Starting phenix.real_space_refine on Sat Jul 4 05:52:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vux_43543/07_2026/8vux_43543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vux_43543/07_2026/8vux_43543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vux_43543/07_2026/8vux_43543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vux_43543/07_2026/8vux_43543.map" model { file = "/net/cci-nas-00/data/ceres_data/8vux_43543/07_2026/8vux_43543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vux_43543/07_2026/8vux_43543.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3561 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 92 5.16 5 C 10464 2.51 5 N 2598 2.21 5 O 2817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15973 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7929 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 42, 'TRANS': 962} Chain breaks: 4 Chain: "B" Number of atoms: 7929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7929 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 42, 'TRANS': 962} Chain breaks: 4 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'1SY': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.14, per 1000 atoms: 0.20 Number of scatterers: 15973 At special positions: 0 Unit cell: (169.728, 113.984, 162.24, 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 92 16.00 P 2 15.00 O 2817 8.00 N 2598 7.00 C 10464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 32 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 32 " 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: 1.27 Conformation dependent library (CDL) restraints added in 677.7 milliseconds 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 6 sheets defined 71.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 3.673A pdb=" N GLY A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 30 through 58 removed outlier: 4.146A pdb=" N LEU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 51 - end of helix Processing helix chain 'A' and resid 68 through 99 removed outlier: 3.557A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 98 " --> pdb=" O TRP A 94 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.875A pdb=" N PHE A 106 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 130 removed outlier: 3.685A pdb=" N LEU A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 161 removed outlier: 3.653A pdb=" N LEU A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 189 Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.802A pdb=" N LEU A 227 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.654A pdb=" N LEU A 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 3.589A pdb=" N VAL A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Proline residue: A 255 - end of helix removed outlier: 3.606A pdb=" N THR A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 321 removed outlier: 4.276A pdb=" N VAL A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 331 through 355 removed outlier: 3.695A pdb=" N PHE A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 361 through 408 removed outlier: 3.670A pdb=" N PHE A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS A 386 " --> pdb=" O HIS A 382 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 434 Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.755A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 462 Proline residue: A 448 - end of helix Processing helix chain 'A' and resid 463 through 477 removed outlier: 4.279A pdb=" N LEU A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 572 Proline residue: A 557 - end of helix removed outlier: 3.596A pdb=" N ASP A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 599 removed outlier: 3.591A pdb=" N PHE A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 601 through 621 Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 735 through 744 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 755 through 759 removed outlier: 3.667A pdb=" N THR A 759 " --> pdb=" O GLY A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 784 Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 860 through 869 Processing helix chain 'A' and resid 974 through 1000 Processing helix chain 'A' and resid 1012 through 1044 Processing helix chain 'A' and resid 1088 through 1110 Processing helix chain 'A' and resid 1112 through 1118 Processing helix chain 'A' and resid 1119 through 1147 removed outlier: 4.156A pdb=" N ILE A1125 " --> pdb=" O PRO A1121 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A1139 " --> pdb=" O ALA A1135 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1161 removed outlier: 4.222A pdb=" N TYR A1152 " --> pdb=" O ARG A1148 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A1161 " --> pdb=" O GLU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1168 Processing helix chain 'A' and resid 1172 through 1221 Proline residue: A1191 - end of helix removed outlier: 3.537A pdb=" N VAL A1206 " --> pdb=" O ARG A1202 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A1221 " --> pdb=" O PHE A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1225 removed outlier: 3.519A pdb=" N LEU A1225 " --> pdb=" O ARG A1222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1222 through 1225' Processing helix chain 'A' and resid 1226 through 1251 removed outlier: 3.774A pdb=" N SER A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A1238 " --> pdb=" O VAL A1234 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 removed outlier: 4.043A pdb=" N SER B 8 " --> pdb=" O ARG B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.532A pdb=" N TRP B 22 " --> pdb=" O TRP B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 58 removed outlier: 4.019A pdb=" N LEU B 38 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL B 39 " --> pdb=" O ASN B 35 " (cutoff:3.500A) Proline residue: B 42 - end of helix removed outlier: 3.569A pdb=" N CYS B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 3.754A pdb=" N SER B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 98 removed outlier: 3.868A