Starting phenix.real_space_refine on Sun Jul 5 03:00:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e82_27942/07_2026/8e82_27942.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e82_27942/07_2026/8e82_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8e82_27942/07_2026/8e82_27942.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e82_27942/07_2026/8e82_27942.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e82_27942/07_2026/8e82_27942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e82_27942/07_2026/8e82_27942.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e82_27942/07_2026/8e82_27942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e82_27942/07_2026/8e82_27942.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} 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, 'ASP:plan': 1, 'ARG: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: 5.26, per 1000 atoms: 0.21 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: 2.19 Conformation dependent library (CDL) restraints added in 963.2 milliseconds 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: 2.76 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: 5.40 Time building geometry restraints manager: 2.85 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=" C1' DT P 135 " pdb=" N1 DT P 135 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" C1' DT P 118 " pdb=" N1 DT P 118 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.14e+01 bond pdb=" C1' DC P 139 " pdb=" N1 DC P 139 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" C1' DT Q 44 " pdb=" N1 DT Q 44 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" C1' DT P 117 " pdb=" N1 DT P 117 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.07e+01 ... (remaining 25462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 34073 1.96 - 3.92: 654 3.92 - 5.88: 68 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=" O4' DT P 115 " pdb=" C4' DT P 115 " pdb=" C3' DT P 115 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.43e+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=" O4' DA P 127 " pdb=" C4' DA P 127 " pdb=" C3' DA P 127 " ideal model delta sigma weight residual 106.00 103.40 2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 34798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 14896 33.44 - 66.87: 462 66.87 - 100.31: 8 100.31 - 133.75: 1 133.75 - 167.19: 1 Dihedral angle restraints: 15368 sinusoidal: 6696 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 15365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 3910 0.128 - 0.256: 61 0.256 - 0.385: 0 0.385 - 0.513: 4 0.513 - 0.641: 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 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 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 2.34 -2.83 -0.49 2.00e-01 2.50e+01 6.11e+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 2.34 -2.81 -0.48 2.00e-01 2.50e+01 5.68e+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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.800 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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= 0.235 Angle : 0.787 47.589 34815 Z= 0.427 Chirality : 0.048 0.641 3976 Planarity : 0.004 0.099 4342 Dihedral : 14.264 167.185 9794 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.57 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (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 ARG 0.003 0.000 ARG D 427 TYR 0.010 0.001 TYR D 586 PHE 0.011 0.001 PHE C 439 TRP 0.010 0.001 TRP C 938 HIS 0.005 0.001 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.23 (25467) covalent geometry : angle 0.67088 / 0.42 (34803) hydrogen bonds : bond 0.16587 / 11.46 ( 1051) hydrogen bonds : angle 6.84543 / 4.65 ( 2896) metal coordination : bond 0.08255 / 4.08 ( 8) metal coordination : angle 22.20010 / 12.74 ( 12) *********************** 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 : 0.880 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: 0.8608 (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: 0.2099 time to fit residues: 190.6069 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 : 0.961 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.0670 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 D1227 GLN E 65 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.173236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134255 restraints weight = 35741.552| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.05 r_work: 0.3609 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25475 Z= 0.158 Angle : 0.672 12.238 34815 Z= 0.350 Chirality : 0.046 0.382 3976 Planarity : 0.005 0.106 4342 Dihedral : 13.948 168.640 4108 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.61 % Favored : 93.96 % Rotamer: Outliers : 3.58 % Allowed : 11.53 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 3013 helix: 0.73 (0.16), residues: 1116 sheet: -1.30 (0.28), residues: 347 loop : -1.33 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Z 124 TYR 0.021 0.001 TYR Z 78 PHE 0.016 0.002 PHE D 131 TRP 0.012 0.001 TRP D 223 HIS 0.010 0.001 HIS D 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (25467) covalent geometry : angle 0.66203 / 0.35 (34803) hydrogen bonds : bond 0.04794 / 3.30 ( 1051) hydrogen bonds : angle 5.28433 / 3.63 ( 2896) metal coordination : bond 0.00924 / 0.40 ( 8) metal coordination : angle 6.35773 / 3.69 ( 12) *********************** 