Starting phenix.real_space_refine on Sat Jun 21 18:45:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e82_27942/06_2025/8e82_27942.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e82_27942/06_2025/8e82_27942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e82_27942/06_2025/8e82_27942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e82_27942/06_2025/8e82_27942.map" model { file = "/net/cci-nas-00/data/ceres_data/8e82_27942/06_2025/8e82_27942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e82_27942/06_2025/8e82_27942.cif" } resolution = 3.03 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= 0.005 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 68 5.49 5 Mg 1 5.21 5 S 88 5.16 5 C 15399 2.51 5 N 4423 2.21 5 O 4919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.49s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24900 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 221} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8485 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1033} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 9916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9916 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1208} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 75} Chain: "Z" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "P" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 666 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "Q" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12487 SG CYS D 60 67.030 110.672 99.732 1.00137.72 S ATOM 12505 SG CYS D 62 67.894 112.719 97.049 1.00143.00 S ATOM 12614 SG CYS D 75 63.872 112.760 97.458 1.00144.11 S ATOM 12640 SG CYS D 78 64.803 110.397 96.450 1.00134.53 S ATOM 19055 SG CYS D 891 22.575 63.767 121.780 1.00 75.54 S ATOM 19622 SG CYS D 968 26.077 64.208 119.367 1.00 63.09 S ATOM 19664 SG CYS D 975 26.094 63.408 122.666 1.00 48.32 S ATOM 19682 SG CYS D 978 25.314 61.326 121.877 1.00 65.28 S Time building chain proxies: 14.92, per 1000 atoms: 0.60 Number of scatterers: 24900 At special positions: 0 Unit cell: (130.196, 125.892, 194.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 88 16.00 P 68 15.00 Mg 1 11.99 O 4919 8.00 N 4423 7.00 C 15399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.11 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " Number of angles added : 12 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5574 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 44 sheets defined 39.0% alpha, 14.6% beta 30 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 9.29 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.546A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 203 through 222 Processing helix chain 'B' and resid 29 through 44 removed outlier: 4.130A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.520A pdb=" N GLU B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.800A pdb=" N TRP C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.576A pdb=" N GLU C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 270 through 282 removed outlier: 3.808A pdb=" N LYS C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.104A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 349 Processing helix chain 'C' and resid 380 through 404 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.713A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.754A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 539 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 3.846A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.650A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.711A pdb=" N ALA C1075 " --> pdb=" O MET C1071 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C1076 " --> pdb=" O GLU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.857A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1108 Processing helix chain 'C' and resid 1118 through 1132 removed outlier: 3.503A pdb=" N CYS C1132 " --> pdb=" O LEU C1128 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 147 through 187 removed outlier: 3.591A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 227 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.635A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 4.011A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.860A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.574A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 361 removed outlier: 3.559A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 407 removed outlier: 3.566A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.130A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 491 removed outlier: 3.749A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 557 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.695A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.540A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.900A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.589A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.560A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.908A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.315A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1196 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1254 removed outlier: 3.542A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.752A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.807A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 removed outlier: 4.018A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 72 removed outlier: 3.569A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'Z' and resid 34 through 45 removed outlier: 3.873A pdb=" N SER Z 44 " --> pdb=" O ALA Z 40 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS Z 45 " --> pdb=" O GLU Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 73 Processing helix chain 'Z' and resid 116 through 125 Processing helix chain 'Z' and resid 143 through 152 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 3.507A pdb=" N LEU A 14 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 15 removed outlier: 3.507A pdb=" N LEU A 14 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 189 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 100 removed outlier: 7.176A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA6, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 15 removed outlier: 