix: 1.18 (0.18), residues: 777 sheet: -0.55 (0.34), residues: 281 loop : -1.47 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 803 HIS 0.010 0.001 HIS A1112 PHE 0.021 0.002 PHE C 50 TYR 0.014 0.002 TYR B 41 ARG 0.004 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.05750 ( 690) hydrogen bonds : angle 4.44370 ( 1983) SS BOND : bond 0.00659 ( 5) SS BOND : angle 1.72823 ( 10) covalent geometry : bond 0.00423 (12889) covalent geometry : angle 0.60182 (17459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5775.28 seconds wall clock time: 106 minutes 12.58 seconds (6372.58 seconds total)