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 405 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 314 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8519 (ptpp) cc_final: 0.8185 (pttt) REVERT: A 184 GLU cc_start: 0.6586 (mm-30) cc_final: 0.6138 (pp20) REVERT: B 213 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7370 (tttt) REVERT: C 127 MET cc_start: 0.7482 (mtm) cc_final: 0.6675 (mmp) REVERT: C 159 MET cc_start: 0.8321 (mmm) cc_final: 0.8058 (mmm) REVERT: C 232 GLN cc_start: 0.7880 (pt0) cc_final: 0.7627 (pt0) REVERT: C 304 LYS cc_start: 0.6488 (tptt) cc_final: 0.6240 (tptt) REVERT: C 305 ARG cc_start: 0.7046 (mtp85) cc_final: 0.6843 (mtp85) REVERT: C 347 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7904 (mpt-90) REVERT: C 415 GLN cc_start: 0.7099 (tt0) cc_final: 0.6346 (tm-30) REVERT: C 421 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7166 (ttt180) REVERT: C 797 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.7002 (ttp80) REVERT: C 963 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8476 (mt) REVERT: D 124 ASP cc_start: 0.7785 (m-30) cc_final: 0.7450 (m-30) REVERT: D 144 ARG cc_start: 0.7533 (tpp80) cc_final: 0.7024 (tpp80) REVERT: D 205 MET cc_start: 0.4166 (OUTLIER) cc_final: 0.3632 (mtp) REVERT: D 214 ARG cc_start: 0.7509 (ptm-80) cc_final: 0.6907 (mpp80) REVERT: D 478 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7399 (mtp85) REVERT: D 793 TYR cc_start: 0.7201 (m-80) cc_final: 0.6737 (m-80) REVERT: D 1112 MET cc_start: 0.6855 (mmt) cc_final: 0.6461 (mmm) REVERT: E 68 TYR cc_start: 0.8205 (m-80) cc_final: 0.7900 (m-80) REVERT: Z 67 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.4985 (pp20) REVERT: Z 87 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: Z 112 ARG cc_start: 0.7345 (ttp80) cc_final: 0.6788 (ttp-110) REVERT: Z 113 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7243 (ptp) REVERT: Z 117 ASP cc_start: 0.7313 (m-30) cc_final: 0.6745 (t0) REVERT: Z 146 ASP cc_start: 0.7453 (m-30) cc_final: 0.7054 (m-30) outliers start: 91 outliers final: 46 residues processed: 378 average time/residue: 0.1955 time to fit residues: 113.0757 Evaluate side-chains 314 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 120 ASP Chi-restraints excluded: chain C residue 122 CYS 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 217 ASP 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 400 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 520 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 963 LEU 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 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 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP 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 87 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 45 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 301 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN B 36 ASN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.171168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.132057 restraints weight = 35821.834| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.13 r_work: 0.3575 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25475 Z= 0.182 Angle : 0.653 15.633 34815 Z= 0.335 Chirality : 0.045 0.238 3976 Planarity : 0.005 0.105 4342 Dihedral : 13.825 167.735 4082 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.61 % Favored : 94.06 % Rotamer: Outliers : 3.62 % Allowed : 12.95 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 3013 helix: 0.79 (0.16), residues: 1122 sheet: -1.52 (0.26), residues: 374 loop : -1.27 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 182 TYR 0.011 0.001 TYR Z 78 PHE 0.023 0.002 PHE B 219 TRP 0.011 0.001 TRP C 938 HIS 0.008 0.001 HIS C1035 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (25467) covalent geometry : angle 0.63391 / 0.33 (34803) hydrogen bonds : bond 0.04646 / 3.19 ( 1051) hydrogen bonds : angle 5.06288 / 3.49 ( 2896) metal coordination : bond 0.01523 / 0.73 ( 8) metal coordination : angle 8.39252 / 4.18 ( 12) *********************** 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 367 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 275 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8362 (m110) cc_final: 0.7927 (m110) REVERT: A 177 LYS cc_start: 0.8514 (ptpp) cc_final: 0.8126 (pttt) REVERT: C 92 GLU cc_start: 0.7305 (tp30) cc_final: 0.6361 (pt0) REVERT: C 127 MET cc_start: 0.7634 (mtm) cc_final: 0.6735 (mmp) REVERT: C 159 MET cc_start: 0.8233 (mmm) cc_final: 0.7957 (mmm) REVERT: C 232 GLN cc_start: 0.7681 (pt0) cc_final: 0.7383 (pt0) REVERT: C 347 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7726 (mpt-90) REVERT: C 401 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7263 (mmm-85) REVERT: C 415 GLN cc_start: 0.7173 (tt0) cc_final: 0.6404 (tm-30) REVERT: C 421 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7228 (ttt180) REVERT: C 797 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.6980 (ttp80) REVERT: D 43 LYS cc_start: 0.7191 (tptp) cc_final: 0.6975 (tptt) REVERT: D 124 ASP cc_start: 0.7821 (m-30) cc_final: 0.7544 (m-30) REVERT: D 205 MET cc_start: 0.4168 (OUTLIER) cc_final: 0.3641 (mtp) REVERT: D 214 ARG cc_start: 0.7399 (ptm-80) cc_final: 0.6856 (mpp80) REVERT: D 219 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7332 (mt) REVERT: D 327 MET cc_start: 0.7100 (mtm) cc_final: 0.6747 (mtm) REVERT: D 478 