6.626A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.533A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.452A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 627 " --> pdb=" O VAL C 972 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.919A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB7, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.240A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 184 through 186 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'C' and resid 519 through 520 Processing sheet with id=AC3, first strand: chain 'C' and resid 541 through 542 removed outlier: 4.053A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 562 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.561A pdb=" N VAL C 660 " --> pdb=" O ARG C 668 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 885 through 886 removed outlier: 8.733A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 885 through 886 Processing sheet with id=AC8, first strand: chain 'C' and resid 748 through 756 removed outlier: 3.883A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 759 through 760 removed outlier: 4.027A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.703A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 807 through 808 removed outlier: 3.853A pdb=" N ARG C 833 " --> pdb=" O THR C 807 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD4, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.335A pdb=" N ALA D 521 " --> pdb=" O PRO D 444 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD6, first strand: chain 'C' and resid 1136 through 1137 Processing sheet with id=AD7, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.591A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.514A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 327 through 330 Processing sheet with id=AE1, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.967A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1051 through 1052 Processing sheet with id=AE4, first strand: chain 'D' and resid 1064 through 1066 Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.407A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1273 through 1274 Processing sheet with id=AE7, first strand: chain 'Z' and resid 81 through 83 removed outlier: 3.975A pdb=" N GLN Z 81 " --> pdb=" O ARG Z 112 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET Z 113 " --> pdb=" O ASP Z 48 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL Z 51 " --> pdb=" O PHE Z 132 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE Z 132 " --> pdb=" O VAL Z 51 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS Z 53 " --> pdb=" O THR Z 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 89 through 93 991 hydrogen bonds defined for protein. 2736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 11.42 Time building geometry restraints manager: 8.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6132 1.33 - 1.45: 4899 1.45 - 1.57: 14149 1.57 - 1.70: 132 1.70 - 1.82: 155 Bond restraints: 25467 Sorted by residual: bond pdb=" N GLY D -1 " pdb=" CA GLY D -1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.01e+00 bond pdb=" N ILE B 23 " pdb=" CA ILE B 23 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 5.96e+00 bond pdb=" N GLU B 24 " pdb=" CA GLU B 24 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.41e-02 5.03e+03 5.59e+00 bond pdb=" CA PRO D 739 " pdb=" C PRO D 739 " ideal model delta sigma weight residual 1.514 1.526 -0.012 5.50e-03 3.31e+04 4.38e+00 bond pdb=" N LEU B 26 " pdb=" CA LEU B 26 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.23e-02 6.61e+03 4.35e+00 ... (remaining 25462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 34161 1.96 - 3.92: 568 3.92 - 5.88: 66 5.88 - 7.85: 6 7.85 - 9.81: 2 Bond angle restraints: 34803 Sorted by residual: angle pdb=" C3' DA P 111 " pdb=" O3' DA P 111 " pdb=" P DG P 112 " ideal model delta sigma weight residual 120.20 110.39 9.81 1.50e+00 4.44e-01 4.28e+01 angle pdb=" C3' DG P 112 " pdb=" O3' DG P 112 " pdb=" P DG P 113 " ideal model delta sigma weight residual 120.20 111.37 8.83 1.50e+00 4.44e-01 3.47e+01 angle pdb=" N PRO B 25 " pdb=" CA PRO B 25 " pdb=" CB PRO B 25 " ideal model delta sigma weight residual 103.25 98.56 4.69 1.05e+00 9.07e-01 1.99e+01 angle pdb=" CA ILE B 23 " pdb=" C ILE B 23 " pdb=" O ILE B 23 " ideal model delta sigma weight residual 120.78 115.87 4.91 1.25e+00 6.40e-01 1.54e+01 angle pdb=" N ARG D1041 " pdb=" CA ARG D1041 " pdb=" C ARG D1041 " ideal model delta sigma weight residual 112.13 106.77 5.36 1.37e+00 5.33e-01 1.53e+01 ... (remaining 34798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 14914 33.44 - 66.87: 481 66.87 - 100.31: 9 100.31 - 133.75: 1 133.75 - 167.19: 1 Dihedral angle restraints: 15406 sinusoidal: 6734 harmonic: 8672 Sorted by residual: dihedral pdb=" O4' C R 11 " pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sinusoidal sigma weight residual 200.00 32.81 167.19 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" CA SER B 44 " pdb=" C SER B 44 " pdb=" N SER B 45 " pdb=" CA SER B 45 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA PRO C 975 " pdb=" C PRO C 975 " pdb=" N VAL C 976 " pdb=" CA VAL C 976 " ideal model delta harmonic sigma weight residual 180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 15403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3949 0.126 - 0.252: 22 0.252 - 0.378: 0 0.378 - 0.505: 4 0.505 - 0.631: 1 Chirality restraints: 3976 Sorted by residual: chirality pdb=" P DG P 110 " pdb=" OP1 DG P 110 " pdb=" OP2 DG P 110 " pdb=" O5' DG P 110 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 9.94e+00 chirality pdb=" P DA P 111 " pdb=" OP1 DA P 111 " pdb=" OP2 DA P 111 " pdb=" O5' DA P 111 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" P DG P 114 " pdb=" OP1 DG P 114 " pdb=" OP2 DG P 114 " pdb=" O5' DG P 114 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.44e+00 ... (remaining 3973 not shown) Planarity restraints: 4342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D1039 " -0.065 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO D1040 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO D1040 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO D1040 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 22 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C VAL B 22 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL B 22 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 23 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 413 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.99e+00 pdb=" N PRO C 414 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " -0.031 5.00e-02 4.00e+02 ... (remaining 4339 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 95 2.42 - 3.04: 16391 3.04 - 3.66: 37314 3.66 - 4.28: 56886 4.28 - 4.90: 95423 Nonbonded interactions: 206109 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 1.803 2.170 nonbonded pdb=" O3' A R 20 " pdb="MG MG D2002 " model vdw 1.923 2.170 nonbonded pdb=" OD1 ASN Z 65 " pdb=" OG1 THR Z 126 " model vdw 1.944 3.040 nonbonded pdb=" OG1 THR D 970 " pdb=" O GLY D 973 " model vdw 1.967 3.040 nonbonded pdb=" OE1 GLN C 150 " pdb=" OG1 THR C 413 " model vdw 1.989 3.040 ... (remaining 206104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and resid 1 through 226) } 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 individual isotropic 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 69.870 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 25475 Z= 0.173 Angle : 0.771 47.589 34815 Z= 0.384 Chirality : 0.045 0.631 3976 Planarity : 0.004 0.099 4342 Dihedral : 14.497 167.185 9832 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.17 % Favored : 93.33 % Rotamer: Outliers : 3.94 % Allowed : 7.67 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.16), residues: 3013 helix: 0.65 (0.16), residues: 1096 sheet: -1.78 (0.26), residues: 367 loop : -1.41 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 938 HIS 0.005 0.001 HIS D 689 PHE 0.011 0.001 PHE C 439 TYR 0.010 0.001 TYR D 586 ARG 0.003 0.000 ARG D 427 Details of bonding type rmsd hydrogen bonds : bond 0.16587 ( 1051) hydrogen bonds : angle 6.84543 ( 2896) metal coordination : bond 0.08255 ( 8) metal coordination : angle 22.20010 ( 12) covalent geometry : bond 0.00327 (25467) covalent geometry : angle 0.65120 (34803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 540 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8836 (mt) cc_final: 0.8248 (mt) REVERT: A 177 LYS cc_start: 0.8607 (ptpp) cc_final: 0.8290 (pttt) REVERT: A 184 GLU cc_start: 0.6419 (mm-30) cc_final: 0.6143 (pp20) REVERT: B 191 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8690 (tttt) REVERT: C 58 THR cc_start: 0.8592 (m) cc_final: 0.8299 (p) REVERT: C 127 MET cc_start: 0.7177 (mtm) cc_final: 0.6391 (mmp) REVERT: C 159 MET cc_start: 0.8247 (mmm) cc_final: 0.7930 (mmm) REVERT: C 274 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6904 (mp) REVERT: C 415 GLN cc_start: 0.6941 (tt0) cc_final: 0.6266 (tm-30) REVERT: C 421 ARG cc_start: 0.7101 (mmm-85) cc_final: 0.6520 (ttt180) REVERT: C 789 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.6789 (mt) REVERT: D 11 ARG cc_start: 0.8139 (ttp-170) cc_final: 0.7868 (ttp-170) REVERT: D 56 ARG cc_start: 0.7817 (mmt180) cc_final: 0.7455 (mmm160) REVERT: D 120 LEU cc_start: 0.8757 (mt) cc_final: 0.8550 (mp) REVERT: D 123 LYS cc_start: 0.7025 (mmtt) cc_final: 0.6739 (mmtm) REVERT: D 124 ASP cc_start: 0.7651 (m-30) cc_final: 0.7228 (m-30) REVERT: D 205 MET cc_start: 0.4230 (OUTLIER) cc_final: 0.3552 (ptt) REVERT: D 353 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6941 (ttm170) REVERT: D 478 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.7183 (mtp85) REVERT: E 100 HIS cc_start: 0.7911 (t-90) cc_final: 0.7643 (t70) REVERT: Z 51 VAL cc_start: 0.8195 (t) cc_final: 0.7925 (m) REVERT: Z 113 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7130 (ptp) REVERT: Z 117 ASP cc_start: 0.7354 (m-30) cc_final: 0.6572 (t0) REVERT: Z 146 ASP cc_start: 0.7423 (m-30) cc_final: 0.6991 (m-30) REVERT: Z 149 LYS cc_start: 0.8706 (tttp) cc_final: 0.8361 (ttpt) outliers start: 100 outliers final: 32 residues processed: 612 average time/residue: 0.4370 time to fit residues: 393.5210 Evaluate side-chains 316 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 106 HIS Chi-restraints excluded: chain Z residue 67 GLU Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 113 MET Chi-restraints excluded: chain Z residue 116 THR Chi-restraints excluded: chain Z residue 126 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 30.0000 chunk 231 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 239 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 277 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN B 124 HIS C 141 ASN C 718 ASN C 930 GLN C 935 HIS C1055 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS E 65 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.173832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.134794 restraints weight = 35756.899| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.10 r_work: 0.3605 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25475 Z= 0.149 Angle : 0.641 11.828 34815 Z= 0.331 Chirality : 0.044 0.255 3976 Planarity : 0.005 0.104 4342 Dihedral : 14.386 168.775 4146 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.24 % Favored : 94.32 % Rotamer: Outliers : 3.23 % Allowed : 11.92 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.77 (0.16), residues: 3013 helix: 0.79 (0.16), residues: 1116 sheet: -1.29 (0.28), residues: 347 loop : -1.30 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 223 HIS 0.010 0.001 HIS D 748 PHE 0.016 0.002 PHE D 131 TYR 0.021 0.001 TYR Z 78 ARG 0.006 0.001 ARG C 347 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 1051) hydrogen bonds : angle 5.14989 ( 2896) metal coordination : bond 0.00928 ( 8) metal coordination : angle 5.49380 ( 12) covalent geometry : bond 0.00341 (25467) covalent geometry : angle 0.63264 (34803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 321 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8515 (ptpp) cc_final: 0.8152 (pttt) REVERT: A 184 GLU cc_start: 0.6663 (mm-30) cc_final: 0.6156 (pp20) REVERT: B 213 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7414 (tttt) REVERT: C 127 MET cc_start: 0.7511 (mtm) cc_final: 0.6692 (mmp) REVERT: C 159 MET cc_start: 0.8258 (mmm) cc_final: 0.8025 (mmm) REVERT: C 192 ASP cc_start: 0.4232 (t0) cc_final: 0.3999 (t0) REVERT: C 304 LYS cc_start: 0.6454 (tptt) cc_final: 0.6230 (tptt) REVERT: C 415 GLN cc_start: 0.7126 (tt0) cc_final: 0.6343 (tm-30) REVERT: C 421 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.7259 (ttt180) REVERT: C 797 ARG