Starting phenix.real_space_refine on Wed Jan 15 16:01:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xa7_38196/01_2025/8xa7_38196.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xa7_38196/01_2025/8xa7_38196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xa7_38196/01_2025/8xa7_38196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xa7_38196/01_2025/8xa7_38196.map" model { file = "/net/cci-nas-00/data/ceres_data/8xa7_38196/01_2025/8xa7_38196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xa7_38196/01_2025/8xa7_38196.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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: 5 Type Number sf(0) Gaussians S 90 5.16 5 C 16221 2.51 5 N 4492 2.21 5 O 4931 1.98 5 H 25990 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 1.41s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 51724 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3456 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3456 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain: "C" Number of atoms: 17931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 17931 Classifications: {'peptide': 1139} Link IDs: {'PTRANS': 54, 'TRANS': 1084} Chain breaks: 1 Chain: "D" Number of atoms: 18775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 18775 Classifications: {'peptide': 1176} Link IDs: {'CIS': 2, 'PTRANS': 52, 'TRANS': 1121} Chain breaks: 1 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 990 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "G" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2946 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "H" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1554 Classifications: {'peptide': 94} Modifications used: {'NH3': 1} Link IDs: {'CIS': 4, 'TRANS': 89} Chain: "L" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1503 Classifications: {'peptide': 92} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 87} Chain: "E" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1113 Classifications: {'peptide': 69} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 17.91, per 1000 atoms: 0.35 Number of scatterers: 51724 At special positions: 0 Unit cell: (136.8, 149.15, 168.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 O 4931 8.00 N 4492 7.00 C 16221 6.00 H 25990 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 78 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.06 Conformation dependent library (CDL) restraints added in 3.2 seconds 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 41 sheets defined 38.8% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 31 through 48 removed outlier: 3.732A pdb=" N SER A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.658A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 205 through 226 removed outlier: 4.488A pdb=" N ILE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 removed outlier: 3.543A pdb=" N THR C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 191 through 197 removed outlier: 4.182A pdb=" N LEU C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 217 through 224 removed outlier: 3.524A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 238 removed outlier: 3.782A pdb=" N GLU C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 268 through 280 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 377 through 393 Processing helix chain 'C' and resid 411 through 439 Processing helix chain 'C' and resid 444 through 449 removed outlier: 4.055A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 464 Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.665A pdb=" N TYR C 511 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 570 Processing helix chain 'C' and resid 614 through 618 removed outlier: 3.898A pdb=" N VAL C 618 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 removed outlier: 3.700A pdb=" N ILE C 626 " --> pdb=" O THR C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 632 Processing helix chain 'C' and resid 633 through 645 Processing helix chain 'C' and resid 661 through 671 removed outlier: 4.543A pdb=" N VAL C 665 " --> pdb=" O GLY C 661 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY C 671 " --> pdb=" O GLY C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 773 removed outlier: 6.432A pdb=" N GLU C 772 " --> pdb=" O TYR C 769 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C 773 " --> pdb=" O ASN C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'C' and resid 817 through 821 Processing helix chain 'C' and resid 959 through 966 Proline residue: C 963 - end of helix removed outlier: 3.572A pdb=" N MET C 966 " --> pdb=" O PRO C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 984 Processing helix chain 'C' and resid 996 through 1007 Processing helix chain 'C' and resid 1043 through 1047 Processing helix chain 'C' and resid 1076 through 1087 Processing helix chain 'C' and resid 1088 through 1097 Processing helix chain 'C' and resid 1102 through 1116 Processing helix chain 'C' and resid 1125 through 1137 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.705A pdb=" N LEU D 118 " --> pdb=" O GLY D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 152 through 159 removed outlier: 3.833A pdb=" N ARG D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 182 removed outlier: 3.565A pdb=" N ALA D 174 " --> pdb=" O MET D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 200 through 219 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 252 through 273 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 366 through 377 removed outlier: 3.979A pdb=" N VAL D 375 " --> pdb=" O MET D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 393 Processing helix chain 'D' and resid 394 through 405 removed outlier: 4.281A pdb=" N TRP D 398 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 442 through 447 Processing helix chain 'D' and resid 462 through 472 Processing helix chain 'D' and resid 493 through 503 Processing helix chain 'D' and resid 518 through 529 Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 550 through 555 removed outlier: 3.913A pdb=" N SER D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 569 Processing helix chain 'D' and resid 582 through 588 Processing helix chain 'D' and resid 591 through 593 No H-bonds generated for 'chain 'D' and resid 591 through 593' Processing