Starting phenix.real_space_refine on Mon May 4 10:14:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yrh_73368/05_2026/9yrh_73368.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yrh_73368/05_2026/9yrh_73368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yrh_73368/05_2026/9yrh_73368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yrh_73368/05_2026/9yrh_73368.map" model { file = "/net/cci-nas-00/data/ceres_data/9yrh_73368/05_2026/9yrh_73368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yrh_73368/05_2026/9yrh_73368.cif" } resolution = 3.8 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= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 112 5.16 5 C 12506 2.51 5 N 3356 2.21 5 O 3743 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19725 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7495 Classifications: {'peptide': 927} Link IDs: {'PTRANS': 32, 'TRANS': 894} Chain breaks: 1 Chain: "B" Number of atoms: 7478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 7478 Classifications: {'peptide': 925} Link IDs: {'PTRANS': 32, 'TRANS': 892} Chain breaks: 1 Chain: "C" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "D" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "E" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "F" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'2OW': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'2OW': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.06, per 1000 atoms: 0.21 Number of scatterers: 19725 At special positions: 0 Unit cell: (92.96, 187.58, 168.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 112 16.00 P 6 15.00 F 2 9.00 O 3743 8.00 N 3356 7.00 C 12506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 14 sheets defined 60.7% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 19 through 28 removed outlier: 3.583A pdb=" N GLN A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 201 removed outlier: 4.200A pdb=" N ALA A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 removed outlier: 3.771A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.580A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 removed outlier: 4.030A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 340 Processing helix chain 'A' and resid 342 through 362 Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 472 through 495 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 544 through 556 Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 614 through 621 removed outlier: 3.509A pdb=" N PHE A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 664 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 697 through 708 removed outlier: 3.729A pdb=" N GLY A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 737 through 748 Processing helix chain 'A' and resid 766 through 782 Processing helix chain 'A' and resid 783 through 824 removed outlier: 3.552A pdb=" N ARG A 787 " --> pdb=" O ARG A 783 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 841 Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 843 through 943 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 97 through 111 removed outlier: 3.665A pdb=" N VAL B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.538A pdb=" N VAL B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 removed outlier: 4.116A pdb=" N ILE B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.685A pdb=" N VAL B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 215 through 232 removed outlier: 3.504A pdb=" N GLN B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Proline residue: B 225 - end of helix removed outlier: 3.749A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.621A pdb=" N ARG B 272 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 273 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.868A pdb=" N TYR B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.792A pdb=" N ASP B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 300' Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.773A pdb=" N GLN B 315 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 316 " --> pdb=" O ILE B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 312 through 316' Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.541A pdb=" N MET B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 360 removed outlier: 3.947A pdb=" N GLY