pdb=" N LEU B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 130 Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 137 through 161 removed outlier: 3.631A pdb=" N LEU B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 189 Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.665A pdb=" N SER B 211 " --> pdb=" O CYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.591A pdb=" N ARG B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.970A pdb=" N ASP B 240 " --> pdb=" O GLU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 313 through 321 removed outlier: 4.265A pdb=" N LYS B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 328 Processing helix chain 'B' and resid 329 through 354 removed outlier: 3.998A pdb=" N ILE B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) Proline residue: B 343 - end of helix removed outlier: 3.510A pdb=" N ASN B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 406 removed outlier: 4.304A pdb=" N GLY B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR B 364 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 369 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS B 386 " --> pdb=" O HIS B 382 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 404 " --> pdb=" O ILE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 423 removed outlier: 3.529A pdb=" N GLU B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 423' Processing helix chain 'B' and resid 423 through 433 Processing helix chain 'B' and resid 435 through 442 removed outlier: 3.962A pdb=" N THR B 439 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 463 removed outlier: 3.643A pdb=" N SER B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Proline residue: B 448 - end of helix removed outlier: 3.510A pdb=" N VAL B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 477 removed outlier: 3.859A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 572 Proline residue: B 557 - end of helix removed outlier: 4.356A pdb=" N ASP B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 621 removed outlier: 3.504A pdb=" N ALA B 582 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE B 594 " --> pdb=" O ASN B 590 " (cutoff:3.500A) Proline residue: B 595 - end of helix Proline residue: B 600 - end of helix removed outlier: 4.186A pdb=" N ILE B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER B 604 " --> pdb=" O PRO B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 721 through 728 Processing helix chain 'B' and resid 733 through 743 removed outlier: 3.655A pdb=" N ILE B 741 " --> pdb=" O TYR B 737 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN B 742 " --> pdb=" O ARG B 738 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 753 removed outlier: 3.546A pdb=" N ILE B 752 " --> pdb=" O PRO B 748 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 784 Processing helix chain 'B' and resid 799 through 810 Processing helix chain 'B' and resid 815 through 820 removed outlier: 4.002A pdb=" N ASN B 819 " --> pdb=" O MET B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 859 Processing helix chain 'B' and resid 860 through 870 Processing helix chain 'B' and resid 974 through 1000 Processing helix chain 'B' and resid 1012 through 1044 Processing helix chain 'B' and resid 1088 through 1112 Processing helix chain 'B' and resid 1113 through 1117 Processing helix chain 'B' and resid 1118 through 1138 removed outlier: 3.542A pdb=" N LEU B1122 " --> pdb=" O ILE B1118 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE B1132 " --> pdb=" O PHE B1128 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG B1138 " --> pdb=" O VAL B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1147 removed outlier: 3.859A pdb=" N GLU B1144 " --> pdb=" O LEU B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1161 removed outlier: 3.976A pdb=" N TYR B1152 " --> pdb=" O ARG B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1168 Processing helix chain 'B' and resid 1172 through 1221 removed outlier: 3.723A pdb=" N VAL B1182 " --> pdb=" O SER B1178 " (cutoff:3.500A) Proline residue: B1191 - end of helix removed outlier: 4.049A pdb=" N PHE B1217 " --> pdb=" O PHE B1213 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B1218 " --> pdb=" O ALA B1214 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B1221 " --> pdb=" O PHE B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1226 through 1251 removed outlier: 3.727A pdb=" N SER B1237 " --> pdb=" O SER B1233 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU B1238 " --> pdb=" O VAL B1234 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN B1239 " --> pdb=" O SER B1235 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 664 through 669 removed outlier: 5.787A pdb=" N ILE A 664 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 668 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A 644 " --> pdb=" O ILE A 668 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 651 through 652 removed outlier: 3.552A pdb=" N THR A 652 " --> pdb=" O ASP A 696 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP A 696 " --> pdb=" O THR A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 709 removed outlier: 4.148A pdb=" N LEU A 790 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR A 789 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL A 825 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE A 791 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 674 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR A 826 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 676 " --> pdb=" O THR A 826 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE A 838 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET A 849 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A 840 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 667 through 669 removed outlier: 5.050A pdb=" N ALA B 649 " --> pdb=" O GLU B 699 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLU B 699 " --> pdb=" O ALA B 649 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE B 651 " --> pdb=" O LYS B 697 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LYS B 697 " --> pdb=" O PHE B 651 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 791 through 792 removed outlier: 3.637A pdb=" N PHE B 791 " --> pdb=" O ILE B 823 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU B 824 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 676 " --> pdb=" O LEU B 824 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 675 " --> pdb=" O VAL B 837 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 708 through 709 removed outlier: 3.877A pdb=" N ALA B 709 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 974 hydrogen bonds defined for protein. 