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7460 (mtp85) REVERT: D 635 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8411 (p) REVERT: D 741 ARG cc_start: 0.6385 (mtp-110) cc_final: 0.6183 (ptm160) REVERT: E 68 TYR cc_start: 0.8248 (m-80) cc_final: 0.7974 (m-80) REVERT: Z 45 LYS cc_start: 0.6210 (mtpt) cc_final: 0.5996 (mtmt) REVERT: Z 67 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5110 (pp20) REVERT: Z 87 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: Z 112 ARG cc_start: 0.7341 (ttp80) cc_final: 0.7127 (ttp-110) REVERT: Z 113 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7253 (ptp) REVERT: Z 117 ASP cc_start: 0.7168 (m-30) cc_final: 0.6677 (t0) REVERT: Z 146 ASP cc_start: 0.7455 (m-30) cc_final: 0.7113 (m-30) outliers start: 92 outliers final: 52 residues processed: 346 average time/residue: 0.1945 time to fit residues: 103.0471 Evaluate side-chains 299 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 240 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER 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 236 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 401 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 458 LEU 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 1087 GLU 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 360 LEU Chi-restraints excluded: chain D residue 423 ASP 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 635 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 87 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 73 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 271 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 241 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 230 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.170448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.131170 restraints weight = 35299.163| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.06 r_work: 0.3576 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2605 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= 0.165 Angle : 0.631 14.696 34815 Z= 0.322 Chirality : 0.044 0.180 3976 Planarity : 0.005 0.107 4342 Dihedral : 13.747 167.231 4072 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.64 % Favored : 94.06 % Rotamer: Outliers : 3.66 % Allowed : 14.36 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 3013 helix: 0.89 (0.16), residues: 1127 sheet: -1.36 (0.26), residues: 381 loop : -1.27 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1087 TYR 0.011 0.001 TYR D 424 PHE 0.026 0.002 PHE C 214 TRP 0.012 0.001 TRP C 938 HIS 0.005 0.001 HIS D1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (25467) covalent geometry : angle 0.61375 / 0.32 (34803) hydrogen bonds : bond 0.04277 / 2.95 ( 1051) hydrogen bonds : angle 4.94502 / 3.42 ( 2896) metal coordination : bond 0.00739 / 0.33 ( 8) metal coordination : angle 7.99087 / 3.87 ( 12) *********************** 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 355 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 262 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8348 (m110) cc_final: 0.7870 (m110) REVERT: A 138 LEU cc_start: 0.7148 (mp) cc_final: 0.6920 (mt) REVERT: A 177 LYS cc_start: 0.8507 (ptpp) cc_final: 0.8115 (ptmt) REVERT: C 92 GLU cc_start: 0.7418 (tp30) cc_final: 0.6310 (pt0) REVERT: C 127 MET cc_start: 0.7630 (mtm) cc_final: 0.6675 (mmp) REVERT: C 159 MET cc_start: 0.8194 (mmm) cc_final: 0.7860 (mmm) REVERT: C 203 LYS cc_start: 0.7440 (mtmt) cc_final: 0.7115 (mttp) REVERT: C 232 GLN cc_start: 0.7674 (pt0) cc_final: 0.7362 (pt0) REVERT: C 421 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7137 (ttt180) REVERT: C 467 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7909 (mtp85) REVERT: C 661 MET cc_start: 0.7800 (tpp) cc_final: 0.7491 (tpt) REVERT: C 797 ARG cc_start: 0.7285 (ttm-80) cc_final: 0.6954 (ttp80) REVERT: C 1063 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: C 1111 ASN cc_start: 0.6109 (p0) cc_final: 0.5806 (m-40) REVERT: D 124 ASP cc_start: 0.7852 (m-30) cc_final: 0.7567 (m-30) REVERT: D 214 ARG cc_start: 0.7320 (ptm-80) cc_final: 0.6771 (mpp80) REVERT: D 219 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7388 (mt) REVERT: D 478 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7394 (mtp85) REVERT: D 793 TYR cc_start: 0.7137 (m-80) cc_final: 0.6741 (m-80) REVERT: Z 66 LEU cc_start: 0.5077 (OUTLIER) cc_final: 0.4830 (mt) REVERT: Z 67 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5179 (pp20) REVERT: Z 113 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7283 (ptp) REVERT: Z 146 ASP cc_start: 0.7571 (m-30) cc_final: 0.7239 (m-30) outliers start: 93 outliers final: 59 residues processed: 335 average time/residue: 0.1880 time to fit residues: 97.3188 Evaluate side-chains 303 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 239 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 140 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 56 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 128 THR 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 302 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 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 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 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 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 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 423 ASP 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 