B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.580A pdb=" N LEU B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 448 Processing helix chain 'B' and resid 472 through 494 Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 517 through 525 Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 544 through 557 Processing helix chain 'B' and resid 592 through 597 removed outlier: 4.145A pdb=" N ASN B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 646 through 664 removed outlier: 3.899A pdb=" N LEU B 650 " --> pdb=" O THR B 646 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 698 through 707 Processing helix chain 'B' and resid 714 through 721 Processing helix chain 'B' and resid 722 through 726 Processing helix chain 'B' and resid 739 through 747 Processing helix chain 'B' and resid 768 through 827 removed outlier: 3.845A pdb=" N LEU B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 834 removed outlier: 4.606A pdb=" N LYS B 831 " --> pdb=" O TRP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 943 removed outlier: 3.830A pdb=" N ARG B 925 " --> pdb=" O GLU B 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 66 through 76 removed outlier: 4.039A pdb=" N ASP C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 93 through 98 removed outlier: 4.059A pdb=" N ASN C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.887A pdb=" N PHE C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 153 Processing helix chain 'C' and resid 158 through 166 removed outlier: 3.542A pdb=" N VAL C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'D' and resid 42 through 57 removed outlier: 3.829A pdb=" N LEU D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 77 removed outlier: 4.061A pdb=" N ASP D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 93 through 99 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 107 through 116 removed outlier: 3.763A pdb=" N MET D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 134 Processing helix chain 'D' and resid 143 through 153 Processing helix chain 'D' and resid 158 through 167 removed outlier: 3.798A pdb=" N VAL D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 79 through 90 removed outlier: 3.964A pdb=" N GLU E 89 " --> pdb=" O THR E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 108 removed outlier: 3.715A pdb=" N ASP E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 126 removed outlier: 3.794A pdb=" N THR E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 141 removed outlier: 3.992A pdb=" N ILE E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 162 removed outlier: 3.540A pdb=" N ILE E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 35 Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 51 through 56 removed outlier: 3.799A pdb=" N ALA F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 74 removed outlier: 3.655A pdb=" N ALA F 74 " --> pdb=" O MET F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 96 through 108 Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.524A pdb=" N LEU F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 removed outlier: 3.659A pdb=" N PHE F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 161 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.264A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG A 54 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 117 removed outlier: 7.174A pdb=" N CYS A 122 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE A 673 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR A 124 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A 177 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 260 removed outlier: 6.855A pdb=" N HIS A 251 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 246 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 455 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN A 172 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU A 460 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 173 " --> pdb=" O HIS A 666 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 364 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564 removed outlier: 3.827A pdb=" N GLY A 584 " --> pdb=" O HIS A 581 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.833A pdb=" N ILE A 713 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 763 " --> pdb=" O ILE A 713 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 