cc_start: 0.7231 (ttm-80) cc_final: 0.6984 (ttp80) REVERT: C 1031 MET cc_start: 0.8940 (mtm) cc_final: 0.8736 (ptp) REVERT: D 56 ARG cc_start: 0.8061 (mmt180) cc_final: 0.7729 (mtp-110) REVERT: D 120 LEU cc_start: 0.8620 (mt) cc_final: 0.8415 (mp) REVERT: D 124 ASP cc_start: 0.7813 (m-30) cc_final: 0.7469 (m-30) REVERT: D 205 MET cc_start: 0.4170 (OUTLIER) cc_final: 0.3636 (mtp) REVERT: D 214 ARG cc_start: 0.7454 (ptm-80) cc_final: 0.6872 (mpp80) REVERT: D 353 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7069 (ttm170) REVERT: D 478 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7443 (mtp85) REVERT: D 1112 MET cc_start: 0.6957 (mmt) cc_final: 0.6600 (mmm) REVERT: E 68 TYR cc_start: 0.8198 (m-80) cc_final: 0.7812 (m-80) REVERT: Z 66 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4959 (mt) REVERT: Z 67 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.5014 (pp20) REVERT: Z 77 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7912 (p0) REVERT: Z 87 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: Z 117 ASP cc_start: 0.7177 (m-30) cc_final: 0.6662 (t0) REVERT: Z 146 ASP cc_start: 0.7500 (m-30) cc_final: 0.7099 (m-30) outliers start: 82 outliers final: 44 residues processed: 381 average time/residue: 0.4062 time to fit residues: 236.4175 Evaluate side-chains 303 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 67 GLU Chi-restraints excluded: chain Z residue 77 ASP Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Chi-restraints excluded: chain Z residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 235 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 47 optimal weight: 0.0030 chunk 73 optimal weight: 2.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN B 5 GLN B 36 ASN C1035 HIS ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS D 959 GLN D1032 GLN E 65 ASN E 100 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.171318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131264 restraints weight = 35247.603| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.04 r_work: 0.3594 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25475 Z= 0.164 Angle : 0.613 11.742 34815 Z= 0.315 Chirality : 0.043 0.203 3976 Planarity : 0.005 0.108 4342 Dihedral : 14.178 167.512 4116 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.68 % Favored : 93.99 % Rotamer: Outliers : 3.78 % Allowed : 12.63 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: -0.69 (0.16), residues: 3013 helix: 0.88 (0.16), residues: 1122 sheet: -1.22 (0.27), residues: 376 loop : -1.28 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 938 HIS 0.007 0.001 HIS C1035 PHE 0.019 0.002 PHE B 219 TYR 0.013 0.001 TYR Z 55 ARG 0.005 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 1051) hydrogen bonds : angle 4.95887 ( 2896) metal coordination : bond 0.00778 ( 8) metal coordination : angle 4.07250 ( 12) covalent geometry : bond 0.00388 (25467) covalent geometry : angle 0.60797 (34803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 280 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8348 (m110) cc_final: 0.7887 (m110) REVERT: A 177 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8133 (pttt) REVERT: C 92 GLU cc_start: 0.7372 (tp30) cc_final: 0.6274 (pt0) REVERT: C 127 MET cc_start: 0.7560 (mtm) cc_final: 0.6647 (mmp) REVERT: C 159 MET cc_start: 0.8183 (mmm) cc_final: 0.7903 (mmm) REVERT: C 192 ASP cc_start: 0.5010 (t0) cc_final: 0.4792 (t0) REVERT: C 203 LYS cc_start: 0.7412 (mtmt) cc_final: 0.7082 (mttm) REVERT: C 421 ARG cc_start: 0.7493 (mmm-85) cc_final: 0.7185 (ttt180) REVERT: C 797 ARG cc_start: 0.7251 (ttm-80) cc_final: 0.6942 (ttp80) REVERT: D 56 ARG cc_start: 0.8119 (mmt180) cc_final: 0.7741 (mtp-110) REVERT: D 124 ASP cc_start: 0.7811 (m-30) cc_final: 0.7535 (m-30) REVERT: D 214 ARG cc_start: 0.7354 (ptm-80) cc_final: 0.6816 (mpp80) REVERT: D 219 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7401 (mt) REVERT: D 327 MET cc_start: 0.7088 (mtm) cc_final: 0.6770 (mtm) REVERT: D 353 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.7066 (ttm170) REVERT: D 478 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7395 (mtp85) REVERT: D 793 TYR cc_start: 0.7118 (m-80) cc_final: 0.6891 (m-80) REVERT: E 68 TYR cc_start: 0.8265 (m-80) cc_final: 0.8030 (m-80) REVERT: Z 66 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.4785 (mt) REVERT: Z 67 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5173 (pp20) REVERT: Z 90 THR cc_start: 0.5662 (OUTLIER) cc_final: 0.5145 (p) REVERT: Z 146 ASP cc_start: 0.7486 (m-30) cc_final: 0.7179 (m-30) outliers start: 96 outliers final: 58 residues processed: 352 average time/residue: 0.4205 time to fit residues: 225.8272 Evaluate side-chains 307 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 244 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1111 ASN Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 67 GLU Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 2 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN C 141 ASN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS E 65 ASN ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.170483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130798 restraints weight = 35657.035| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.07 r_work: 0.3565 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25475 Z= 0.167 Angle : 0.603 12.227 34815 Z= 0.310 Chirality : 0.043 0.173 3976 Planarity : 0.005 0.107 4342 Dihedral : 14.109 166.695 4110 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.61 % Favored : 94.09 % Rotamer: Outliers : 3.90 % Allowed : 13.97 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: -0.60 (0.16), residues: 3013 helix: 0.99 (0.16), residues: 1119 sheet: -1.18 (0.27), residues: 368 loop : -1.26 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 120 HIS 0.006 0.001 HIS D1150 PHE 0.017 0.002 PHE C 906 TYR 0.011 0.001 TYR D 749 ARG 0.005 0.000 ARG Z 102 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1051) hydrogen bonds : angle 4.84941 ( 2896) metal coordination : bond 0.00687 ( 8) metal coordination : angle 3.31723 ( 12) covalent geometry : bond 0.00396 (25467) covalent geometry : angle 0.60039 (34803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 268 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8360 (m110) cc_final: 0.7916 (m110) REVERT: A 151 GLN cc_start: 0.7841 (tp40) cc_final: 