2862 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2457 1.31 - 1.44: 4558 1.44 - 1.57: 9214 1.57 - 1.69: 4 1.69 - 1.82: 144 Bond restraints: 16377 Sorted by residual: bond pdb=" C36 1SY B1601 " pdb=" N42 1SY B1601 " ideal model delta sigma weight residual 1.357 1.496 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C40 1SY B1601 " pdb=" N39 1SY B1601 " ideal model delta sigma weight residual 1.304 1.437 -0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" C6 1SY B1601 " pdb=" N01 1SY B1601 " ideal model delta sigma weight residual 1.334 1.454 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C40 1SY B1601 " pdb=" N41 1SY B1601 " ideal model delta sigma weight residual 1.345 1.449 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C40 1SY B1601 " pdb=" N42 1SY B1601 " ideal model delta sigma weight residual 1.367 1.459 -0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 16372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 22192 4.09 - 8.18: 94 8.18 - 12.27: 12 12.27 - 16.37: 2 16.37 - 20.46: 4 Bond angle restraints: 22304 Sorted by residual: angle pdb=" C32 1SY B1601 " pdb=" N33 1SY B1601 " pdb=" C34 1SY B1601 " ideal model delta sigma weight residual 125.84 105.38 20.46 3.00e+00 1.11e-01 4.65e+01 angle pdb=" O19 1SY B1601 " pdb=" P18 1SY B1601 " pdb=" O44 1SY B1601 " ideal model delta sigma weight residual 123.21 104.74 18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" O29 1SY B1601 " pdb=" P27 1SY B1601 " pdb=" O30 1SY B1601 " ideal model delta sigma weight residual 123.47 106.72 16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" C32 1SY B1601 " pdb=" N33 1SY B1601 " pdb=" C36 1SY B1601 " ideal model delta sigma weight residual 128.83 145.50 -16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" C21 1SY B1601 " pdb=" O20 1SY B1601 " pdb=" P18 1SY B1601 " ideal model delta sigma weight residual 121.36 107.21 14.15 3.00e+00 1.11e-01 2.22e+01 ... (remaining 22299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.01: 8888 26.01 - 52.01: 765 52.01 - 78.02: 79 78.02 - 104.03: 24 104.03 - 130.03: 5 Dihedral angle restraints: 9761 sinusoidal: 3899 harmonic: 5862 Sorted by residual: dihedral pdb=" CA ILE B 65 " pdb=" C ILE B 65 " pdb=" N GLN B 66 " pdb=" CA GLN B 66 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" C25 1SY B1601 " pdb=" O26 1SY B1601 " pdb=" P27 1SY B1601 " pdb=" O28 1SY B1601 " ideal model delta sinusoidal sigma weight residual 96.37 -133.60 -130.03 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C25 1SY B1601 " pdb=" O26 1SY B1601 " pdb=" P27 1SY B1601 " pdb=" O29 1SY B1601 " ideal model delta sinusoidal sigma weight residual -150.39 -21.67 -128.72 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 9758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1985 0.045 - 0.091: 489 0.091 - 0.136: 110 0.136 - 0.181: 11 0.181 - 0.226: 3 Chirality restraints: 2598 Sorted by residual: chirality pdb=" C2' 1SY B1601 " pdb=" C1' 1SY B1601 " pdb=" C3' 1SY B1601 " pdb=" O2' 1SY B1601 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU A1199 " pdb=" CB LEU A1199 " pdb=" CD1 LEU A1199 " pdb=" CD2 LEU A1199 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A 224 " pdb=" N ILE A 224 " pdb=" C ILE A 224 " pdb=" CB ILE A 224 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.56e-01 ... (remaining 2595 not shown) Planarity restraints: 2739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 50 " -0.067 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO B 51 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 446 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C SER A 446 " 0.046 2.00e-02 2.50e+03 pdb=" O SER A 446 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 447 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 322 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 323 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.034 5.00e-02 4.00e+02 ... (remaining 2736 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 614 2.72 - 3.27: 16877 3.27 - 3.81: 26697 3.81 - 4.36: 28940 4.36 - 4.90: 50101 Nonbonded interactions: 123229 Sorted by model distance: nonbonded pdb=" OD1 ASP B 720 " pdb=" N SER B 721 " model vdw 2.176 3.120 nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASN A 71 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR A 53 " pdb=" OE2 GLU A 127 " model vdw 2.222 3.040 nonbonded pdb=" N GLN A 714 " pdb=" OE1 GLN A 714 " model vdw 2.261 3.120 nonbonded pdb=" O GLU A 864 " pdb=" OG1 THR A 868 " model vdw 2.293 3.040 ... (remaining 123224 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 1254) selection = (chain 'B' and resid 1 through 1254) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.660 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 0.139 16379 Z= 0.206 Angle : 0.728 20.457 22308 Z= 0.346 Chirality : 0.041 0.226 2598 Planarity : 0.005 0.099 2739 Dihedral : 18.502 130.033 5963 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.40 % Allowed : 32.40 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1990 helix: 1.26 (0.15), residues: 1282 sheet: 0.06 (0.58), residues: 80 loop : -1.38 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 230 TYR 0.024 0.001 TYR A1033 PHE 0.023 0.001 PHE A 6 TRP 0.013 0.001 TRP B1198 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.21 (16377) covalent geometry : angle 0.72770 / 0.35 (22304) SS BOND : bond 0.00449 / 0.22 ( 2) SS BOND : angle 2.06108 / 0.93 ( 4) hydrogen bonds : bond 0.12658 / 7.97 ( 974) hydrogen bonds : angle 5.44043 / 3.85 ( 2862) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7467 (t80) REVERT: A 456 TYR cc_start: 0.6762 (t80) cc_final: 0.6524 (t80) REVERT: A 1204 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 1250 MET cc_start: 0.6351 (ttt) cc_final: 0.5273 (mmt) outliers start: 7 outliers final: 4 residues processed: 169 average time/residue: 0.0938 time to fit residues: 25.3785 Evaluate side-chains 164 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 53 TYR Chi-restraints excluded: chain B residue 458 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN B 34 GLN B 362 GLN B 608 GLN ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.194728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126463 restraints weight = 22839.