helix chain 'D' and resid 601 through 609 Processing helix chain 'D' and resid 616 through 631 Processing helix chain 'D' and resid 633 through 653 Processing helix chain 'D' and resid 659 through 664 removed outlier: 3.533A pdb=" N VAL D 664 " --> pdb=" O VAL D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 689 Processing helix chain 'D' and resid 693 through 720 Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 737 through 746 removed outlier: 3.692A pdb=" N GLN D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 809 removed outlier: 3.622A pdb=" N HIS D 781 " --> pdb=" O PHE D 777 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY D 782 " --> pdb=" O ILE D 778 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 843 removed outlier: 3.516A pdb=" N LEU D 843 " --> pdb=" O GLU D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 879 Processing helix chain 'D' and resid 888 through 892 Processing helix chain 'D' and resid 900 through 904 Processing helix chain 'D' and resid 918 through 929 Processing helix chain 'D' and resid 930 through 932 No H-bonds generated for 'chain 'D' and resid 930 through 932' Processing helix chain 'D' and resid 952 through 962 removed outlier: 4.384A pdb=" N ALA D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 986 removed outlier: 3.695A pdb=" N ASP D 986 " --> pdb=" O GLU D 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 983 through 986' Processing helix chain 'D' and resid 1030 through 1038 removed outlier: 3.931A pdb=" N LEU D1035 " --> pdb=" O PRO D1031 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS D1036 " --> pdb=" O LYS D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1058 removed outlier: 3.835A pdb=" N GLN D1058 " --> pdb=" O VAL D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1075 removed outlier: 3.939A pdb=" N VAL D1067 " --> pdb=" O GLY D1063 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1108 Processing helix chain 'D' and resid 1122 through 1128 removed outlier: 3.717A pdb=" N LEU D1128 " --> pdb=" O THR D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1138 Processing helix chain 'D' and resid 1141 through 1153 Processing helix chain 'D' and resid 1161 through 1168 Processing helix chain 'D' and resid 1173 through 1176 Processing helix chain 'D' and resid 1177 through 1182 removed outlier: 3.625A pdb=" N LYS D1182 " --> pdb=" O MET D1178 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 15 through 34 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'G' and resid 118 through 126 removed outlier: 4.360A pdb=" N TYR G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 154 removed outlier: 3.903A pdb=" N ASN G 142 " --> pdb=" O LEU G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 177 removed outlier: 4.335A pdb=" N ILE G 164 " --> pdb=" O PHE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 195 removed outlier: 4.008A pdb=" N ILE G 194 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG G 195 " --> pdb=" O TRP G 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 195' Processing helix chain 'G' and resid 196 through 204 removed outlier: 3.700A pdb=" N ASP G 204 " --> pdb=" O ARG G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 304 removed outlier: 3.536A pdb=" N ALA G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS G 300 " --> pdb=" O TYR G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 311 Processing helix chain 'G' and resid 313 through 319 removed outlier: 3.671A pdb=" N ASN G 316 " --> pdb=" O ARG G 313 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL G 317 " --> pdb=" O GLU G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 338 Processing helix chain 'G' and resid 342 through 354 removed outlier: 4.286A pdb=" N ILE G 346 " --> pdb=" O THR G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 370 removed outlier: 3.613A pdb=" N ASP G 368 " --> pdb=" O LYS G 364 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 9 Processing helix chain 'H' and resid 22 through 37 removed outlier: 3.647A pdb=" N LYS H 37 " --> pdb=" O ALA H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 93 Processing helix chain 'L' and resid 7 through 13 removed outlier: 3.588A pdb=" N GLU L 13 " --> pdb=" O GLU L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 44 Processing helix chain 'L' and resid 51 through 65 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 83 through 92 removed outlier: 3.986A pdb=" N LEU L 87 " --> pdb=" O PRO L 83 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU L 89 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU L 90 " --> pdb=" O GLN L 86 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR L 91 " --> pdb=" O LEU L 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 29 through 38 Processing helix chain 'E' and resid 51 through 61 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14 removed outlier: 6.734A pdb=" N LYS A 22 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE A 14 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE A 20 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR A 191 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 6.569A pdb=" N GLN A 143 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL A 53 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 145 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA A 51 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 14 removed outlier: 4.508A pdb=" N ILE B 14 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 20 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LYS B 22 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL B 198 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL B 24 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 196 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU B 26 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU B 194 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 113 removed outlier: 4.294A pdb=" N VAL B 138 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE B 56 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AB2, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AB3, first strand: chain 'C' and resid 4 through 7 removed outlier: 7.100A pdb=" N ALA C 988 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ARG C 15 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 62 