0.7587 (tp-100) REVERT: A 177 LYS cc_start: 0.8513 (ptpp) cc_final: 0.8141 (ptmt) REVERT: C 92 GLU cc_start: 0.7507 (tp30) cc_final: 0.6552 (pt0) REVERT: C 127 MET cc_start: 0.7644 (mtm) cc_final: 0.6697 (mmp) REVERT: C 159 MET cc_start: 0.8183 (mmm) cc_final: 0.7866 (mmm) REVERT: C 192 ASP cc_start: 0.5119 (t0) cc_final: 0.4894 (t0) REVERT: C 203 LYS cc_start: 0.7504 (mtmt) cc_final: 0.7175 (mttm) REVERT: C 305 ARG cc_start: 0.6975 (mtp85) cc_final: 0.6364 (mtm180) REVERT: C 421 ARG cc_start: 0.7434 (mmm-85) cc_final: 0.7188 (ttt180) REVERT: C 467 ARG cc_start: 0.7928 (mtt-85) cc_final: 0.7651 (mtt90) REVERT: C 797 ARG cc_start: 0.7258 (ttm-80) cc_final: 0.6951 (ttp80) REVERT: C 1063 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: C 1111 ASN cc_start: 0.6194 (p0) cc_final: 0.5940 (m-40) REVERT: D 56 ARG cc_start: 0.8185 (mmt180) cc_final: 0.7819 (mtp-110) REVERT: D 124 ASP cc_start: 0.7812 (m-30) cc_final: 0.7559 (m-30) REVERT: D 214 ARG cc_start: 0.7256 (ptm-80) cc_final: 0.6734 (mpp80) REVERT: D 247 ARG cc_start: 0.7538 (ttm170) cc_final: 0.6962 (tpp80) REVERT: D 353 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7107 (ttm170) REVERT: D 478 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7460 (mtp85) REVERT: D 677 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8196 (mt) REVERT: D 793 TYR cc_start: 0.7276 (m-80) cc_final: 0.6946 (m-80) REVERT: E 68 TYR cc_start: 0.8261 (m-80) cc_final: 0.8060 (m-80) REVERT: Z 66 LEU cc_start: 0.4777 (OUTLIER) cc_final: 0.4544 (mt) REVERT: Z 90 THR cc_start: 0.5709 (OUTLIER) cc_final: 0.5199 (p) REVERT: Z 113 MET cc_start: 0.6623 (ptp) cc_final: 0.5953 (ptt) REVERT: Z 146 ASP cc_start: 0.7523 (m-30) cc_final: 0.7152 (m-30) outliers start: 99 outliers final: 59 residues processed: 348 average time/residue: 0.3827 time to fit residues: 205.9285 Evaluate side-chains 312 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 248 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain Z residue 51 VAL Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 67 GLU Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Chi-restraints excluded: chain Z residue 119 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 83 optimal weight: 0.0010 chunk 139 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 299 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 288 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.171234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.131909 restraints weight = 35535.474| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.02 r_work: 0.3586 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25475 Z= 0.145 Angle : 0.583 12.564 34815 Z= 0.300 Chirality : 0.042 0.166 3976 Planarity : 0.005 0.104 4342 Dihedral : 14.011 166.062 4105 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.38 % Favored : 94.32 % Rotamer: Outliers : 3.50 % Allowed : 15.19 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: -0.52 (0.16), residues: 3013 helix: 1.06 (0.16), residues: 1126 sheet: -1.17 (0.27), residues: 356 loop : -1.22 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 938 HIS 0.006 0.001 HIS D 748 PHE 0.023 0.001 PHE C 214 TYR 0.014 0.001 TYR Z 58 ARG 0.005 0.000 ARG Z 102 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 1051) hydrogen bonds : angle 4.78520 ( 2896) metal coordination : bond 0.00575 ( 8) metal coordination : angle 2.76281 ( 12) covalent geometry : bond 0.00337 (25467) covalent geometry : angle 0.58119 (34803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 277 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7848 (tp40) cc_final: 0.7628 (tp-100) REVERT: A 177 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8065 (pttt) REVERT: C 92 GLU cc_start: 0.7538 (tp30) cc_final: 0.6587 (pt0) REVERT: C 93 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7823 (tp) REVERT: C 127 MET cc_start: 0.7580 (mtm) cc_final: 0.6639 (mmp) REVERT: C 159 MET cc_start: 0.8176 (mmm) cc_final: 0.7844 (mmm) REVERT: C 203 LYS cc_start: 0.7475 (mtmt) cc_final: 0.7182 (mttm) REVERT: C 421 ARG cc_start: 0.7188 (mmm-85) cc_final: 0.6974 (ttt180) REVERT: C 538 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7471 (mmp80) REVERT: C 797 ARG cc_start: 0.7225 (ttm-80) cc_final: 0.6928 (ttp80) REVERT: C 1063 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: D 56 ARG cc_start: 0.8224 (mmt180) cc_final: 0.7834 (mtp-110) REVERT: D 124 ASP cc_start: 0.7823 (m-30) cc_final: 0.7572 (m-30) REVERT: D 221 ASP cc_start: 0.7428 (m-30) cc_final: 0.7175 (m-30) REVERT: D 247 ARG cc_start: 0.7547 (ttm170) cc_final: 0.7004 (tpp80) REVERT: D 353 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7135 (ttm170) REVERT: D 478 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7470 (mtp85) REVERT: D 793 TYR cc_start: 0.7298 (m-80) cc_final: 0.6970 (m-80) REVERT: Z 45 LYS cc_start: 0.7002 (mtmm) cc_final: 0.6501 (mtmt) REVERT: Z 90 THR cc_start: 0.5802 (OUTLIER) cc_final: 0.5328 (p) REVERT: Z 113 MET cc_start: 0.6547 (ptp) cc_final: 0.5888 (ptt) REVERT: Z 146 ASP cc_start: 0.7489 (m-30) cc_final: 0.7135 (m-30) outliers start: 89 outliers final: 59 residues processed: 347 average time/residue: 0.4218 time to fit residues: 225.2673 Evaluate side-chains 321 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain Z residue 51 VAL Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 102 ARG Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 153 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 227 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 241 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS E 65 ASN ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.169187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129782 restraints weight = 35414.713| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.08 r_work: 0.3560 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25475 Z= 0.181 Angle : 0.617 12.502 34815 Z= 0.316 Chirality : 0.043 0.177 3976 Planarity : 0.005 0.104 4342 Dihedral : 14.003 164.929 4100 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.84 % Favored : 93.86 % Rotamer: Outliers : 3.78 % Allowed : 15.19 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: -0.58 (0.16), residues: 3013 helix: 1.02 (0.16), residues: 1121 sheet: -1.45 (0.26), residues: 385 loop : -1.17 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 120 HIS 0.008 0.001 HIS D 