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130308 restraints weight = 12329.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132842 restraints weight = 9002.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134179 restraints weight = 7688.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134552 restraints weight = 7125.060| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16379 Z= 0.131 Angle : 0.593 12.900 22308 Z= 0.293 Chirality : 0.040 0.165 2598 Planarity : 0.004 0.061 2739 Dihedral : 8.834 90.400 2373 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.54 % Allowed : 29.83 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1990 helix: 1.57 (0.15), residues: 1310 sheet: 0.14 (0.61), residues: 70 loop : -1.47 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.024 0.001 TYR A1033 PHE 0.012 0.001 PHE A 6 TRP 0.011 0.001 TRP B1198 HIS 0.005 0.001 HIS B 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16377) covalent geometry : angle 0.59297 / 0.29 (22304) SS BOND : bond 0.00424 / 0.21 ( 2) SS BOND : angle 1.28214 / 0.55 ( 4) hydrogen bonds : bond 0.04440 / 2.89 ( 974) hydrogen bonds : angle 4.16099 / 2.94 ( 2862) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 384 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.8207 (t80) REVERT: A 608 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8072 (mp-120) REVERT: A 1204 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6902 (mm-30) REVERT: A 1236 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.6305 (m-10) REVERT: A 1250 MET cc_start: 0.6542 (ttt) cc_final: 0.5396 (mmt) REVERT: B 127 GLU cc_start: 0.7314 (tt0) cc_final: 0.7060 (tt0) REVERT: B 133 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: B 362 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7708 (mt0) REVERT: B 430 ASP cc_start: 0.8005 (m-30) cc_final: 0.7747 (m-30) REVERT: B 616 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8038 (mp) REVERT: B 1172 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6290 (tm-30) REVERT: B 1236 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6637 (m-10) outliers start: 62 outliers final: 30 residues processed: 212 average time/residue: 0.0865 time to fit residues: 30.0095 Evaluate side-chains 194 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 143 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN B 608 GLN ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.194859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130333 restraints weight = 23213.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.131608 restraints weight = 14661.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131312 restraints weight = 10572.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.131560 restraints weight = 10196.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131898 restraints weight = 10158.740| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16379 Z= 0.120 Angle : 0.576 11.911 22308 Z= 0.282 Chirality : 0.040 0.162 2598 Planarity : 0.004 0.057 2739 Dihedral : 7.660 74.556 2365 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.74 % Allowed : 29.09 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1990 helix: 1.74 (0.15), residues: 1316 sheet: 0.04 (0.60), residues: 70 loop : -1.42 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.024 0.001 TYR A1033 PHE 0.011 0.001 PHE B 329 TRP 0.012 0.001 TRP B 22 HIS 0.004 0.001 HIS B 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (16377) covalent geometry : angle 0.57558 / 0.28 (22304) SS BOND : bond 0.00685 / 0.33 ( 2) SS BOND : angle 2.03294 / 0.89 ( 4) hydrogen bonds : bond 0.04183 / 2.72 ( 974) hydrogen bonds : angle 3.98639 / 2.82 ( 2862) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 171 time to evaluate : 0.598 Fit side-chains REVERT: A 25 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7468 (t) REVERT: A 384 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8242 (t80) REVERT: A 608 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8115 (mp-120) REVERT: A 763 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: A 764 LYS cc_start: 0.7858 (mmtm) cc_final: 0.7180 (mmtp) REVERT: A 849 MET cc_start: -0.2011 (tpt) cc_final: -0.2506 (tpt) REVERT: A 1144 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: A 1236 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.6267 (m-10) REVERT: A 1250 MET cc_start: 0.6824 (ttt) cc_final: 0.5502 (mmt) REVERT: B 118 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7738 (mp) REVERT: B 133 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: B 430 ASP cc_start: 0.7916 (m-30) cc_final: 0.7698 (m-30) REVERT: B 616 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7996 (mp) REVERT: B 1236 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.6579 (m-10) outliers start: 83 outliers final: 45 residues processed: 232 average time/residue: 0.0943 time to fit residues: 35.3976 Evaluate side-chains 213 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 445 TRP Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1168 PHE Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1205 CYS Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1236 TYR Chi-restraints excluded: chain B residue 1238 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 41 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 189 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN B 608 GLN B 648 ASN ** B1186 GLN ** 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 = 0.4452 r_free = 0.4452 target = 0.195074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132600 restraints weight = 22840.