through 68 removed outlier: 6.975A pdb=" N LYS C 95 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY C 114 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL C 94 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE C 112 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL C 96 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ASP C 110 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU C 98 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASP C 108 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 410 removed outlier: 6.603A pdb=" N SER C 136 " --> pdb=" O SER C 487 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 144 through 145 removed outlier: 3.765A pdb=" N ALA C 160 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 170 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 345 through 350 Processing sheet with id=AB9, first strand: chain 'C' and resid 536 through 537 removed outlier: 5.395A pdb=" N ARG C 560 " --> pdb=" O ARG C 549 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 536 through 537 Processing sheet with id=AC2, first strand: chain 'C' and resid 591 through 592 Processing sheet with id=AC3, first strand: chain 'C' and resid 674 through 675 removed outlier: 6.447A pdb=" N VAL C 674 " --> pdb=" O LEU C 742 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 727 " --> pdb=" O ASP C 744 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 707 through 711 removed outlier: 6.818A pdb=" N ASN C 689 " --> pdb=" O VAL C 685 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL C 685 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP C 691 " --> pdb=" O GLU C 683 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 749 Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 763 removed outlier: 7.211A pdb=" N ILE C 775 " --> pdb=" O SER C 936 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE C 938 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET C 777 " --> pdb=" O ILE C 938 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 805 through 806 removed outlier: 6.463A pdb=" N ASP C 801 " --> pdb=" O VAL C 905 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL C 905 " --> pdb=" O ASP C 801 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ASN C 906 " --> pdb=" O ASN C 894 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN C 894 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 908 " --> pdb=" O VAL C 892 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL C 892 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG C 910 " --> pdb=" O VAL C 890 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL C 890 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYR C 912 " --> pdb=" O HIS C 888 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 808 through 809 Processing sheet with id=AC9, first strand: chain 'C' and resid 841 through 843 removed outlier: 7.036A pdb=" N LEU C 877 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1073 through 1075 removed outlier: 3.714A pdb=" N GLN C1073 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS D 334 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1143 through 1145 removed outlier: 3.573A pdb=" N MET D 10 " --> pdb=" O ASP D1156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 93 through 102 removed outlier: 9.812A pdb=" N LEU D 97 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 10.288A pdb=" N ALA D 99 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL D 230 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 339 through 346 removed outlier: 7.592A pdb=" N ILE D 436 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 343 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU D 438 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL D 345 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS D 355 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 431 " --> pdb=" O CYS D 355 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU D 357 " --> pdb=" O VAL D 431 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 515 through 516 removed outlier: 4.259A pdb=" N LEU D 557 " --> pdb=" O LEU D 596 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 813 through 815 Processing sheet with id=AD7, first strand: chain 'D' and resid 825 through 826 removed outlier: 4.526A pdb=" N PHE D 847 " --> pdb=" O ARG D 887 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG D 846 " --> pdb=" O ILE D 868 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 829 through 831 removed outlier: 6.621A pdb=" N LEU D 829 " --> pdb=" O ILE D 836 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 852 through 853 removed outlier: 4.046A pdb=" N VAL D 862 " --> pdb=" O VAL D 852 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 977 through 981 Processing sheet with id=AE2, first strand: chain 'D' and resid 1077 through 1079 Processing sheet with id=AE3, first strand: chain 'H' and resid 56 through 61 removed outlier: 6.836A pdb=" N VAL H 67 " --> pdb=" O GLU H 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 69 through 70 Processing sheet with id=AE5, first strand: chain 'E' and resid 43 through 50 removed outlier: 5.295A pdb=" N ILE E 44 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN E 8 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE E 2 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N LEU E 67 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N TYR E 24 " --> pdb=" O LEU E 67 " (cutoff:3.500A) 997 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.70 Time building geometry restraints manager: 12.