748 PHE 0.018 0.002 PHE C 906 TYR 0.013 0.001 TYR Z 55 ARG 0.007 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 1051) hydrogen bonds : angle 4.81353 ( 2896) metal coordination : bond 0.00656 ( 8) metal coordination : angle 2.73080 ( 12) covalent geometry : bond 0.00430 (25467) covalent geometry : angle 0.61461 (34803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 272 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8366 (m110) cc_final: 0.7945 (m110) REVERT: A 151 GLN cc_start: 0.7763 (tp40) cc_final: 0.7532 (tp-100) REVERT: A 177 LYS cc_start: 0.8467 (ptpp) cc_final: 0.8048 (pttt) REVERT: C 92 GLU cc_start: 0.7658 (tp30) cc_final: 0.6546 (pt0) REVERT: C 93 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7740 (tp) REVERT: C 127 MET cc_start: 0.7570 (mtm) cc_final: 0.6512 (mmp) REVERT: C 159 MET cc_start: 0.8157 (mmm) cc_final: 0.7730 (mmm) REVERT: C 203 LYS cc_start: 0.7492 (mtmt) cc_final: 0.7147 (mttm) REVERT: C 305 ARG cc_start: 0.7148 (mtp85) cc_final: 0.6385 (mtm110) REVERT: C 538 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7460 (mmp80) REVERT: C 797 ARG cc_start: 0.7264 (ttm-80) cc_final: 0.6957 (ttp80) REVERT: C 1063 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7353 (m-80) REVERT: D 56 ARG cc_start: 0.8265 (mmt180) cc_final: 0.7794 (mtp-110) REVERT: D 124 ASP cc_start: 0.7838 (m-30) cc_final: 0.7570 (m-30) REVERT: D 221 ASP cc_start: 0.7488 (m-30) cc_final: 0.7204 (m-30) REVERT: D 247 ARG cc_start: 0.7470 (ttm170) cc_final: 0.6916 (tpp80) REVERT: D 353 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7104 (ttm170) REVERT: D 478 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7481 (mtp85) REVERT: D 677 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8180 (mt) REVERT: E 68 TYR cc_start: 0.8298 (m-80) cc_final: 0.8033 (m-80) REVERT: Z 45 LYS cc_start: 0.6918 (mtmm) cc_final: 0.6542 (mtmt) REVERT: Z 90 THR cc_start: 0.5897 (OUTLIER) cc_final: 0.5486 (p) REVERT: Z 113 MET cc_start: 0.6556 (ptp) cc_final: 0.5890 (ptt) REVERT: Z 146 ASP cc_start: 0.7434 (m-30) cc_final: 0.7096 (m-30) outliers start: 96 outliers final: 67 residues processed: 346 average time/residue: 0.4015 time to fit residues: 212.0932 Evaluate side-chains 323 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 251 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain Z residue 51 VAL Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 102 ARG Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Chi-restraints excluded: chain Z residue 137 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 265 optimal weight: 0.9990 chunk 284 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 111 optimal weight: 0.0170 chunk 163 optimal weight: 7.9990 chunk 207 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.170328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130746 restraints weight = 35463.292| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.05 r_work: 0.3581 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25475 Z= 0.141 Angle : 0.591 13.189 34815 Z= 0.302 Chirality : 0.042 0.181 3976 Planarity : 0.005 0.102 4342 Dihedral : 13.950 164.603 4100 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.71 % Favored : 94.03 % Rotamer: Outliers : 3.42 % Allowed : 16.25 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: -0.45 (0.16), residues: 3013 helix: 1.14 (0.16), residues: 1123 sheet: -1.31 (0.27), residues: 373 loop : -1.12 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 120 HIS 0.012 0.001 HIS D 748 PHE 0.024 0.001 PHE C 214 TYR 0.012 0.001 TYR Z 55 ARG 0.007 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 1051) hydrogen bonds : angle 4.71551 ( 2896) metal coordination : bond 0.00525 ( 8) metal coordination : angle 2.39612 ( 12) covalent geometry : bond 0.00328 (25467) covalent geometry : angle 0.58958 (34803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 264 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8372 (m110) cc_final: 0.7962 (m110) REVERT: A 151 GLN cc_start: 0.7886 (tp40) cc_final: 0.7682 (tp-100) REVERT: A 177 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8034 (pttt) REVERT: C 92 GLU cc_start: 0.7631 (tp30) cc_final: 0.6554 (pt0) REVERT: C 93 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7866 (tp) REVERT: C 127 MET cc_start: 0.7527 (mtm) cc_final: 0.6552 (mmp) REVERT: C 159 MET cc_start: 0.8157 (mmm) cc_final: 0.7762 (mmm) REVERT: C 203 LYS cc_start: 0.7483 (mtmt) cc_final: 0.7167 (mttm) REVERT: C 305 ARG cc_start: 0.6836 (mtp85) cc_final: 0.6131 (mtm180) REVERT: C 538 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7447 (mmp80) REVERT: C 661 MET cc_start: 0.7866 (tpp) cc_final: 0.7629 (tpp) REVERT: C 797 ARG cc_start: 0.7353 (ttm-80) cc_final: 0.7070 (ttp80) REVERT: C 1063 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: D 56 ARG cc_start: 0.8238 (mmt180) cc_final: 0.7777 (mtp-110) REVERT: D 124 ASP cc_start: 0.7880 (m-30) cc_final: 0.7604 (m-30) REVERT: D 221 ASP cc_start: 0.7538 (m-30) cc_final: 0.7308 (m-30) REVERT: D 247 ARG cc_start: 0.7388 (ttm170) cc_final: 0.6888 (tpp80) REVERT: D 478 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7497 (mtp85) REVERT: D 677 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8155 (mt) REVERT: D 741 ARG cc_start: 0.5468 (ptm160) cc_final: 0.5193 (ptm160) REVERT: E 42 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.5695 (mp0) REVERT: E 68 TYR cc_start: 0.8219 (m-80) cc_final: 0.8019 (m-80) REVERT: Z 45 LYS cc_start: 0.6919 (mtmm) cc_final: 0.6474 (mtmt) REVERT: Z 90 THR cc_start: 0.5802 (OUTLIER) cc_final: 0.5378 (p) REVERT: Z 113 MET cc_start: 0.6592 (ptp) cc_final: 0.5988 (ptt) REVERT: Z 146 ASP cc_start: 0.7601 (m-30) cc_final: 0.7304 (m-30) outliers start: 87 outliers final: 67 residues processed: 333 average time/residue: 0.4423 time to fit residues: 227.7022 Evaluate side-chains 323 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 251 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 102 ARG Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Chi-restraints excluded: chain Z residue 137 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 301 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 204 optimal weight: 0.5980 chunk 154 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS E 88 GLN E 100 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.166586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127173 