47 removed outlier: 4.282A pdb=" N MET B 77 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 49 through 53 removed outlier: 7.152A pdb=" N THR B 60 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 117 removed outlier: 6.160A pdb=" N CYS B 122 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE B 673 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR B 124 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER B 173 " --> pdb=" O HIS B 668 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL B 670 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 175 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N CYS B 672 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B 177 " --> pdb=" O CYS B 672 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLN B 172 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 459 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 248 " --> pdb=" O VAL B 459 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB4, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'D' and resid 141 through 142 1054 hydrogen bonds defined for protein. 3093 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: 3.80 Time building geometry restraints manager: 2.44 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: 3420 1.31 - 1.44: 5007 1.44 - 1.56: 11457 1.56 - 1.69: 8 1.69 - 1.82: 198 Bond restraints: 20090 Sorted by residual: bond pdb=" C14 2OW A1401 " pdb=" N15 2OW A1401 " ideal model delta sigma weight residual 1.398 1.493 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C14 2OW B1401 " pdb=" N15 2OW B1401 " ideal model delta sigma weight residual 1.398 1.493 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C19 2OW A1401 " pdb=" N18 2OW A1401 " ideal model delta sigma weight residual 1.391 1.486 -0.095 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C19 2OW B1401 " pdb=" N18 2OW B1401 " ideal model delta sigma weight residual 1.391 1.484 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C16 2OW A1401 " pdb=" N18 2OW A1401 " ideal model delta sigma weight residual 1.367 1.460 -0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 20085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 26325 2.25 - 4.49: 621 4.49 - 6.74: 70 6.74 - 8.98: 6 8.98 - 11.23: 2 Bond angle restraints: 27024 Sorted by residual: angle pdb=" C HIS A 666 " pdb=" CA HIS A 666 " pdb=" CB HIS A 666 " ideal model delta sigma weight residual 110.08 116.40 -6.32 1.15e+00 7.56e-01 3.02e+01 angle pdb=" N PRO A 667 " pdb=" CA PRO A 667 " pdb=" C PRO A 667 " ideal model delta sigma weight residual 111.57 118.17 -6.60 1.52e+00 4.33e-01 1.89e+01 angle pdb=" CA ASP A 107 " pdb=" CB ASP A 107 " pdb=" CG ASP A 107 " ideal model delta sigma weight residual 112.60 116.77 -4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" N PRO A 667 " pdb=" CD PRO A 667 " pdb=" CG PRO A 667 " ideal model delta sigma weight residual 103.20 97.01 6.19 1.50e+00 4.44e-01 1.71e+01 angle pdb=" N15 2OW A1401 " pdb=" C16 2OW A1401 " pdb=" N18 2OW A1401 " ideal model delta sigma weight residual 112.53 123.76 -11.23 3.00e+00 1.11e-01 1.40e+01 ... (remaining 27019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.33: 10681 19.33 - 38.67: 1237 38.67 - 58.00: 238 58.00 - 77.34: 90 77.34 - 96.67: 25 Dihedral angle restraints: 12271 sinusoidal: 5181 harmonic: 7090 Sorted by residual: dihedral pdb=" C06 2OW B1401 " pdb=" C29 2OW B1401 " pdb=" N05 2OW B1401 " pdb=" C28 2OW B1401 " ideal model delta sinusoidal sigma weight residual 53.31 -43.36 96.67 1 3.00e+01 1.11e-03 1.19e+01 dihedral pdb=" CA ASP E 146 " pdb=" CB ASP E 146 " pdb=" CG ASP E 146 " pdb=" OD1 ASP E 146 " ideal model delta sinusoidal sigma weight residual -30.00 -89.64 59.64 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" C06 2OW A1401 " pdb=" C29 2OW A1401 " pdb=" N05 2OW A1401 " pdb=" C28 2OW A1401 " ideal model delta sinusoidal sigma weight residual 53.31 -42.95 96.26 1 3.00e+01 1.11e-03 1.18e+01 ... (remaining 12268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2398 0.053 - 0.106: 390 0.106 - 0.158: 104 0.158 - 0.211: 15 0.211 - 0.264: 5 Chirality restraints: 2912 Sorted by residual: chirality pdb=" CA ILE A 462 " pdb=" N ILE A 462 " pdb=" C ILE A 462 " pdb=" CB ILE A 462 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE A 674 " pdb=" N ILE A 674 " pdb=" C ILE A 674 " pdb=" CB ILE A 674 