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 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 Z residue 66 LEU Chi-restraints excluded: chain Z residue 67 GLU Chi-restraints excluded: chain Z residue 105 LEU 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 119 SER Chi-restraints excluded: chain Z residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 204 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 102 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 273 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.170452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.131005 restraints weight = 35555.875| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.10 r_work: 0.3565 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25475 Z= 0.166 Angle : 0.625 15.004 34815 Z= 0.318 Chirality : 0.044 0.165 3976 Planarity : 0.005 0.106 4342 Dihedral : 13.733 166.682 4071 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.97 % Favored : 93.73 % Rotamer: Outliers : 4.13 % Allowed : 15.07 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.16), residues: 3013 helix: 0.93 (0.16), residues: 1120 sheet: -1.43 (0.26), residues: 392 loop : -1.24 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 43 TYR 0.027 0.001 TYR E 68 PHE 0.016 0.002 PHE C 906 TRP 0.011 0.001 TRP C 938 HIS 0.014 0.001 HIS D 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (25467) covalent geometry : angle 0.60734 / 0.32 (34803) hydrogen bonds : bond 0.04191 / 2.88 ( 1051) hydrogen bonds : angle 4.88908 / 3.38 ( 2896) metal coordination : bond 0.00742 / 0.34 ( 8) metal coordination : angle 7.90539 / 3.78 ( 12) *********************** 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 368 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 263 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7189 (mp) cc_final: 0.6933 (mt) REVERT: A 151 GLN cc_start: 0.7812 (tp40) cc_final: 0.7545 (tp-100) REVERT: A 177 LYS cc_start: 0.8362 (ptpp) cc_final: 0.7969 (pttt) REVERT: B 5 GLN cc_start: 0.7335 (pt0) cc_final: 0.7105 (pt0) REVERT: C 92 GLU cc_start: 0.7312 (tp30) cc_final: 0.6342 (pt0) REVERT: C 127 MET cc_start: 0.7454 (mtm) cc_final: 0.6599 (mmp) REVERT: C 159 MET cc_start: 0.8094 (mmm) cc_final: 0.7770 (mmm) REVERT: C 203 LYS cc_start: 0.7223 (mtmt) cc_final: 0.6893 (mttp) REVERT: C 232 GLN cc_start: 0.7604 (pt0) cc_final: 0.7319 (pt0) REVERT: C 304 LYS cc_start: 0.6337 (tptt) cc_final: 0.6053 (tptt) REVERT: C 661 MET cc_start: 0.7658 (tpp) cc_final: 0.7315 (tpt) REVERT: C 797 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6852 (ttp80) REVERT: C 1063 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: C 1111 ASN cc_start: 0.6159 (p0) cc_final: 0.5946 (m-40) REVERT: D 124 ASP cc_start: 0.7705 (m-30) cc_final: 0.7439 (m-30) REVERT: D 214 ARG cc_start: 0.7273 (ptm-80) cc_final: 0.6743 (mpp80) REVERT: D 221 ASP cc_start: 0.7395 (m-30) cc_final: 0.7166 (m-30) REVERT: D 247 ARG cc_start: 0.7504 (ttm170) cc_final: 0.6918 (tpp80) REVERT: D 478 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7377 (mtp85) REVERT: D 793 TYR cc_start: 0.7057 (m-80) cc_final: 0.6671 (m-80) REVERT: Z 66 LEU cc_start: 0.4917 (OUTLIER) cc_final: 0.4686 (mt) REVERT: Z 67 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5037 (pp20) REVERT: Z 90 THR cc_start: 0.5488 (OUTLIER) cc_final: 0.4948 (p) REVERT: Z 113 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7222 (ptp) REVERT: Z 146 ASP cc_start: 0.7322 (m-30) cc_final: 0.7039 (m-30) outliers start: 105 outliers final: 71 residues processed: 344 average time/residue: 0.1905 time to fit residues: 101.9705 Evaluate side-chains 317 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 241 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 88 GLU 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 140 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 140 ILE 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 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 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 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 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 423 ASP 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 635 VAL 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 862 ASP 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 66 LEU Chi-restraints excluded: chain Z residue 67 GLU Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 105 LEU 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 119 SER Chi-restraints excluded: chain Z residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 55 optimal weight: 8.9990 chunk 155 optimal weight: 0.5980 chunk 227 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 37 optimal weight: 0.0870 chunk 271 optimal weight: 1.9990 chunk 222 optimal weight: 0.0170 chunk 79 optimal weight: 7.9990 chunk 256 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 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 ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4277 r_free = 0.4277 target = 0.173833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.133767 restraints weight = 35821.537| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.18 r_work: 0.3600 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25475 Z= 0.120 Angle : 0.589 12.996 34815 Z= 0.301 Chirality : 0.042 0.171 3976 Planarity : 0.005 0.103 4342 Dihedral : 13.667 166.521 4069 