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 25976 1.03 - 1.23: 75 1.23 - 1.42: 10513 1.42 - 1.62: 15416 1.62 - 1.81: 164 Bond restraints: 52144 Sorted by residual: bond pdb=" N ASN G 113 " pdb=" CA ASN G 113 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N GLU B 5 " pdb=" CA GLU B 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N THR C 2 " pdb=" CA THR C 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N GLU A 5 " pdb=" CA GLU A 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" CB PRO C 164 " pdb=" CG PRO C 164 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.88e+00 ... (remaining 52139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.41: 94527 7.41 - 14.83: 9 14.83 - 22.24: 0 22.24 - 29.66: 2 29.66 - 37.07: 4 Bond angle restraints: 94542 Sorted by residual: angle pdb=" C LEU E 69 " pdb=" CA LEU E 69 " pdb=" HA LEU E 69 " ideal model delta sigma weight residual 109.00 71.93 37.07 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C GLN L 92 " pdb=" CA GLN L 92 " pdb=" HA GLN L 92 " ideal model delta sigma weight residual 109.00 73.43 35.57 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N GLN L 92 " pdb=" CA GLN L 92 " pdb=" HA GLN L 92 " ideal model delta sigma weight residual 110.00 74.94 35.06 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N LEU E 69 " pdb=" CA LEU E 69 " pdb=" HA LEU E 69 " ideal model delta sigma weight residual 110.00 76.81 33.19 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CB GLN L 92 " pdb=" CA GLN L 92 " pdb=" HA GLN L 92 " ideal model delta sigma weight residual 109.00 79.66 29.34 3.00e+00 1.11e-01 9.56e+01 ... (remaining 94537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 20885 17.93 - 35.85: 2296 35.85 - 53.78: 773 53.78 - 71.70: 189 71.70 - 89.63: 66 Dihedral angle restraints: 24209 sinusoidal: 13626 harmonic: 10583 Sorted by residual: dihedral pdb=" CA LYS C1039 " pdb=" C LYS C1039 " pdb=" N LEU C1040 " pdb=" CA LEU C1040 " ideal model delta harmonic sigma weight residual -180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ARG D 50 " pdb=" C ARG D 50 " pdb=" N ILE D 51 " pdb=" CA ILE D 51 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CB CYS D 62 " pdb=" SG CYS D 62 " pdb=" SG CYS D 78 " pdb=" CB CYS D 78 " ideal model delta sinusoidal sigma weight residual -86.00 -122.70 36.70 1 1.00e+01 1.00e-02 1.90e+01 ... (remaining 24206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3747 0.094 - 0.187: 241 0.187 - 0.281: 1 0.281 - 0.374: 0 0.374 - 0.468: 2 Chirality restraints: 3991 Sorted by residual: chirality pdb=" CA LEU E 69 " pdb=" N LEU E 69 " pdb=" C LEU E 69 " pdb=" CB LEU E 69 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CA GLN L 92 " pdb=" N GLN L 92 " pdb=" C GLN L 92 " pdb=" CB GLN L 92 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CA PRO D1113 " pdb=" N PRO D1113 " pdb=" C PRO D1113 " pdb=" CB PRO D1113 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 3988 not shown) Planarity restraints: 7716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 190 " -0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO C 191 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 359 " 0.053 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO G 360 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO G 360 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 360 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 31 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO L 32 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO L 32 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 32 " 0.035 5.00e-02 4.00e+02 ... (remaining 7713 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 1436 2.11 - 2.73: 94787 2.73 - 3.35: 155341 3.35 - 3.98: 199521 3.98 - 4.60: 313461 Nonbonded interactions: 764546 Sorted by model distance: nonbonded pdb=" OE1 GLU C 25 " pdb=" H GLU C 25 " model vdw 1.482 2.450 nonbonded pdb=" OE1 GLN D 951 " pdb=" H GLN D 951 " model vdw 1.568 2.450 nonbonded pdb="HE21 GLN D 553 " pdb=" OD1 ASP D 592 " model vdw 1.587 2.450 nonbonded pdb=" H GLN L 92 " pdb=" HA GLN L 92 " model vdw 1.593 1.816 nonbonded pdb=" O GLN G 196 " pdb=" HG1 THR G 199 " model vdw 1.607 2.450 ... (remaining 764541 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' selection = chain 'B' } 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=0.00 max=1.00 mean=0.99 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.690 Extract box with map and model: 1.430 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 82.500 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 0.085 26154 Z= 0.262 Angle : 0.558 11.945 35315 Z= 0.293 Chirality : 0.044 0.468 3991 Planarity : 0.004 0.082 4603 Dihedral : 17.702 88.130 10022 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.11 % Favored : 92.55 % Rotamer: Outliers : 0.32 % Allowed : 26.70 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3233 helix: 0.81 (0.16), residues: 1091 sheet: -0.78 (0.27), residues: 356 loop : -1.00 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 199 HIS 0.012 0.001 HIS D 176 PHE 0.015 0.001 PHE D 450 TYR 0.014 0.001 TYR D 500 ARG 0.009 0.000 ARG D1144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 366 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 357 time to evaluate : 2.978 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: symmetry clash REVERT: A 215 LYS cc_start: 0.8360 (mttm) cc_final: 0.8085 (mttp) REVERT: C 185 ASP cc_start: 0.7106 (t0) cc_final: 0.6751 (t0) REVERT: D 217 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7821 (ttm170) REVERT: D 1095 ASP cc_start: 0.7653 (m-30) cc_final: 0.7431 (t0) REVERT: E 38 LYS cc_start: 0.8442 (ptmt) cc_final: 0.7969 (ptmt) outliers start: 9 outliers final: 5 residues processed: 361 average time/residue: 2.2592 time to fit residues: 962.2429 Evaluate side-chains 337 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 332 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 349 ILE Chi-restraints excluded: chain H residue 73 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 187 GLN C 441 ASN ** C 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.177651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130475 restraints weight = 90035.722| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.07 r_work: 0.3376 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26154 Z= 0.249 Angle : 0.572 10.594 35315 Z= 0.305 Chirality : 0.044 0.464 3991 Planarity : 0.004 0.069 4603 Dihedral : 4.912 56.292 3587 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.46 % Favored : 93.20 % Rotamer: Outliers : 2.21 % Allowed : 26.45 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3233 helix: 0.96 (0.16), residues: 1088 sheet: -0.95 (0.28), residues: 335 loop : -1.05 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.012 0.001 HIS D 176 PHE 0.012 0.001 PHE D 450 TYR 0.014 0.001 TYR D 155 ARG 0.006 0.000 ARG C 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 423 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 361 time to evaluate : 3.023 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: A 166 