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE A 457 " pdb=" N ILE A 457 " pdb=" C ILE A 457 " pdb=" CB ILE A 457 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2909 not shown) Planarity restraints: 3513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 925 " -0.462 9.50e-02 1.11e+02 2.07e-01 2.63e+01 pdb=" NE ARG B 925 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 925 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 925 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 925 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 144 " -0.059 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO E 145 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO E 145 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 145 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 739 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C ARG B 739 " 0.054 2.00e-02 2.50e+03 pdb=" O ARG B 739 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS B 740 " -0.018 2.00e-02 2.50e+03 ... (remaining 3510 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 238 2.49 - 3.09: 16157 3.09 - 3.70: 33961 3.70 - 4.30: 47904 4.30 - 4.90: 75774 Nonbonded interactions: 174034 Sorted by model distance: nonbonded pdb=" O GLU A 269 " pdb=" OH TYR A 283 " model vdw 1.888 3.040 nonbonded pdb=" O GLU B 269 " pdb=" OH TYR B 283 " model vdw 1.932 3.040 nonbonded pdb=" OH TYR A 287 " pdb=" O ILE A 313 " model vdw 1.966 3.040 nonbonded pdb=" O LYS A 184 " pdb=" OG1 THR A 188 " model vdw 1.986 3.040 nonbonded pdb=" OG SER A 180 " pdb=" O3 PO4 A1403 " model vdw 2.020 3.040 ... (remaining 174029 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 4 through 629 or resid 645 through 1403)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.940 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 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 : 0.005 0.095 20091 Z= 0.323 Angle : 0.760 11.231 27024 Z= 0.454 Chirality : 0.045 0.264 2912 Planarity : 0.006 0.207 3513 Dihedral : 17.707 96.672 7687 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.43 % Allowed : 21.67 % Favored : 77.91 % 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: -0.74 (0.17), residues: 2424 helix: 0.51 (0.14), residues: 1328 sheet: -2.87 (0.43), residues: 124 loop : -1.52 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 721 TYR 0.019 0.002 TYR B 432 PHE 0.013 0.001 PHE B 709 TRP 0.017 0.001 TRP B 827 HIS 0.007 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00532 (20090) covalent geometry : angle 0.75994 (27024) hydrogen bonds : bond 0.15542 ( 1054) hydrogen bonds : angle 6.69601 ( 3093) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 249 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7210 (mmt) cc_final: 0.6922 (mmt) REVERT: A 90 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7520 (mtt) REVERT: A 113 MET cc_start: 0.7183 (mmt) cc_final: 0.6215 (mmt) REVERT: A 723 ARG cc_start: 0.4107 (ptt90) cc_final: 0.2891 (ptt180) REVERT: B 113 MET cc_start: 0.4926 (mmp) cc_final: 0.4389 (mmm) REVERT: B 779 GLU cc_start: 0.6662 (tm-30) cc_final: 0.6402 (tm-30) REVERT: B 922 MET cc_start: 0.1020 (ttm) cc_final: 0.0406 (ttm) REVERT: B 926 LEU cc_start: 0.2551 (OUTLIER) cc_final: 0.2210 (mt) REVERT: B 932 MET cc_start: 0.4193 (ppp) cc_final: 0.2638 (tpt) REVERT: C 71 ASP cc_start: 0.6636 (m-30) cc_final: 0.6263 (m-30) REVERT: C 94 ASN cc_start: 0.3960 (p0) cc_final: 0.3472 (m-40) REVERT: E 123 LEU cc_start: 0.8243 (mt) cc_final: 0.7899 (pp) outliers start: 9 outliers final: 3 residues processed: 253 average time/residue: 0.1267 time to fit residues: 51.7032 Evaluate side-chains 214 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 209 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 926 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.0870 chunk 194 optimal weight: 0.3980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 0.0030 overall best weight: 0.2968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 415 GLN A 437 ASN A 486 GLN A 490 ASN ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 ASN ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN B 890 GLN C 117 ASN D 91 ASN E 24 GLN E 155 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.143575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.122223 restraints weight = 65984.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.121281 restraints weight = 75491.