restraints weight = 35402.662| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.06 r_work: 0.3527 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 25475 Z= 0.238 Angle : 0.677 13.420 34815 Z= 0.345 Chirality : 0.045 0.201 3976 Planarity : 0.005 0.103 4342 Dihedral : 14.022 162.864 4095 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.41 % Favored : 93.33 % Rotamer: Outliers : 3.70 % Allowed : 16.57 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: -0.72 (0.15), residues: 3013 helix: 0.83 (0.16), residues: 1123 sheet: -1.65 (0.26), residues: 379 loop : -1.14 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 944 HIS 0.012 0.001 HIS D 748 PHE 0.022 0.002 PHE C 906 TYR 0.017 0.002 TYR C1027 ARG 0.007 0.001 ARG D 572 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 1051) hydrogen bonds : angle 4.91237 ( 2896) metal coordination : bond 0.00770 ( 8) metal coordination : angle 2.53288 ( 12) covalent geometry : bond 0.00570 (25467) covalent geometry : angle 0.67575 (34803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 253 time to evaluate : 2.835 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6933 (mp) REVERT: A 79 ASN cc_start: 0.8394 (m110) cc_final: 0.7964 (m110) REVERT: A 151 GLN cc_start: 0.7957 (tp-100) cc_final: 0.7419 (tp40) REVERT: A 177 LYS cc_start: 0.8453 (ptpp) cc_final: 0.8060 (pttt) REVERT: C 93 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8095 (tp) REVERT: C 127 MET cc_start: 0.7794 (mtm) cc_final: 0.6569 (mmp) REVERT: C 159 MET cc_start: 0.8240 (mmm) cc_final: 0.7771 (mmm) REVERT: C 421 ARG cc_start: 0.7904 (ttt180) cc_final: 0.7211 (tpt-90) REVERT: C 661 MET cc_start: 0.7924 (tpp) cc_final: 0.7662 (tpt) REVERT: C 797 ARG cc_start: 0.7375 (ttm-80) cc_final: 0.7081 (ttp80) REVERT: C 891 ASN cc_start: 0.8539 (p0) cc_final: 0.8150 (p0) REVERT: C 1063 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: D 56 ARG cc_start: 0.8379 (mmt180) cc_final: 0.7870 (mtp-110) REVERT: D 124 ASP cc_start: 0.7848 (m-30) cc_final: 0.7592 (m-30) REVERT: D 214 ARG cc_start: 0.7221 (ptm-80) cc_final: 0.6721 (mpp80) REVERT: D 221 ASP cc_start: 0.7422 (m-30) cc_final: 0.7160 (m-30) REVERT: D 247 ARG cc_start: 0.7414 (ttm170) cc_final: 0.7018 (tpp80) REVERT: D 478 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7392 (mtp85) REVERT: D 677 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8336 (mt) REVERT: D 741 ARG cc_start: 0.5751 (ptm160) cc_final: 0.5373 (ptm160) REVERT: E 42 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6010 (mp0) REVERT: E 68 TYR cc_start: 0.8322 (m-80) cc_final: 0.8040 (m-80) REVERT: Z 45 LYS cc_start: 0.6928 (mtmm) cc_final: 0.6460 (mtmt) REVERT: Z 90 THR cc_start: 0.5778 (OUTLIER) cc_final: 0.5391 (p) REVERT: Z 113 MET cc_start: 0.6651 (ptp) cc_final: 0.6071 (ptt) REVERT: Z 146 ASP cc_start: 0.7528 (m-30) cc_final: 0.7184 (m-30) outliers start: 94 outliers final: 74 residues processed: 329 average time/residue: 0.4249 time to fit residues: 214.8870 Evaluate side-chains 317 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 237 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain Z residue 51 VAL Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 102 ARG Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Chi-restraints excluded: chain Z residue 137 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 293 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 242 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 244 optimal weight: 0.0270 chunk 45 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 262 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 HIS ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS D 761 GLN ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.169065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.129839 restraints weight = 35583.967| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.05 r_work: 0.3569 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25475 Z= 0.149 Angle : 0.615 13.649 34815 Z= 0.312 Chirality : 0.043 0.192 3976 Planarity : 0.005 0.101 4342 Dihedral : 13.940 163.222 4095 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.91 % Favored : 93.86 % Rotamer: Outliers : 3.62 % Allowed : 17.00 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: -0.53 (0.16), residues: 3013 helix: 1.00 (0.16), residues: 1125 sheet: -1.48 (0.26), residues: 379 loop : -1.07 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Z 120 HIS 0.025 0.001 HIS D 748 PHE 0.029 0.001 PHE C 214 TYR 0.016 0.001 TYR Z 55 ARG 0.007 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 1051) hydrogen bonds : angle 4.76251 ( 2896) metal coordination : bond 0.00550 ( 8) metal coordination : angle 2.28679 ( 12) covalent geometry : bond 0.00349 (25467) covalent geometry : angle 0.61315 (34803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 260 time to evaluate : 4.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8365 (m110) cc_final: 0.7942 (m110) REVERT: A 177 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8045 (pttt) REVERT: C 93 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8013 (tp) REVERT: C 127 MET cc_start: 0.7720 (mtm) cc_final: 0.6541 (mmp) REVERT: C 159 MET cc_start: 0.8162 (mmm) cc_final: 0.7683 (mmm) REVERT: C 421 ARG cc_start: 0.7919 (ttt180) cc_final: 0.7185 (tpt-90) REVERT: C 538 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7441 (mmp80) REVERT: C 580 ASP cc_start: 0.8115 (m-30) cc_final: 0.7878 (m-30) REVERT: C 797 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.7087 (ttp80) REVERT: C 891 ASN cc_start: 0.8412 (p0) cc_final: 0.8010 (p0) REVERT: C 1063 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7352 (m-80) REVERT: D 56 ARG cc_start: 0.8333 (mmt180) cc_final: 0.7838 (mtp-110) REVERT: D 124 ASP cc_start: 0.7894 (m-30) cc_final: 0.7618 (m-30) REVERT: D 214 ARG cc_start: 0.7210 (ptm-80) cc_final: 0.6731 (mpp80) REVERT: D 221 ASP cc_start: 0.7479 (m-30) cc_final: 0.7226 (m-30) REVERT: D 247 ARG cc_start: 0.7432 (ttm170) cc_final: 0.7021 (tpp80) REVERT: D 478 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7438 (mtp85) REVERT: D 677 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8241 (mt) REVERT: D 741 ARG cc_start: 0.5563 (ptm160) cc_final: 0.5174 (ptm160) REVERT: E 42 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.5840 (mp0) REVERT: Z 45 LYS cc_start: 0.6918 (mtmm) cc_final: 0.6479 (mtmt) REVERT: Z 90 THR cc_start: 0.5926 (OUTLIER) cc_final: 0.5501 (p) REVERT: Z 113 MET cc_start: 0.6555 (ptp) cc_final: 0.6054 (ptt) REVERT: Z 120 TRP cc_start: 0.6633 (t60) cc_final: 0.5210 (t60) REVERT: Z 146 ASP cc_start: 0.7408 (m-30) cc_final: 0.7108 (m-30) outliers start: 92 outliers final: 73 residues processed: 330 average time/residue: 0.6520 time to fit residues: 338.1764 Evaluate side-chains 324 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 246 time to evaluate : 5.