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132611 restraints weight = 14161.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.132038 restraints weight = 10341.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132728 restraints weight = 10567.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132840 restraints weight = 9734.608| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16379 Z= 0.119 Angle : 0.579 11.816 22308 Z= 0.281 Chirality : 0.040 0.170 2598 Planarity : 0.004 0.056 2739 Dihedral : 7.046 59.533 2365 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.63 % Allowed : 29.60 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.20), residues: 1990 helix: 1.76 (0.15), residues: 1328 sheet: -0.04 (0.59), residues: 70 loop : -1.41 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.024 0.001 TYR A1033 PHE 0.014 0.001 PHE A 6 TRP 0.011 0.001 TRP B1198 HIS 0.004 0.001 HIS B 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16377) covalent geometry : angle 0.57921 / 0.28 (22304) SS BOND : bond 0.00424 / 0.21 ( 2) SS BOND : angle 1.39998 / 0.64 ( 4) hydrogen bonds : bond 0.03999 / 2.59 ( 974) hydrogen bonds : angle 3.90059 / 2.76 ( 2862) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 172 time to evaluate : 0.563 Fit side-chains REVERT: A 25 SER cc_start: 0.7652 (OUTLIER) cc_final: 0.7444 (t) REVERT: A 384 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8246 (t80) REVERT: A 608 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8104 (mp-120) REVERT: A 763 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: A 764 LYS cc_start: 0.7939 (mmtm) cc_final: 0.7583 (mmtp) REVERT: A 849 MET cc_start: -0.2105 (tpt) cc_final: -0.2608 (tpt) REVERT: A 1144 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: A 1236 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.6267 (m-10) REVERT: A 1250 MET cc_start: 0.6880 (ttt) cc_final: 0.5599 (mmt) REVERT: B 83 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8273 (mt) REVERT: B 118 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7798 (mp) REVERT: B 127 GLU cc_start: 0.7449 (tt0) cc_final: 0.7031 (tt0) REVERT: B 133 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: B 616 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7981 (mp) REVERT: B 695 MET cc_start: 0.4340 (mmt) cc_final: 0.3670 (mmt) REVERT: B 1015 ARG cc_start: 0.6292 (mmt180) cc_final: 0.6061 (mmt180) REVERT: B 1187 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8413 (ttmt) REVERT: B 1236 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6587 (m-10) outliers start: 81 outliers final: 48 residues processed: 232 average time/residue: 0.0971 time to fit residues: 36.2661 Evaluate side-chains 216 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 156 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 445 TRP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1236 TYR Chi-restraints excluded: chain B residue 1238 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 14 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 155 optimal weight: 0.0470 chunk 33 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 0.4980 chunk 114 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.196127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.131859 restraints weight = 23121.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132854 restraints weight = 13670.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133853 restraints weight = 10329.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134782 restraints weight = 9508.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134448 restraints weight = 9038.329| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16379 Z= 0.113 Angle : 0.562 11.332 22308 Z= 0.275 Chirality : 0.040 0.192 2598 Planarity : 0.004 0.055 2739 Dihedral : 6.525 56.140 2365 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.23 % Allowed : 30.57 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1990 helix: 1.92 (0.15), residues: 1318 sheet: -0.24 (0.56), residues: 80 loop : -1.20 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.024 0.001 TYR A1033 PHE 0.010 0.001 PHE B 175 TRP 0.011 0.001 TRP B1198 HIS 0.004 0.001 HIS B 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (16377) covalent geometry : angle 0.56159 / 0.27 (22304) SS BOND : bond 0.00298 / 0.15 ( 2) SS BOND : angle 1.04036 / 0.47 ( 4) hydrogen bonds : bond 0.03792 / 2.46 ( 974) hydrogen bonds : angle 3.77666 / 2.68 ( 2862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 164 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 572 ASP cc_start: 0.4788 (m-30) cc_final: 0.3431 (t0) REVERT: A 608 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8110 (mp-120) REVERT: A 763 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: A 764 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7613 (mmtp) REVERT: A 849 MET cc_start: -0.1851 (tpt) cc_final: -0.2310 (tpt) REVERT: A 1236 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.6209 (m-10) REVERT: A 1250 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.5658 (mmt) REVERT: B 83 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8297 (mt) REVERT: B 118 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7860 (mp) REVERT: B 133 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: B 599 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7675 (mm) REVERT: B 616 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8004 (mp) REVERT: B 1015 ARG cc_start: 0.6320 (mmt180) cc_final: 0.6024 (mmt180) REVERT: B 1187 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8440 (ttmt) REVERT: B 1236 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6549 (m-10) outliers start: 74 outliers final: 42 residues processed: 219 average time/residue: 0.0963 time to fit residues: 33.7328 Evaluate side-chains 212 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 445 TRP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1250 MET Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1205 CYS Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1236 TYR Chi-restraints excluded: chain B residue 1238 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 170 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 147 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.193577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129449 restraints weight = 23087.