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.122706 restraints weight = 56110.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.122810 restraints weight = 38665.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.123277 restraints weight = 37032.802| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20091 Z= 0.144 Angle : 0.658 8.743 27024 Z= 0.335 Chirality : 0.043 0.175 2912 Planarity : 0.004 0.057 3513 Dihedral : 6.818 91.181 2677 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.41 % Allowed : 19.44 % Favored : 77.15 % 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: -0.52 (0.17), residues: 2424 helix: 0.68 (0.14), residues: 1357 sheet: -2.56 (0.50), residues: 93 loop : -1.57 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 819 TYR 0.026 0.002 TYR E 153 PHE 0.033 0.002 PHE C 181 TRP 0.015 0.002 TRP A 438 HIS 0.009 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00306 (20090) covalent geometry : angle 0.65751 (27024) hydrogen bonds : bond 0.04750 ( 1054) hydrogen bonds : angle 5.52947 ( 3093) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 250 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 MET cc_start: 0.5735 (mmm) cc_final: 0.5292 (mmm) REVERT: A 723 ARG cc_start: 0.3680 (ptt90) cc_final: 0.3007 (ptt180) REVERT: B 932 MET cc_start: 0.4725 (ppp) cc_final: 0.2782 (tpt) REVERT: C 71 ASP cc_start: 0.6205 (m-30) cc_final: 0.5919 (m-30) REVERT: C 94 ASN cc_start: 0.4351 (p0) cc_final: 0.3844 (m110) REVERT: C 157 MET cc_start: 0.4980 (mmt) cc_final: 0.4634 (mmp) REVERT: E 70 MET cc_start: 0.6737 (pmm) cc_final: 0.4758 (mmt) REVERT: E 123 LEU cc_start: 0.8207 (mt) cc_final: 0.7884 (pp) REVERT: F 50 LEU cc_start: 0.7303 (tp) cc_final: 0.6940 (mt) outliers start: 72 outliers final: 24 residues processed: 301 average time/residue: 0.1233 time to fit residues: 59.9598 Evaluate side-chains 234 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 827 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 73 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 1 optimal weight: 0.0770 chunk 118 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 186 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 182 optimal weight: 20.0000 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.143022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.121896 restraints weight = 67801.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.120727 restraints weight = 80574.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.122160 restraints weight = 60426.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.122471 restraints weight = 40381.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.122842 restraints weight = 39281.431| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20091 Z= 0.142 Angle : 0.642 8.248 27024 Z= 0.327 Chirality : 0.042 0.184 2912 Planarity : 0.004 0.084 3513 Dihedral : 6.575 90.088 2671 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.32 % Allowed : 21.57 % Favored : 76.11 % 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: -0.53 (0.17), residues: 2424 helix: 0.68 (0.14), residues: 1359 sheet: -2.58 (0.49), residues: 97 loop : -1.59 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 870 TYR 0.024 0.001 TYR A 283 PHE 0.031 0.002 PHE C 181 TRP 0.015 0.001 TRP F 140 HIS 0.016 0.001 HIS C 148 Details of bonding type rmsd covalent geometry : bond 0.00311 (20090) covalent geometry : angle 0.64154 (27024) hydrogen bonds : bond 0.04387 ( 1054) hydrogen bonds : angle 5.39535 ( 3093) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6836 (mmt) cc_final: 0.6475 (mmt) REVERT: A 684 MET cc_start: 0.5630 (mmm) cc_final: 0.5250 (mmm) REVERT: A 723 ARG cc_start: 0.3808 (ptt90) cc_final: 0.3544 (ptt180) REVERT: A 838 PRO cc_start: 0.7790 (Cg_exo) cc_final: 0.7582 (Cg_endo) REVERT: B 419 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6201 (mp10) REVERT: B 422 TYR cc_start: 0.6725 (t80) cc_final: 0.6456 (t80) REVERT: B 932 MET cc_start: 0.4760 (ppp) cc_final: 0.2913 (tpt) REVERT: C 71 ASP cc_start: 0.6268 (m-30) cc_final: 0.5927 (m-30) REVERT: C 94 ASN cc_start: 0.4311 (p0) cc_final: 0.3754 (m110) REVERT: C 157 MET cc_start: 0.5154 (mmt) cc_final: 0.4863 (mmp) REVERT: E 70 MET cc_start: 0.6726 (pmm) cc_final: 0.4794 (mmt) REVERT: E 123 LEU cc_start: 0.8290 (mt) cc_final: 0.7957 (pp) REVERT: F 51 ARG cc_start: 0.7968 (mmp80) cc_final: 0.7673 (mmp80) outliers start: 49 outliers final: 30 residues processed: 265 average time/residue: 0.1226 time to fit residues: 53.3928 Evaluate side-chains 241 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 0 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 150 ASN E 155 ASN F 162 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.142528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.121983 restraints weight = 67674.