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain Z residue 51 VAL Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 102 ARG Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 137 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 49 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 240 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.169452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.129848 restraints weight = 35410.328| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.06 r_work: 0.3575 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25475 Z= 0.145 Angle : 0.617 13.698 34815 Z= 0.313 Chirality : 0.043 0.198 3976 Planarity : 0.005 0.101 4342 Dihedral : 13.888 162.856 4093 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.11 % Favored : 93.69 % Rotamer: Outliers : 3.07 % Allowed : 17.83 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: -0.43 (0.16), residues: 3013 helix: 1.08 (0.16), residues: 1120 sheet: -1.42 (0.26), residues: 374 loop : -1.00 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 120 HIS 0.033 0.001 HIS D 748 PHE 0.035 0.001 PHE C 214 TYR 0.014 0.001 TYR Z 58 ARG 0.008 0.000 ARG C 671 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 1051) hydrogen bonds : angle 4.73781 ( 2896) metal coordination : bond 0.00511 ( 8) metal coordination : angle 2.17347 ( 12) covalent geometry : bond 0.00342 (25467) covalent geometry : angle 0.61571 (34803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6026 Ramachandran restraints generated. 3013 Oldfield, 0 Emsley, 3013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 254 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8378 (m110) cc_final: 0.7965 (m110) REVERT: A 177 LYS cc_start: 0.8436 (ptpp) cc_final: 0.8053 (pttt) REVERT: B 97 LEU cc_start: 0.7576 (tp) cc_final: 0.7191 (tt) REVERT: C 93 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8094 (tp) REVERT: C 127 MET cc_start: 0.7675 (mtm) cc_final: 0.6520 (mmp) REVERT: C 159 MET cc_start: 0.8146 (mmm) cc_final: 0.7678 (mmm) REVERT: C 203 LYS cc_start: 0.7615 (mtmt) cc_final: 0.7348 (mttm) REVERT: C 305 ARG cc_start: 0.6788 (mtp85) cc_final: 0.6107 (mtm110) REVERT: C 538 ARG cc_start: 0.7703 (ttm-80) cc_final: 0.7433 (mmp80) REVERT: C 580 ASP cc_start: 0.8096 (m-30) cc_final: 0.7855 (m-30) REVERT: C 671 ARG cc_start: 0.7366 (mmt180) cc_final: 0.6922 (tpp-160) REVERT: C 797 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.7079 (ttp80) REVERT: C 891 ASN cc_start: 0.8396 (p0) cc_final: 0.7975 (p0) REVERT: C 1063 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: D 56 ARG cc_start: 0.8325 (mmt180) cc_final: 0.7827 (mtp-110) REVERT: D 124 ASP cc_start: 0.7884 (m-30) cc_final: 0.7607 (m-30) REVERT: D 214 ARG cc_start: 0.7184 (ptm-80) cc_final: 0.6745 (mpp80) REVERT: D 221 ASP cc_start: 0.7417 (m-30) cc_final: 0.7159 (m-30) REVERT: D 247 ARG cc_start: 0.7432 (ttm170) cc_final: 0.7023 (tpp80) REVERT: D 478 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7421 (mtp85) REVERT: D 677 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8177 (mt) REVERT: D 741 ARG cc_start: 0.5542 (ptm160) cc_final: 0.5177 (ptm160) REVERT: D 750 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7511 (mp0) REVERT: D 776 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7917 (tt0) REVERT: E 42 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.5797 (mp0) REVERT: E 68 TYR cc_start: 0.8363 (m-80) cc_final: 0.8000 (m-80) REVERT: Z 45 LYS cc_start: 0.6902 (mtmm) cc_final: 0.6469 (mtmt) REVERT: Z 90 THR cc_start: 0.5918 (OUTLIER) cc_final: 0.5502 (p) REVERT: Z 113 MET cc_start: 0.6749 (ptp) cc_final: 0.6229 (ptt) REVERT: Z 120 TRP cc_start: 0.6385 (t60) cc_final: 0.5207 (t60) REVERT: Z 146 ASP cc_start: 0.7435 (m-30) cc_final: 0.7159 (m-30) outliers start: 78 outliers final: 68 residues processed: 316 average time/residue: 0.3996 time to fit residues: 193.1635 Evaluate side-chains 320 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 247 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain Z residue 51 VAL Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 102 ARG Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Chi-restraints excluded: chain Z residue 137 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 164 optimal weight: 0.0980 chunk 141 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 283 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 270 optimal weight: 0.8980 chunk 281 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 ASN C 141 ASN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 ASN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 761 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.166188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.126534 restraints weight = 35814.504| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.07 r_work: 0.3506 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 25475 Z= 0.288 Angle : 0.732 13.388 34815 Z= 0.372 Chirality : 0.047 0.215 3976 Planarity : 0.006 0.102 4342 Dihedral : 14.034 160.750 4093 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.67 % Favored : 93.13 % Rotamer: Outliers : 3.27 % Allowed : 17.63 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: -0.81 (0.15), residues: 3013 helix: 0.67 (0.15), residues: 1124 sheet: -1.68 (0.26), residues: 375 loop : -1.13 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 944 HIS 0.007 0.001 HIS D1150 PHE 0.027 0.002 PHE C 214 TYR 0.021 0.002 TYR Z 55 ARG 0.007 0.001 ARG D 572 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 1051) hydrogen bonds : angle 5.00515 ( 2896) metal coordination : bond 0.00894 ( 8) metal coordination : angle 2.41975 ( 12) covalent geometry : bond 0.00692 (25467) covalent geometry : angle 0.73119 (34803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17547.12 seconds wall clock time: 304 minutes 59.20 seconds (18299.20 seconds total)