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.34 % Favored : 94.36 % Rotamer: Outliers : 3.58 % Allowed : 15.66 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 3013 helix: 1.11 (0.16), residues: 1120 sheet: -1.04 (0.27), residues: 365 loop : -1.21 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 11 TYR 0.013 0.001 TYR E 68 PHE 0.014 0.001 PHE B 219 TRP 0.018 0.001 TRP Z 120 HIS 0.004 0.001 HIS D1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (25467) covalent geometry : angle 0.57563 / 0.30 (34803) hydrogen bonds : bond 0.03783 / 2.61 ( 1051) hydrogen bonds : angle 4.77370 / 3.30 ( 2896) metal coordination : bond 0.00586 / 0.28 ( 8) metal coordination : angle 6.82147 / 3.32 ( 12) *********************** 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 367 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 276 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8177 (m110) cc_final: 0.7732 (m110) REVERT: A 138 LEU cc_start: 0.7271 (mp) cc_final: 0.6993 (mt) REVERT: A 151 GLN cc_start: 0.7835 (tp40) cc_final: 0.7621 (tp-100) REVERT: A 177 LYS cc_start: 0.8362 (ptpp) cc_final: 0.7946 (pttt) REVERT: C 92 GLU cc_start: 0.7361 (tp30) cc_final: 0.6372 (pt0) REVERT: C 93 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7604 (tp) REVERT: C 127 MET cc_start: 0.7369 (mtm) cc_final: 0.6526 (mmp) REVERT: C 159 MET cc_start: 0.8063 (mmm) cc_final: 0.7725 (mmm) REVERT: C 203 LYS cc_start: 0.7102 (mtmt) cc_final: 0.6796 (mttp) REVERT: C 232 GLN cc_start: 0.7515 (pt0) cc_final: 0.7202 (pt0) REVERT: C 304 LYS cc_start: 0.6158 (tptt) cc_final: 0.5891 (tptt) REVERT: C 421 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6915 (tpt-90) REVERT: C 661 MET cc_start: 0.7639 (tpp) cc_final: 0.7357 (tpt) REVERT: C 797 ARG cc_start: 0.7138 (ttm-80) cc_final: 0.6871 (ttp80) REVERT: C 909 ASP cc_start: 0.7911 (p0) cc_final: 0.7691 (p0) REVERT: C 1063 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: D 124 ASP cc_start: 0.7726 (m-30) cc_final: 0.7447 (m-30) REVERT: D 214 ARG cc_start: 0.7206 (ptm-80) cc_final: 0.6671 (mpp80) REVERT: D 221 ASP cc_start: 0.7403 (m-30) cc_final: 0.7157 (m-30) REVERT: D 247 ARG cc_start: 0.7485 (ttm170) cc_final: 0.6936 (tpp80) REVERT: D 478 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7419 (mtp85) REVERT: D 793 TYR cc_start: 0.7161 (m-80) cc_final: 0.6725 (m-80) REVERT: Z 45 LYS cc_start: 0.6807 (mtmm) cc_final: 0.6343 (mtmt) REVERT: Z 66 LEU cc_start: 0.4743 (OUTLIER) cc_final: 0.4537 (mt) REVERT: Z 78 TYR cc_start: 0.6512 (m-80) cc_final: 0.6303 (m-10) REVERT: Z 84 VAL cc_start: 0.7965 (p) cc_final: 0.7580 (m) REVERT: Z 90 THR cc_start: 0.5762 (OUTLIER) cc_final: 0.5314 (p) REVERT: Z 113 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7227 (ptp) REVERT: Z 123 VAL cc_start: 0.7511 (t) cc_final: 0.7217 (t) REVERT: Z 146 ASP cc_start: 0.7362 (m-30) cc_final: 0.7099 (m-30) outliers start: 91 outliers final: 57 residues processed: 347 average time/residue: 0.1856 time to fit residues: 99.4866 Evaluate side-chains 314 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 251 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 131 LYS Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 111 VAL 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 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 236 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 421 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 520 VAL 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 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 635 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 800 ILE Chi-restraints excluded: chain D residue 824 VAL 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 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 90 THR Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 113 MET Chi-restraints excluded: chain Z residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 298 optimal weight: 10.0000 chunk 227 optimal weight: 0.1980 chunk 98 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 294 optimal weight: 0.0060 chunk 262 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4273 r_free = 0.4273 target = 0.173119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.133780 restraints weight = 35349.282| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.08 r_work: 0.3627 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 25475 Z= 0.117 Angle : 0.589 14.034 34815 Z= 0.298 Chirality : 0.042 0.213 3976 Planarity : 0.005 0.102 4342 Dihedral : 13.549 166.239 4061 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.77 % Favored : 94.03 % Rotamer: Outliers : 2.91 % Allowed : 16.29 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 3013 helix: 1.22 (0.16), residues: 1117 sheet: -1.13 (0.27), residues: 377 loop : -1.13 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 11 TYR 0.011 0.001 TYR E 68 PHE 0.020 0.001 PHE C 214 TRP 0.017 0.001 TRP Z 120 HIS 0.003 0.000 HIS D1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (25467) covalent geometry : angle 0.57332 / 0.30 (34803) hydrogen bonds : bond 0.03589 / 2.48 ( 1051) hydrogen bonds : angle 4.69215 / 3.25 ( 2896) metal coordination : bond 0.00553 / 0.26 ( 8) metal coordination : angle 7.25080 / 3.42 ( 12) *********************** 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 345 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 271 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8337 (m110) cc_final: 0.7921 (m110) REVERT: A 138 LEU cc_start: 0.7293 (mp) cc_final: 0.7034 (mt) REVERT: A 151 GLN cc_start: 0.7822 (tp40) cc_final: 0.7613 (tp-100) REVERT: A 177 LYS cc_start: 0.8444 (ptpp) cc_final: 0.8040 (pttt) REVERT: B 5 GLN cc_start: 0.7653 (mt0) cc_final: 0.7352 (mt0) REVERT: C 92 GLU cc_start: 0.7499 (tp30) cc_final: 0.6456 (pt0) REVERT: C 93 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7708 (tp) REVERT: C 127 MET cc_start: 0.7489 (mtm) cc_final: 0.6598 (mmp) REVERT: C 159 MET cc_start: 0.8087 (mmm) cc_final: 0.7771 (mmm) REVERT: C 203 LYS cc_start: 0.7369 (mtmt) cc_final: 0.7114 (mttp) REVERT: C 232 GLN cc_start: 0.7600 (pt0) cc_final: 0.7343 (pt0) REVERT: C 421 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6966 (tpt-90) REVERT: C 580 ASP cc_start: 0.8024 (m-30) cc_final: 0.7789 (m-30) REVERT: C 661 MET cc_start: 0.7786 (tpp) cc_final: 0.7547 (tpt) REVERT: C 797 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6940 (ttp80) REVERT: C 1063 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: D 124 ASP cc_start: 0.7836 (m-30) cc_final: 0.7580 (m-30) REVERT: D 221 ASP cc_start: 0.7414 (m-30) cc_final: 0.7156 (m-30) REVERT: D 247 ARG cc_start: 0.7487 (ttm170) cc_final: 0.6944 (tpp80) REVERT: D 478 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7485 (mtp85) REVERT: D 793 TYR cc_start: 0.7451 (m-80) cc_final: 0.7008 (m-80) REVERT: Z 45 LYS cc_start: 0.6899 (mtmm) cc_final: 0.6333 (mtmt) REVERT: Z 66 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4522 (mt) REVERT: Z 90 THR cc_start: 0.5603 (OUTLIER) cc_final: 0.5183 (p) REVERT: Z 113 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7169 (ptp) REVERT: Z 146 ASP cc_start: 0.7301 (m-30) cc_final: 0.7073 (m-30) outliers start: 74 outliers final: 54 residues processed: 326 average time/residue: 0.1904 time to fit residues: 96.2656 Evaluate side-chains 311 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 140 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 44 LEU 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 236 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 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET 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 635 VAL 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 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU 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 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 109 ILE Chi-restraints excluded: chain Z residue 113 MET Chi-restraints excluded: chain Z residue 116 THR Chi-restraints excluded: chain Z residue 119 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 304 optimal weight: 20.0000 chunk 210 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** 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 = 0.4206 r_free = 0.4206 target = 0.166669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.127531 restraints weight = 35442.128| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.06 r_work: 0.3526 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 25475 Z= 0.290 Angle : 0.724 13.604 34815 Z= 0.366 Chirality : 0.048 0.242 3976 Planarity : 0.006 0.102 4342 Dihedral : 13.710 164.637 4059 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.11 % Favored : 93.69 % Rotamer: Outliers : 3.74 % Allowed : 16.41 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 3013 helix: 0.80 (0.16), residues: 1123 sheet: -1.31 (0.26), residues: 390 loop : -1.20 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 11 TYR 0.030 0.002 TYR Z 58 PHE 0.022 0.002 PHE C 906 TRP 0.015 0.002 TRP C 944 HIS 0.007 0.001 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.29 (25467) covalent geometry : angle 0.71274 / 0.37 (34803) hydrogen bonds : bond 0.04692 / 3.21 ( 1051) hydrogen bonds : angle 4.94081 / 3.39 ( 2896) metal coordination : bond 0.00984 / 0.45 ( 8) metal coordination : angle 6.90670 / 3.34 ( 12) *********************** 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 352 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 257 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8391 (m110) cc_final: 0.7932 (m110) REVERT: A 177 LYS cc_start: 0.8444 (ptpp) cc_final: 0.8022 (pttt) REVERT: C 92 GLU cc_start: 0.7632 (tp30) cc_final: 0.6591 (pt0) REVERT: C 93 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7801 (tp) REVERT: C 127 MET cc_start: 0.7663 (mtm) cc_final: 0.6575 (mmp) REVERT: C 159 MET cc_start: 0.8174 (mmm) cc_final: 0.7775 (mmm) REVERT: C 232 GLN cc_start: 0.7823 (pt0) cc_final: 0.7567 (pt0) REVERT: C 304 LYS cc_start: 0.6313 (tptt) cc_final: 0.6044 (tptt) REVERT: C 305 ARG cc_start: 0.7150 (mtp85) cc_final: 0.6373 (mtm180) REVERT: C 314 TYR cc_start: 0.8564 (t80) cc_final: 0.8358 (t80) REVERT: C 421 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7482 (ttm-80) REVERT: C 661 MET cc_start: 0.7877 (tpp) cc_final: 0.7637 (tpt) REVERT: C 797 ARG cc_start: 0.7402 (ttm-80) cc_final: 0.7106 (ttp80) REVERT: C 1063 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: D 124 ASP cc_start: 0.7842 (m-30) cc_final: 0.7576 (m-30) REVERT: D 214 ARG cc_start: 0.7178 (ptm-80) cc_final: 0.6700 (mpp80) REVERT: D 221 ASP cc_start: 0.7421 (m-30) cc_final: 0.7175 (m-30) REVERT: D 247 ARG cc_start: 0.7513 (ttm170) cc_final: 0.6963 (tpp80) REVERT: D 478 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7422 (mtp85) REVERT: D 612 TYR cc_start: 0.8851 (m-80) cc_final: 0.8507 (m-80) REVERT: Z 45 LYS