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.121656 restraints weight = 74308.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.122678 restraints weight = 62959.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.122870 restraints weight = 43944.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.123766 restraints weight = 39143.784| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20091 Z= 0.154 Angle : 0.630 8.975 27024 Z= 0.320 Chirality : 0.041 0.175 2912 Planarity : 0.004 0.043 3513 Dihedral : 6.511 90.493 2671 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.07 % Allowed : 21.57 % Favored : 75.35 % 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: -0.54 (0.17), residues: 2424 helix: 0.69 (0.14), residues: 1359 sheet: -2.48 (0.50), residues: 92 loop : -1.64 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 721 TYR 0.025 0.001 TYR E 153 PHE 0.029 0.002 PHE C 181 TRP 0.013 0.001 TRP F 140 HIS 0.014 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00340 (20090) covalent geometry : angle 0.63002 (27024) hydrogen bonds : bond 0.04276 ( 1054) hydrogen bonds : angle 5.30461 ( 3093) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7573 (mtp) REVERT: A 684 MET cc_start: 0.5600 (mmm) cc_final: 0.5311 (mmm) REVERT: A 723 ARG cc_start: 0.3856 (ptt90) cc_final: 0.3475 (ptt180) REVERT: A 779 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: B 113 MET cc_start: 0.5253 (mmp) cc_final: 0.4730 (mmm) REVERT: B 388 MET cc_start: 0.4206 (ppp) cc_final: 0.3783 (ppp) REVERT: B 422 TYR cc_start: 0.6639 (t80) cc_final: 0.6397 (t80) REVERT: B 932 MET cc_start: 0.4879 (ppp) cc_final: 0.3410 (tpt) REVERT: C 71 ASP cc_start: 0.6161 (m-30) cc_final: 0.5822 (m-30) REVERT: C 94 ASN cc_start: 0.4263 (p0) cc_final: 0.3692 (m110) REVERT: C 157 MET cc_start: 0.5191 (mmt) cc_final: 0.4824 (mmp) REVERT: E 70 MET cc_start: 0.6650 (pmm) cc_final: 0.5150 (mmp) REVERT: E 123 LEU cc_start: 0.8216 (mt) cc_final: 0.7924 (pp) outliers start: 65 outliers final: 48 residues processed: 270 average time/residue: 0.1189 time to fit residues: 53.3310 Evaluate side-chains 259 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 182 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 188 optimal weight: 0.4980 chunk 132 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.133744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.113162 restraints weight = 68050.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.113673 restraints weight = 78370.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.114535 restraints weight = 61749.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.114598 restraints weight = 43041.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.115471 restraints weight = 38646.900| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20091 Z= 0.180 Angle : 0.654 8.808 27024 Z= 0.333 Chirality : 0.042 0.172 2912 Planarity : 0.004 0.039 3513 Dihedral : 6.553 91.729 2671 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.78 % Allowed : 21.81 % Favored : 74.41 % 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: -0.63 (0.17), residues: 2424 helix: 0.62 (0.14), residues: 1361 sheet: -2.53 (0.51), residues: 89 loop : -1.69 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 51 TYR 0.025 0.002 TYR E 153 PHE 0.024 0.002 PHE B 494 TRP 0.013 0.001 TRP F 140 HIS 0.015 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00403 (20090) covalent geometry : angle 0.65430 (27024) hydrogen bonds : bond 0.04359 ( 1054) hydrogen bonds : angle 5.30534 ( 3093) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 218 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 ARG cc_start: 0.3938 (ptt90) cc_final: 0.3641 (ptt-90) REVERT: B 113 MET cc_start: 0.5474 (mmp) cc_final: 0.5202 (mmp) REVERT: B 388 MET cc_start: 0.4315 (ppp) cc_final: 0.4000 (ppp) REVERT: B 422 TYR cc_start: 0.6538 (t80) cc_final: 0.6315 (t80) REVERT: B 599 ASP cc_start: -0.1057 (OUTLIER) cc_final: -0.1708 (p0) REVERT: B 932 MET cc_start: 0.4178 (ppp) cc_final: 0.2401 (tpt) REVERT: C 71 ASP cc_start: 0.5984 (m-30) cc_final: 0.5628 (m-30) REVERT: C 94 ASN cc_start: 0.4428 (p0) cc_final: 0.3836 (m110) REVERT: C 157 MET cc_start: 0.5310 (mmt) cc_final: 0.4932 (mmp) REVERT: D 97 MET cc_start: 0.1421 (tpt) cc_final: 0.1036 (ttt) REVERT: E 70 MET cc_start: 0.6597 (pmm) cc_final: 0.5131 (mmp) REVERT: E 123 LEU cc_start: 0.8093 (mt) cc_final: 0.7853 (pp) REVERT: E 139 MET cc_start: 0.4553 (tmm) cc_final: 0.4337 (tmm) outliers start: 80 outliers final: 55 residues processed: 277 average time/residue: 0.1176 time to fit residues: 53.5784 Evaluate side-chains 262 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 694 ARG Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 156 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 209 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 98 ASN C 169 GLN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.133164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.112691 restraints weight = 67914.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.112413 restraints weight = 84535.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.113701 restraints weight = 66232.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.113718 restraints weight = 46080.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.114903 restraints weight = 40980.953| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20091 Z= 0.188 Angle : 0.660 7.539 27024 Z= 0.336 Chirality : 0.042 0.184 2912 Planarity : 0.004 0.040 3513 Dihedral : 6.588 93.340 2668 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.12 % Allowed : 21.76 % Favored : 74.12 % 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: -0.66 (0.17), residues: 2424 helix: 0.60 (0.14), residues: 1367 sheet: -2.51 (0.51), residues: 89 loop : -1.73 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 721 TYR 0.026 0.002 TYR E 153 PHE 0.022 0.002 PHE C 181 TRP 0.014 0.001 TRP B 827 HIS 0.016 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00421 (20090) covalent geometry : angle 0.66033 (27024) hydrogen bonds : bond 0.04363 ( 1054) hydrogen bonds : angle 5.31160 ( 3093) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 219 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: A 563 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.5833 (t80) REVERT: A 796 LEU cc_start: 0.3912 (OUTLIER) cc_final: 0.3639 (mm) REVERT: B 422 TYR cc_start: 0.6542 (t80) cc_final: 0.6317 (t80) REVERT: B 599 ASP cc_start: -0.1079 (OUTLIER) cc_final: -0.1809 (p0) REVERT: B 932 MET cc_start: 0.4345 (ppp) cc_final: 0.2760 (tpt) REVERT: C 71 ASP cc_start: 0.6028 (m-30) cc_final: 0.5647 (m-30) REVERT: C 94 ASN cc_start: 0.4475 (p0) cc_final: 0.3649 (m-40) REVERT: C 157 MET cc_start: 0.5328 (mmt) cc_final: 0.4890 (mmp) REVERT: E 70 MET cc_start: 0.6612 (pmm) cc_final: 0.4762 (mmt) REVERT: E 123 LEU cc_start: 0.8050 (mt) cc_final: 0.7815 (pp) REVERT: E 139 MET cc_start: 0.4432 (tmm) cc_final: 0.3919 (tmm) outliers start: 87 outliers final: 58 residues processed: 286 average time/residue: 0.1247 time to fit residues: 57.5391 Evaluate side-chains 270 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 208 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 694 ARG Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 212 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 82 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.133281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.112430 restraints weight = 68364.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.112510 restraints weight = 78662.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.113585 restraints weight = 63623.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.113498 restraints weight = 45905.