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8698 (pt) REVERT: A 215 LYS cc_start: 0.8293 (mttm) cc_final: 0.8010 (mttp) REVERT: C 185 ASP cc_start: 0.7244 (t0) cc_final: 0.6831 (t0) REVERT: C 862 HIS cc_start: 0.3725 (OUTLIER) cc_final: 0.3502 (m-70) REVERT: D 217 ARG cc_start: 0.8400 (ttm170) cc_final: 0.8146 (ttm170) REVERT: D 427 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: D 1095 ASP cc_start: 0.7887 (m-30) cc_final: 0.7519 (t0) REVERT: G 169 MET cc_start: 0.7504 (ttm) cc_final: 0.7266 (ttm) REVERT: G 196 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6955 (pt0) REVERT: G 362 ARG cc_start: 0.4239 (mtp180) cc_final: 0.2775 (mtp-110) REVERT: L 22 GLU cc_start: 0.5036 (OUTLIER) cc_final: 0.4756 (tm-30) REVERT: E 38 LYS cc_start: 0.8440 (ptmt) cc_final: 0.7680 (ptmt) outliers start: 62 outliers final: 24 residues processed: 402 average time/residue: 2.1698 time to fit residues: 1038.2225 Evaluate side-chains 359 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 330 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 862 HIS Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 1143 THR Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 196 GLN Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 349 ILE Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 81 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 164 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN C 359 GLN C 600 ASN ** C 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 HIS C1093 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.176764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129546 restraints weight = 90655.981| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.94 r_work: 0.3386 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26154 Z= 0.346 Angle : 0.590 10.736 35315 Z= 0.311 Chirality : 0.045 0.471 3991 Planarity : 0.004 0.064 4603 Dihedral : 5.022 53.071 3587 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.93 % Favored : 92.73 % Rotamer: Outliers : 2.57 % Allowed : 26.84 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3233 helix: 0.91 (0.16), residues: 1088 sheet: -1.07 (0.27), residues: 348 loop : -1.17 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 885 HIS 0.006 0.001 HIS D 176 PHE 0.012 0.001 PHE D 450 TYR 0.012 0.001 TYR D 500 ARG 0.009 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 343 time to evaluate : 3.513 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: A 215 LYS cc_start: 0.8281 (mttm) cc_final: 0.8002 (mttp) REVERT: B 118 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7763 (p) REVERT: C 185 ASP cc_start: 0.7287 (t0) cc_final: 0.6832 (t0) REVERT: C 1149 GLU cc_start: 0.3669 (OUTLIER) cc_final: 0.1623 (tp30) REVERT: D 217 ARG cc_start: 0.8397 (ttm170) cc_final: 0.8181 (ttm110) REVERT: D 427 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: D 1095 ASP cc_start: 0.7855 (m-30) cc_final: 0.7480 (t0) REVERT: G 362 ARG cc_start: 0.4527 (OUTLIER) cc_final: 0.3553 (mtp85) REVERT: H 41 LYS cc_start: 0.6990 (mmtt) cc_final: 0.6728 (tptt) REVERT: L 22 GLU cc_start: 0.4992 (OUTLIER) cc_final: 0.4743 (tm-30) REVERT: E 38 LYS cc_start: 0.8432 (ptmt) cc_final: 0.7675 (ptmt) outliers start: 72 outliers final: 37 residues processed: 390 average time/residue: 2.2166 time to fit residues: 1033.4590 Evaluate side-chains 370 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 328 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1121 GLU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 608 GLN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 1143 THR Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 349 ILE Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 60 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 192 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 316 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 301 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 chunk 254 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 187 GLN C 600 ASN ** C 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.180198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.133728 restraints weight = 90182.814| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.94 r_work: 0.3403 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26154 Z= 0.250 Angle : 0.559 10.666 35315 Z= 0.294 Chirality : 0.044 0.465 3991 Planarity : 0.004 0.062 4603 Dihedral : 4.954 52.904 3587 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.40 % Favored : 93.26 % Rotamer: Outliers : 2.64 % Allowed : 26.77 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3233 helix: 1.00 (0.17), residues: 1082 sheet: -1.07 (0.28), residues: 338 loop : -1.13 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 39 HIS 0.005 0.001 HIS D 176 PHE 0.022 0.001 PHE G 160 TYR 0.012 0.001 TYR D 500 ARG 0.006 0.000 ARG C 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 423 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 349 time to evaluate : 3.133 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: A 166 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8668 (pt) REVERT: A 215 LYS cc_start: 0.8257 (mttm) cc_final: 0.8023 (mttp) REVERT: B 118 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7755 (p) REVERT: B 126 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.6988 (t-90) REVERT: C 185 ASP cc_start: 0.7380 (t0) cc_final: 0.6868 (t0) REVERT: C 793 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7895 (mm-30) REVERT: C 1149 GLU cc_start: 0.3675 (OUTLIER) cc_final: 0.1625 (tp30) REVERT: D 217 ARG cc_start: 0.8440 (ttm170) cc_final: 0.8201 (ttm110) REVERT: D 427 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: D 1095 ASP cc_start: 0.7814 (m-30) cc_final: 0.7460 (t0) REVERT: G 293 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6786 (t-90) REVERT: G 362 ARG cc_start: 0.4571 (OUTLIER) cc_final: 0.3839 (mtp180) REVERT: H 41 LYS cc_start: 0.7035 (mmtt) cc_final: 0.6771 (tptt) REVERT: L 22 GLU cc_start: 0.4978 (OUTLIER) cc_final: 0.4745 (tm-30) REVERT: L 35 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6879 (tm-30) REVERT: L 39 GLU cc_start: 0.6898 (pt0) cc_final: 0.6424 (pt0) REVERT: E 38 LYS cc_start: 0.8404 (ptmt) cc_final: 0.7643 (ptmt) outliers start: 74 outliers final: 40 residues processed: 403 average time/residue: 2.0734 time to fit residues: 