cc_start: 0.6964 (mtmm) cc_final: 0.6585 (mtmm) REVERT: Z 67 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: Z 90 THR cc_start: 0.5609 (OUTLIER) cc_final: 0.5173 (p) REVERT: Z 146 ASP cc_start: 0.7451 (m-30) cc_final: 0.7135 (m-30) outliers start: 95 outliers final: 73 residues processed: 328 average time/residue: 0.1883 time to fit residues: 95.9205 Evaluate side-chains 323 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 245 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 140 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 56 VAL 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 147 ILE 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 236 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 PHE 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 421 ARG Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 470 LEU 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 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 1107 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 264 LEU 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 635 VAL Chi-restraints excluded: chain D residue 666 THR 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 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 67 GLU Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 143 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 761 GLN ** 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 = 0.170331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130972 restraints weight = 35277.426| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.05 r_work: 0.3583 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25475 Z= 0.136 Angle : 0.619 12.872 34815 Z= 0.313 Chirality : 0.043 0.192 3976 Planarity : 0.005 0.101 4342 Dihedral : 13.597 164.887 4056 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.96 % Rotamer: Outliers : 2.79 % Allowed : 17.16 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 3013 helix: 1.00 (0.16), residues: 1123 sheet: -1.10 (0.27), residues: 364 loop : -1.11 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 11 TYR 0.010 0.001 TYR D 586 PHE 0.021 0.001 PHE C 214 TRP 0.019 0.002 TRP Z 120 HIS 0.005 0.001 HIS D1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (25467) covalent geometry : angle 0.60707 / 0.31 (34803) hydrogen bonds : bond 0.03919 / 2.69 ( 1051) hydrogen bonds : angle 4.80173 / 3.31 ( 2896) metal coordination : bond 0.00685 / 0.31 ( 8) metal coordination : angle 6.43662 / 3.11 ( 12) *********************** 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 330 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 259 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8365 (m110) cc_final: 0.7923 (m110) REVERT: A 151 GLN cc_start: 0.7783 (tp40) cc_final: 0.7533 (tp-100) REVERT: A 177 LYS cc_start: 0.8403 (ptpp) cc_final: 0.7999 (pttt) REVERT: B 5 GLN cc_start: 0.7661 (mt0) cc_final: 0.7387 (mt0) REVERT: C 92 GLU cc_start: 0.7587 (tp30) cc_final: 0.6585 (pt0) REVERT: C 93 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7887 (tp) REVERT: C 127 MET cc_start: 0.7570 (mtm) cc_final: 0.6546 (mmp) REVERT: C 159 MET cc_start: 0.8155 (mmm) cc_final: 0.7743 (mmm) REVERT: C 203 LYS cc_start: 0.7464 (mtmt) cc_final: 0.7152 (mttm) REVERT: C 232 GLN cc_start: 0.7643 (pt0) cc_final: 0.7363 (pt0) REVERT: C 305 ARG cc_start: 0.7085 (mtp85) cc_final: 0.6340 (mtm180) REVERT: C 421 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7509 (ttm-80) REVERT: C 580 ASP cc_start: 0.8164 (m-30) cc_final: 0.7904 (m-30) REVERT: C 661 MET cc_start: 0.7784 (tpp) cc_final: 0.7533 (tpt) REVERT: C 671 ARG cc_start: 0.7314 (mmt180) cc_final: 0.6968 (ttm-80) REVERT: C 797 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.7117 (ttp80) REVERT: C 1063 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: D 124 ASP cc_start: 0.7831 (m-30) cc_final: 0.7556 (m-30) REVERT: D 221 ASP cc_start: 0.7513 (m-30) cc_final: 0.7289 (m-30) REVERT: D 247 ARG cc_start: 0.7547 (ttm170) cc_final: 0.7064 (tpp80) REVERT: D 478 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7508 (mtp85) REVERT: Z 45 LYS cc_start: 0.6907 (mtmm) cc_final: 0.6501 (mtmt) REVERT: Z 87 GLU cc_start: 0.7551 (pp20) cc_final: 0.7159 (pp20) REVERT: Z 90 THR cc_start: 0.5555 (OUTLIER) cc_final: 0.5134 (p) REVERT: Z 102 ARG cc_start: 0.7102 (ptt-90) cc_final: 0.6902 (ptt-90) REVERT: Z 113 MET cc_start: 0.6682 (ptp) cc_final: 0.5935 (ptt) REVERT: Z 120 TRP cc_start: 0.6609 (t60) cc_final: 0.6227 (t60) REVERT: Z 146 ASP cc_start: 0.7213 (m-30) cc_final: 0.6956 (m-30) outliers start: 71 outliers final: 58 residues processed: 313 average time/residue: 0.1906 time to fit residues: 92.5313 Evaluate side-chains 305 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 243 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE 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 150 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 56 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 236 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 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 433 THR 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 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU 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 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 264 LEU 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 635 VAL Chi-restraints excluded: chain D residue 666 THR 