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130803 restraints weight = 14091.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130083 restraints weight = 10147.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.130612 restraints weight = 10545.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130603 restraints weight = 10272.339| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16379 Z= 0.137 Angle : 0.583 11.852 22308 Z= 0.285 Chirality : 0.041 0.205 2598 Planarity : 0.004 0.055 2739 Dihedral : 6.440 57.282 2363 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.91 % Allowed : 30.46 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1990 helix: 1.82 (0.15), residues: 1334 sheet: -0.31 (0.56), residues: 80 loop : -1.31 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 230 TYR 0.024 0.001 TYR A1033 PHE 0.013 0.001 PHE B 175 TRP 0.012 0.001 TRP B1198 HIS 0.004 0.001 HIS B 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16377) covalent geometry : angle 0.58258 / 0.28 (22304) SS BOND : bond 0.00443 / 0.22 ( 2) SS BOND : angle 1.09509 / 0.49 ( 4) hydrogen bonds : bond 0.04024 / 2.60 ( 974) hydrogen bonds : angle 3.81543 / 2.70 ( 2862) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 164 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 572 ASP cc_start: 0.4668 (m-30) cc_final: 0.3311 (t0) REVERT: A 608 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8134 (mp-120) REVERT: A 763 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6789 (tm-30) REVERT: A 764 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7671 (mmtp) REVERT: A 849 MET cc_start: -0.1736 (tpt) cc_final: -0.2186 (tpt) REVERT: A 1144 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: A 1236 TYR cc_start: 0.6635 (OUTLIER) cc_final: 0.6264 (m-10) REVERT: A 1250 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.5610 (mmt) REVERT: B 83 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8293 (mt) REVERT: B 118 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7834 (mp) REVERT: B 133 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 599 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7727 (mm) REVERT: B 616 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7977 (mp) REVERT: B 1187 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8451 (ttmt) REVERT: B 1236 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6628 (m-10) outliers start: 86 outliers final: 57 residues processed: 231 average time/residue: 0.1011 time to fit residues: 37.6147 Evaluate side-chains 225 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 156 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 445 TRP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1168 PHE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1250 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1117 ILE Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1205 CYS Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1235 SER Chi-restraints excluded: chain B residue 1236 TYR Chi-restraints excluded: chain B residue 1238 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 71 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 83 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.195455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131258 restraints weight = 22950.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131747 restraints weight = 14086.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132044 restraints weight = 10336.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132940 restraints weight = 9848.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132961 restraints weight = 8857.336| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16379 Z= 0.115 Angle : 0.574 13.919 22308 Z= 0.277 Chirality : 0.040 0.221 2598 Planarity : 0.004 0.054 2739 Dihedral : 6.357 56.988 2363 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.40 % Allowed : 31.43 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1990 helix: 1.93 (0.15), residues: 1316 sheet: -0.29 (0.56), residues: 80 loop : -1.14 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 230 TYR 0.024 0.001 TYR A1033 PHE 0.033 0.001 PHE A 314 TRP 0.011 0.001 TRP B1198 HIS 0.004 0.001 HIS B 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (16377) covalent geometry : angle 0.57410 / 0.28 (22304) SS BOND : bond 0.00376 / 0.19 ( 2) SS BOND : angle 0.91413 / 0.40 ( 4) hydrogen bonds : bond 0.03805 / 2.46 ( 974) hydrogen bonds : angle 3.74775 / 2.65 ( 2862) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 167 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 ASP cc_start: 0.4716 (m-30) cc_final: 0.3363 (t0) REVERT: A 608 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8133 (mp-120) REVERT: A 763 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: A 764 LYS cc_start: 0.8162 (mmtm) cc_final: 0.7709 (mmtp) REVERT: A 849 MET cc_start: -0.1755 (tpt) cc_final: -0.2179 (tpt) REVERT: A 1236 TYR cc_start: 0.6621 (OUTLIER) cc_final: 0.6256 (m-10) REVERT: A 1250 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.5436 (mmt) REVERT: B 83 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 118 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7764 (mp) REVERT: B 133 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: B 599 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7663 (mm) REVERT: B 616 