1001.3622 Evaluate side-chains 379 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 331 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 1143 THR Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 349 ILE Chi-restraints excluded: chain G residue 361 SER Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 81 TRP Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 60 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 224 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 118 optimal weight: 0.0570 chunk 180 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 211 optimal weight: 2.9990 chunk 309 optimal weight: 0.0980 chunk 269 optimal weight: 0.9980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN C 600 ASN D 585 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.183598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138766 restraints weight = 90172.603| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.87 r_work: 0.3444 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26154 Z= 0.159 Angle : 0.530 10.624 35315 Z= 0.277 Chirality : 0.043 0.459 3991 Planarity : 0.004 0.063 4603 Dihedral : 4.733 52.809 3585 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.03 % Favored : 93.60 % Rotamer: Outliers : 2.46 % Allowed : 26.95 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3233 helix: 1.21 (0.17), residues: 1076 sheet: -0.99 (0.28), residues: 342 loop : -0.99 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 39 HIS 0.004 0.001 HIS D 176 PHE 0.015 0.001 PHE D1099 TYR 0.013 0.001 TYR D 500 ARG 0.006 0.000 ARG C 429 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 429 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 360 time to evaluate : 3.003 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: symmetry clash REVERT: A 166 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8642 (pt) REVERT: A 215 LYS cc_start: 0.8179 (mttm) cc_final: 0.7911 (mttp) REVERT: C 185 ASP cc_start: 0.7278 (t0) cc_final: 0.6825 (t0) REVERT: C 1149 GLU cc_start: 0.3581 (OUTLIER) cc_final: 0.1518 (tp30) REVERT: D 11 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8458 (t0) REVERT: D 217 ARG cc_start: 0.8421 (ttm170) cc_final: 0.8163 (ttm110) REVERT: D 427 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: D 1057 MET cc_start: 0.7791 (mtp) cc_final: 0.7498 (mtm) REVERT: D 1095 ASP cc_start: 0.7717 (m-30) cc_final: 0.7365 (t0) REVERT: G 193 TRP cc_start: 0.7173 (m100) cc_final: 0.6969 (m100) REVERT: G 362 ARG cc_start: 0.4493 (OUTLIER) cc_final: 0.3476 (mtp180) REVERT: L 35 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6813 (tm-30) REVERT: E 38 LYS cc_start: 0.8363 (ptmt) cc_final: 0.7607 (ptmt) outliers start: 69 outliers final: 33 residues processed: 410 average time/residue: 2.0778 time to fit residues: 1016.8591 Evaluate side-chains 374 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 336 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 862 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1143 THR Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 349 ILE Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 81 TRP Chi-restraints excluded: chain E residue 60 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 49 optimal weight: 6.9990 chunk 160 optimal weight: 0.0000 chunk 257 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 187 GLN C 600 ASN ** D 585 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 = 0.4153 r_free = 0.4153 target = 0.181699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136356 restraints weight = 90176.755| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.99 r_work: 0.3423 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26154 Z= 0.199 Angle : 0.535 10.571 35315 Z= 0.280 Chirality : 0.043 0.466 3991 Planarity : 0.004 0.060 4603 Dihedral : 4.706 52.512 3585 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.12 % Favored : 93.50 % Rotamer: Outliers : 2.25 % Allowed : 27.38 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3233 helix: 1.20 (0.17), residues: 1091 sheet: -1.04 (0.27), residues: 348 loop : -0.99 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 199 HIS 0.004 0.001 HIS D 176 PHE 0.022 0.001 PHE G 160 TYR 0.013 0.001 TYR C 76 ARG 0.007 0.000 ARG C 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 413 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 350 time to evaluate : 3.021 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8224 (mttm) cc_final: 0.7970 (mttp) REVERT: B 118 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7675 (p) REVERT: C 185 ASP cc_start: 0.7319 (t0) cc_final: 0.6842 (t0) REVERT: C 1149 GLU cc_start: 0.3640 (OUTLIER) cc_final: 0.1562 (tp30) REVERT: D 11 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (t0) REVERT: D 217 ARG cc_start: 0.8441 (ttm170) cc_final: 0.8205 (ttm110) REVERT: D 427 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: D 1095 ASP cc_start: 0.7784 (m-30) cc_final: 0.7451 (t0) REVERT: G 293 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6799 (t-90) REVERT: G 362 ARG cc_start: 0.4554 (OUTLIER) cc_final: 0.2832 (mtp-110) REVERT: L 35 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6761 (tm-30) REVERT: L 39 GLU cc_start: 0.6739 (pt0) cc_final: 0.6350 (pt0) REVERT: E 38 LYS cc_start: 0.8447 (ptmt) cc_final: 0.7705 (ptmt) outliers start: 63 outliers final: 37 residues processed: 396 average time/residue: 2.1059 time to fit residues: 1000.0970 Evaluate side-chains 379 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 336 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 862 HIS Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1121 GLU Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 1143 THR Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 349 ILE Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 81 TRP Chi-restraints excluded: chain E residue 60 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 224 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 243 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 316 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 137 optimal weight: 0.2980 chunk 207 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN C 600 ASN D 585 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.181783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137307 restraints weight = 