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 824 VAL 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 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 109 ILE Chi-restraints excluded: chain Z residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 168 optimal weight: 9.9990 chunk 180 optimal weight: 0.4980 chunk 99 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 302 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.171915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.132941 restraints weight = 35760.350| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.08 r_work: 0.3593 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25475 Z= 0.132 Angle : 0.617 13.427 34815 Z= 0.313 Chirality : 0.043 0.201 3976 Planarity : 0.005 0.100 4342 Dihedral : 13.557 164.905 4056 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.07 % Favored : 93.76 % Rotamer: Outliers : 2.48 % Allowed : 17.91 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 3013 helix: 1.11 (0.16), residues: 1123 sheet: -0.97 (0.28), residues: 352 loop : -1.06 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 43 TYR 0.009 0.001 TYR D 130 PHE 0.018 0.001 PHE C 252 TRP 0.018 0.001 TRP Z 120 HIS 0.006 0.001 HIS D 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (25467) covalent geometry : angle 0.60734 / 0.31 (34803) hydrogen bonds : bond 0.03794 / 2.62 ( 1051) hydrogen bonds : angle 4.75012 / 3.28 ( 2896) metal coordination : bond 0.00609 / 0.28 ( 8) metal coordination : angle 6.01193 / 2.91 ( 12) ********************** 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 318 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8381 (m110) cc_final: 0.7927 (m110) REVERT: A 151 GLN cc_start: 0.7689 (tp40) cc_final: 0.7436 (tp-100) REVERT: A 177 LYS cc_start: 0.8416 (ptpp) cc_final: 0.7997 (pttt) REVERT: C 92 GLU cc_start: 0.7601 (tp30) cc_final: 0.6543 (pt0) REVERT: C 93 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7897 (tp) REVERT: C 127 MET cc_start: 0.7565 (mtm) cc_final: 0.6513 (mmp) REVERT: C 159 MET cc_start: 0.8146 (mmm) cc_final: 0.7722 (mmm) REVERT: C 203 LYS cc_start: 0.7448 (mtmt) cc_final: 0.7135 (mttm) REVERT: C 232 GLN cc_start: 0.7599 (pt0) cc_final: 0.7379 (pt0) REVERT: C 305 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6306 (mtm180) REVERT: C 421 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7421 (ttm-80) REVERT: C 661 MET cc_start: 0.7780 (tpp) cc_final: 0.7528 (tpt) REVERT: C 671 ARG cc_start: 0.7327 (mmt180) cc_final: 0.6807 (tpp-160) REVERT: C 797 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.7096 (ttp80) REVERT: C 1063 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: D 124 ASP cc_start: 0.7852 (m-30) cc_final: 0.7563 (m-30) REVERT: D 221 ASP cc_start: 0.7517 (m-30) cc_final: 0.7293 (m-30) REVERT: D 247 ARG cc_start: 0.7529 (ttm170) cc_final: 0.7046 (tpp80) REVERT: D 478 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7502 (mtp85) REVERT: D 793 TYR cc_start: 0.7357 (m-80) cc_final: 0.6771 (m-80) REVERT: Z 45 LYS cc_start: 0.6871 (mtmm) cc_final: 0.6464 (mtmt) REVERT: Z 87 GLU cc_start: 0.7539 (pp20) cc_final: 0.7209 (pp20) REVERT: Z 90 THR cc_start: 0.5528 (OUTLIER) cc_final: 0.5131 (p) REVERT: Z 113 MET cc_start: 0.6604 (ptp) cc_final: 0.5862 (ptt) REVERT: Z 120 TRP cc_start: 0.6559 (t60) cc_final: 0.6238 (t60) outliers start: 63 outliers final: 51 residues processed: 303 average time/residue: 0.1866 time to fit residues: 88.1635 Evaluate side-chains 300 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 150 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 56 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 381 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 789 ILE 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 1107 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 264 LEU 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 635 VAL Chi-restraints excluded: chain D residue 666 THR 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 824 VAL 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 50 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 170 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 272 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.169129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130374 restraints weight = 35430.931| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.04 r_work: 0.3565 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25475 Z= 0.182 Angle : 0.639 13.411 34815 Z= 0.323 Chirality : 0.044 0.260 3976 Planarity : 0.005 0.100 4342 Dihedral : 13.593 164.259 4056 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.07 % Favored : 93.76 % Rotamer: Outliers : 2.72 % Allowed : 17.87 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 3013 helix: 1.01 (0.16), residues: 1124 sheet: -1.23 (0.27), residues: 366 loop : -1.04 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 11 TYR 0.011 0.001 TYR C1027 PHE 0.019 0.002 PHE C 252 TRP 0.014 0.002 TRP Z 120 HIS 0.006 0.001 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (25467) covalent geometry : angle 0.62946 / 0.32 (34803) hydrogen bonds : bond 0.04076 / 2.81 ( 1051) hydrogen bonds : angle 4.77649 / 3.29 ( 2896) metal coordination : bond 0.00741 / 0.34 ( 8) metal coordination : angle 5.87218 / 2.85 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8021.83 seconds wall clock time: 137 minutes 47.74 seconds (8267.74 seconds total)