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7933 (mp) REVERT: B 829 MET cc_start: 0.1280 (OUTLIER) cc_final: 0.0994 (mmt) REVERT: B 1187 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8419 (ttmt) REVERT: B 1236 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6569 (m-10) outliers start: 77 outliers final: 52 residues processed: 226 average time/residue: 0.0957 time to fit residues: 34.6480 Evaluate side-chains 218 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 154 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1250 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1117 ILE Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1205 CYS Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1235 SER Chi-restraints excluded: chain B residue 1236 TYR Chi-restraints excluded: chain B residue 1238 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 28 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 overall best weight: 1.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.192743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.128652 restraints weight = 23066.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.127959 restraints weight = 14682.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.128465 restraints weight = 11705.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129330 restraints weight = 10210.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129479 restraints weight = 9605.580| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16379 Z= 0.145 Angle : 0.603 12.286 22308 Z= 0.292 Chirality : 0.042 0.225 2598 Planarity : 0.004 0.054 2739 Dihedral : 6.421 58.199 2363 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.74 % Allowed : 31.20 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1990 helix: 1.79 (0.15), residues: 1324 sheet: -0.39 (0.56), residues: 80 loop : -1.26 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 230 TYR 0.024 0.001 TYR A1033 PHE 0.025 0.001 PHE A 314 TRP 0.012 0.001 TRP B1198 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (16377) covalent geometry : angle 0.60328 / 0.29 (22304) SS BOND : bond 0.00466 / 0.23 ( 2) SS BOND : angle 1.17270 / 0.53 ( 4) hydrogen bonds : bond 0.04064 / 2.62 ( 974) hydrogen bonds : angle 3.86114 / 2.76 ( 2862) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 162 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 572 ASP cc_start: 0.4687 (m-30) cc_final: 0.3385 (t0) REVERT: A 608 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8132 (mp-120) REVERT: A 763 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: A 764 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7763 (mmtp) REVERT: A 849 MET cc_start: -0.1612 (tpt) cc_final: -0.2016 (tpt) REVERT: A 1236 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6323 (m-10) REVERT: A 1250 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.5783 (mmt) REVERT: B 83 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8306 (mt) REVERT: B 118 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7877 (mp) REVERT: B 133 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: B 599 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7722 (mm) REVERT: B 616 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7955 (mp) REVERT: B 829 MET cc_start: 0.1446 (OUTLIER) cc_final: 0.0921 (mmt) REVERT: B 1187 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8454 (ttmt) REVERT: B 1236 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6706 (m-10) outliers start: 83 outliers final: 60 residues processed: 224 average time/residue: 0.1013 time to fit residues: 36.6353 Evaluate side-chains 228 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 156 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1168 PHE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1250 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1117 ILE Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1205 CYS Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1235 SER Chi-restraints excluded: chain B residue 1236 TYR Chi-restraints excluded: chain B residue 1238 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 193 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 189 optimal weight: 0.6980 chunk 179 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.194943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.126811 restraints weight = 23056.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.130729 restraints weight = 12343.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133190 restraints weight = 9032.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134380 restraints weight = 7734.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134889 restraints weight = 7194.420| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16379 Z= 0.116 Angle : 0.587 11.970 22308 Z= 0.283 Chirality : 0.040 0.240 2598 Planarity : 0.004 0.043 2739 Dihedral : 6.339 57.795 2363 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.17 % Allowed : 32.06 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1990 helix: 1.94 (0.15), residues: 1312 sheet: -0.40 (0.57), residues: 80 loop : -1.12 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 230 TYR 0.024 0.001 TYR A1033 PHE 0.025 0.001 PHE A 314 TRP 0.012 0.001 TRP B1198 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (16377) covalent geometry : angle 0.58679 / 0.28 (22304) SS BOND : bond 0.00378 / 0.19 ( 2) SS BOND : angle 0.99845 / 0.44 ( 4) hydrogen bonds : bond 0.03807 / 2.46 ( 974) hydrogen bonds : angle 3.75462 / 2.67 ( 2862) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 162 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 572 ASP cc_start: 0.4601 (m-30) cc_final: 0.3304 (t0) REVERT: A 608 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8086 (mp-120) REVERT: A 763 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: A 764 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7828 (mmtp) REVERT: A 849 MET cc_start: -0.1547 (tpt) cc_final: -0.1877 (tpt) REVERT: A 1204 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6647 (mm-30) REVERT: A 1236 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: A 1250 MET cc_start: 0.6843 (ttt) cc_final: 0.5858 (mmt) REVERT: B 83 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8336 (mt) REVERT: B 118 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7835 (mp) REVERT: B 133 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: B 599 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7727 (mm) REVERT: B 616 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8039 (mp) REVERT: B 829 MET cc_start: 0.1614 (OUTLIER) cc_final: 0.0935 (mmt) REVERT: B 1187 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8436 (ttmt) REVERT: B 1236 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.6616 (m-10) outliers start: 73 outliers final: 60 residues processed: 217 average time/residue: 0.1036 time to fit residues: 36.1900 Evaluate side-chains 230 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 159 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1168 PHE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1117 ILE Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1205 CYS Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1235 SER Chi-restraints excluded: chain B residue 1236 TYR Chi-restraints excluded: chain B residue 1238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 181 optimal weight: 0.0770 chunk 199 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 138 optimal weight: 0.0770 chunk 42 optimal weight: 5.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.194744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131225 restraints weight = 23085.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131488 restraints weight = 13818.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.131357 restraints weight = 11148.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132342 restraints weight = 10173.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132357 restraints weight = 9525.371| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16379 Z= 0.119 Angle : 0.592 12.094 22308 Z= 0.284 Chirality : 0.041 0.241 2598 Planarity : 0.004 0.043 2739 Dihedral : 6.331 58.545 2363 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.34 % Allowed : 32.06 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1990 helix: 1.98 (0.15), residues: 1312 sheet: -0.41 (0.57), residues: 80 loop : -1.10 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 230 TYR 0.025 0.001 TYR A1033 PHE 0.025 0.001 PHE A 314 TRP 0.011 0.001 TRP B1198 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (16377) covalent geometry : angle 0.59203 / 0.28 (22304) SS BOND : bond 0.00365 / 0.18 ( 2) SS BOND : angle 0.94276 / 0.42 ( 4) hydrogen bonds : bond 0.03743 / 2.41 ( 974) hydrogen bonds : angle 3.73236 / 2.65 ( 2862) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 162 time to evaluate : 0.651 Fit side-chains REVERT: A 608 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8112 (mp-120) REVERT: A 849 MET cc_start: -0.1435 (tpt) cc_final: -0.1737 (tpt) REVERT: A 1204 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6715 (mm-30) REVERT: A 1236 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.6236 (m-10) REVERT: A 1250 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.5941 (mmt) REVERT: B 83 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8292 (mt) REVERT: B 118 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7820 (mp) REVERT: B 133 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: B 599 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7646 (mm) REVERT: B 616 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7985 (mp) REVERT: B 829 MET cc_start: 0.1620 (OUTLIER) cc_final: 0.0571 (mmt) REVERT: B 1187 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8418 (ttmt) REVERT: B 1236 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6622 (m-10) outliers start: 76 outliers final: 63 residues processed: 219 average time/residue: 0.1035 time to fit residues: 37.0506 Evaluate side-chains 230 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 156 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1168 PHE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1250 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1117 ILE Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1205 CYS Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1235 SER Chi-restraints excluded: chain B residue 1236 TYR Chi-restraints excluded: chain B residue 1238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 190 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 125 optimal weight: 0.0050 chunk 108 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.195239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.127022 restraints weight = 22835.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131039 restraints weight = 12250.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133542 restraints weight = 8904.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134459 restraints weight = 7630.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135026 restraints weight = 7131.936| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16379 Z= 0.117 Angle : 0.587 12.066 22308 Z= 0.282 Chirality : 0.040 0.240 2598 Planarity : 0.004 0.042 2739 Dihedral : 6.331 59.411 2363 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.23 % Allowed : 32.29 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.20), residues: 1990 helix: 2.01 (0.15), residues: 1316 sheet: -0.43 (0.57), residues: 80 loop : -1.08 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 230 TYR 0.025 0.001 TYR A1033 PHE 0.023 0.001 PHE A 314 TRP 0.020 0.001 TRP A 47 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (16377) covalent geometry : angle 0.58716 / 0.28 (22304) SS BOND : bond 0.00360 / 0.18 ( 2) SS BOND : angle 0.87493 / 0.39 ( 4) hydrogen bonds : bond 0.03675 / 2.37 ( 974) hydrogen bonds : angle 3.69501 / 2.62 ( 2862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2934.03 seconds wall clock time: 51 minutes 18.78 seconds (3078.78 seconds total)