90228.803| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.87 r_work: 0.3429 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26154 Z= 0.183 Angle : 0.531 10.686 35315 Z= 0.277 Chirality : 0.043 0.464 3991 Planarity : 0.004 0.061 4603 Dihedral : 4.664 53.051 3585 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.06 % Favored : 93.57 % Rotamer: Outliers : 2.17 % Allowed : 27.45 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3233 helix: 1.25 (0.17), residues: 1085 sheet: -1.00 (0.28), residues: 344 loop : -0.97 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 199 HIS 0.004 0.001 HIS C 678 PHE 0.013 0.001 PHE D 450 TYR 0.013 0.001 TYR D 500 ARG 0.009 0.000 ARG C 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 354 time to evaluate : 3.107 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: symmetry clash REVERT: A 215 LYS cc_start: 0.8210 (mttm) cc_final: 0.7945 (mttp) REVERT: B 118 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7675 (p) REVERT: C 185 ASP cc_start: 0.7324 (t0) cc_final: 0.6857 (t0) REVERT: C 1149 GLU cc_start: 0.3623 (OUTLIER) cc_final: 0.1554 (tp30) REVERT: D 11 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8477 (t0) REVERT: D 187 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7827 (mp0) REVERT: D 217 ARG cc_start: 0.8445 (ttm170) cc_final: 0.8206 (ttm110) REVERT: D 427 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: D 1058 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7999 (mm-40) REVERT: D 1095 ASP cc_start: 0.7769 (m-30) cc_final: 0.7442 (t0) REVERT: G 293 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.6829 (t-90) REVERT: G 362 ARG cc_start: 0.4687 (OUTLIER) cc_final: 0.2936 (mtp-110) REVERT: L 35 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6729 (tm-30) REVERT: L 39 GLU cc_start: 0.6772 (pt0) cc_final: 0.6379 (pt0) REVERT: E 38 LYS cc_start: 0.8423 (ptmt) cc_final: 0.7700 (ptmt) outliers start: 61 outliers final: 48 residues processed: 399 average time/residue: 2.1959 time to fit residues: 1058.2046 Evaluate side-chains 388 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 334 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 862 HIS Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1121 GLU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1143 THR Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 349 ILE Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 361 SER Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 81 TRP Chi-restraints excluded: chain E residue 60 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 229 optimal weight: 0.2980 chunk 286 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 118 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 252 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 187 GLN C 269 ASN C 600 ASN D 478 ASN D 585 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.180603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135182 restraints weight = 90316.999| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.89 r_work: 0.3444 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26154 Z= 0.166 Angle : 0.526 10.703 35315 Z= 0.273 Chirality : 0.043 0.464 3991 Planarity : 0.004 0.076 4603 Dihedral : 4.593 53.423 3585 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.82 % Favored : 93.81 % Rotamer: Outliers : 2.10 % Allowed : 27.81 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3233 helix: 1.31 (0.17), residues: 1085 sheet: -0.97 (0.28), residues: 344 loop : -0.93 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 199 HIS 0.005 0.001 HIS C 678 PHE 0.014 0.001 PHE D1099 TYR 0.019 0.001 TYR C 76 ARG 0.012 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 406 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 347 time to evaluate : 3.044 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: symmetry clash revert: symmetry clash REVERT: A 107 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8534 (p) REVERT: A 215 LYS cc_start: 0.8190 (mttm) cc_final: 0.7922 (mttp) REVERT: B 118 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7645 (p) REVERT: B 140 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8725 (mt) REVERT: C 185 ASP cc_start: 0.7323 (t0) cc_final: 0.6867 (t0) REVERT: C 1149 GLU cc_start: 0.3544 (OUTLIER) cc_final: 0.1542 (tp30) REVERT: D 11 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8455 (t0) REVERT: D 217 ARG cc_start: 0.8430 (ttm170) cc_final: 0.8183 (ttm110) REVERT: D 427 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: D 1058 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7885 (mm-40) REVERT: D 1095 ASP cc_start: 0.7727 (m-30) cc_final: 0.7400 (t0) REVERT: G 193 TRP cc_start: 0.7372 (m100) cc_final: 0.7050 (m100) REVERT: G 293 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.6773 (t-90) REVERT: G 362 ARG cc_start: 0.4637 (OUTLIER) cc_final: 0.3789 (mtp85) REVERT: H 73 TYR cc_start: 0.4408 (OUTLIER) cc_final: 0.2165 (t80) REVERT: L 35 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6729 (tm-30) REVERT: L 39 GLU cc_start: 0.6732 (pt0) cc_final: 0.6354 (pt0) REVERT: E 38 LYS cc_start: 0.8397 (ptmt) cc_final: 0.7671 (ptmt) outliers start: 59 outliers final: 33 residues processed: 392 average time/residue: 2.1454 time to fit residues: 1010.1703 Evaluate side-chains 382 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 340 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 862 HIS Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 1143 THR Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 349 ILE Chi-restraints excluded: chain G residue 361 SER Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 81 TRP Chi-restraints excluded: chain E residue 60 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 223 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 199 optimal weight: 0.4980 chunk 189 optimal weight: 0.0770 chunk 138 optimal weight: 1.9990 chunk 118 optimal weight: 0.0170 chunk 185 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 229 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN C 600 ASN D 585 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.181293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135002 restraints weight = 90150.814| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.07 r_work: 0.3458 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26154 Z= 0.160 Angle : 0.523 10.711 35315 Z= 0.272 Chirality : 0.043 0.464 3991 Planarity : 0.004 0.075 4603 Dihedral : 4.543 53.659 3585 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.47 % Favored : 94.18 % Rotamer: Outliers : 2.00 % Allowed : 28.24 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3233 helix: 1.35 (0.17), residues: 1086 sheet: -0.93 (0.28), residues: 343 loop : -0.90 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 199 HIS 0.005 0.001 HIS C 678 PHE 0.033 0.001 PHE G 160 TYR 0.012 0.001 TYR D 500 ARG 0.011 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 396 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 3.016 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8526 (p) REVERT: A 215 LYS cc_start: 0.8184 (mttm) cc_final: 0.7919 (mttp) REVERT: B 118 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7666 (p) REVERT: B 140 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8728 (mt) REVERT: C 185 ASP cc_start: 0.7334 (t0) cc_final: 0.6879 (t0) REVERT: D 11 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8436 (t0) REVERT: D 1095 ASP cc_start: 0.7720 (m-30) cc_final: 0.7398 (t0) REVERT: G 196 GLN cc_start: 0.7408 (pp30) cc_final: 0.7129 (pt0) REVERT: G 293 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.6812 (t-90) REVERT: G 362 ARG cc_start: 0.4566 (OUTLIER) cc_final: 0.3717 (mtp85) REVERT: H 73 TYR cc_start: 0.4383 (OUTLIER) cc_final: 0.2359 (t80) REVERT: L 35 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6706 (tm-30) REVERT: E 38 LYS cc_start: 0.8407 (ptmt) cc_final: 0.7684 (ptmt) outliers start: 56 outliers final: 36 residues processed: 384 average time/residue: 2.0951 time to fit residues: 971.8253 Evaluate side-chains 376 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 333 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 862 HIS Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 264 ARG Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1143 THR Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 349 ILE Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 361 SER Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 81 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 259 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 chunk 273 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 254 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 187 GLN C 600 ASN D 585 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.182654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137770 restraints weight = 90197.279| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.97 r_work: 0.3450 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26154 Z= 0.189 Angle : 0.530 10.715 35315 Z= 0.276 Chirality : 0.043 0.466 3991 Planarity : 0.004 0.075 4603 Dihedral : 4.548 53.987 3585 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.66 % Favored : 94.00 % Rotamer: Outliers : 1.82 % Allowed : 28.45 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3233 helix: 1.34 (0.17), residues: 1088 sheet: -0.97 (0.28), residues: 344 loop : -0.89 (0.15), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 193 HIS 0.005 0.001 HIS D 632 PHE 0.031 0.001 PHE G 160 TYR 0.023 0.001 TYR C 76 ARG 0.012 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 395 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 344 time to evaluate : 3.072 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8547 (p) REVERT: A 166 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8641 (pt) REVERT: A 215 LYS cc_start: 0.8186 (mttm) cc_final: 0.7920 (mttp) REVERT: B 118 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7680 (p) REVERT: B 140 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8701 (mt) REVERT: C 185 ASP cc_start: 0.7337 (t0) cc_final: 0.6888 (t0) REVERT: C 879 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8594 (p) REVERT: D 7 PHE cc_start: 0.7615 (m-10) cc_final: 0.7400 (m-10) REVERT: D 1095 ASP cc_start: 0.7730 (m-30) cc_final: 0.7413 (t0) REVERT: G 193 TRP cc_start: 0.7402 (m100) cc_final: 0.7181 (m100) REVERT: G 196 GLN cc_start: 0.7426 (pp30) cc_final: 0.7181 (pt0) REVERT: G 293 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6806 (t-90) REVERT: G 362 ARG cc_start: 0.4632 (OUTLIER) cc_final: 0.3964 (ttt-90) REVERT: H 73 TYR cc_start: 0.4469 (OUTLIER) cc_final: 0.2261 (t80) REVERT: L 35 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6733 (tm-30) REVERT: E 38 LYS cc_start: 0.8411 (ptmt) cc_final: 0.7689 (ptmt) outliers start: 51 outliers final: 38 residues processed: 384 average time/residue: 2.1016 time to fit residues: 977.6189 Evaluate side-chains 387 residues out of total 2810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 341 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 862 HIS Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 264 ARG Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 1143 THR Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 349 ILE Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 361 SER Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 81 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 107 optimal weight: 1.9990 chunk 312 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 238 optimal weight: 0.0770 chunk 128 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 288 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN C 600 ASN D 585 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.182326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137576 restraints weight = 90217.681| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.93 r_work: 0.3445 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26154 Z= 0.208 Angle : 0.534 10.662 35315 Z= 0.278 Chirality : 0.043 0.466 3991 Planarity : 0.004 0.072 4603 Dihedral : 4.571 54.265 3585 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.03 % Favored : 93.63 % Rotamer: Outliers : 1.89 % Allowed : 28.34 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3233 helix: 1.32 (0.17), residues: 1093 sheet: -0.99 (0.28), residues: 345 loop : -0.89 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 193 HIS 0.004 0.001 HIS C 678 PHE 0.031 0.001 PHE G 160 TYR 0.014 0.001 TYR G 296 ARG 0.012 0.000 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30200.35 seconds wall clock time: 513 minutes 37.18 seconds (30817.18 seconds total)