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.114131 restraints weight = 40402.183| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20091 Z= 0.179 Angle : 0.681 10.759 27024 Z= 0.346 Chirality : 0.043 0.247 2912 Planarity : 0.004 0.041 3513 Dihedral : 6.624 94.057 2668 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.50 % Allowed : 22.89 % Favored : 73.60 % 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: -0.69 (0.17), residues: 2424 helix: 0.57 (0.14), residues: 1362 sheet: -2.45 (0.51), residues: 89 loop : -1.74 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 721 TYR 0.027 0.002 TYR E 153 PHE 0.025 0.002 PHE B 494 TRP 0.014 0.001 TRP B 827 HIS 0.016 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00404 (20090) covalent geometry : angle 0.68061 (27024) hydrogen bonds : bond 0.04366 ( 1054) hydrogen bonds : angle 5.32453 ( 3093) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 218 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6839 (mmt) cc_final: 0.6114 (mmt) REVERT: A 465 PHE cc_start: 0.7946 (t80) cc_final: 0.7684 (m-80) REVERT: A 563 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.5785 (t80) REVERT: A 679 LYS cc_start: 0.7308 (tttt) cc_final: 0.7063 (mttm) REVERT: B 240 ASN cc_start: 0.6255 (OUTLIER) cc_final: 0.5429 (m110) REVERT: B 422 TYR cc_start: 0.6690 (t80) cc_final: 0.6475 (t80) REVERT: B 599 ASP cc_start: -0.1050 (OUTLIER) cc_final: -0.1847 (p0) REVERT: B 709 PHE cc_start: 0.0772 (OUTLIER) cc_final: -0.0505 (p90) REVERT: B 932 MET cc_start: 0.4175 (ppp) cc_final: 0.2687 (tpt) REVERT: C 71 ASP cc_start: 0.5979 (m-30) cc_final: 0.5581 (m-30) REVERT: C 94 ASN cc_start: 0.4478 (p0) cc_final: 0.3640 (m-40) REVERT: C 110 MET cc_start: 0.1090 (tpp) cc_final: 0.0788 (tpp) REVERT: C 157 MET cc_start: 0.5440 (mmt) cc_final: 0.4976 (mmp) REVERT: D 97 MET cc_start: 0.1508 (tpt) cc_final: 0.1254 (ttt) REVERT: E 70 MET cc_start: 0.6646 (pmm) cc_final: 0.5066 (mmp) REVERT: E 123 LEU cc_start: 0.8069 (mt) cc_final: 0.7815 (pp) REVERT: E 139 MET cc_start: 0.4609 (tmm) cc_final: 0.4081 (tmm) outliers start: 74 outliers final: 59 residues processed: 274 average time/residue: 0.1242 time to fit residues: 54.9846 Evaluate side-chains 272 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 694 ARG Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 827 TRP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 154 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 192 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 197 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.131773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.111429 restraints weight = 68164.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.112787 restraints weight = 81435.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.113259 restraints weight = 62940.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.113516 restraints weight = 42271.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.114380 restraints weight = 37662.988| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20091 Z= 0.229 Angle : 0.722 11.127 27024 Z= 0.368 Chirality : 0.044 0.214 2912 Planarity : 0.004 0.043 3513 Dihedral : 6.735 95.344 2668 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.83 % Allowed : 22.89 % Favored : 73.27 % 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: -0.81 (0.17), residues: 2424 helix: 0.46 (0.14), residues: 1359 sheet: -2.22 (0.59), residues: 73 loop : -1.81 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 51 TYR 0.026 0.002 TYR E 153 PHE 0.020 0.002 PHE A 38 TRP 0.016 0.002 TRP B 827 HIS 0.017 0.002 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00520 (20090) covalent geometry : angle 0.72160 (27024) hydrogen bonds : bond 0.04620 ( 1054) hydrogen bonds : angle 5.38848 ( 3093) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 218 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: A 563 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.5683 (t80) REVERT: A 922 MET cc_start: 0.0461 (tmm) cc_final: 0.0029 (ttp) REVERT: B 240 ASN cc_start: 0.6515 (OUTLIER) cc_final: 0.5955 (m110) REVERT: B 388 MET cc_start: 0.4127 (ppp) cc_final: 0.3826 (ppp) REVERT: B 422 TYR cc_start: 0.6648 (t80) cc_final: 0.6437 (t80) REVERT: B 599 ASP cc_start: -0.1169 (OUTLIER) cc_final: -0.2029 (p0) REVERT: B 709 PHE cc_start: 0.0851 (OUTLIER) cc_final: -0.0411 (p90) REVERT: B 932 MET cc_start: 0.4279 (ppp) cc_final: 0.2810 (tpt) REVERT: C 71 ASP cc_start: 0.5884 (m-30) cc_final: 0.5491 (m-30) REVERT: C 94 ASN cc_start: 0.4567 (p0) cc_final: 0.3645 (m-40) REVERT: C 157 MET cc_start: 0.5569 (mmt) cc_final: 0.5084 (mmp) REVERT: D 97 MET cc_start: 0.1493 (tpt) cc_final: 0.1145 (ttt) REVERT: E 70 MET cc_start: 0.6586 (pmm) cc_final: 0.4944 (mmp) REVERT: E 123 LEU cc_start: 0.8024 (mt) cc_final: 0.7768 (pp) REVERT: E 139 MET cc_start: 0.4380 (tmm) cc_final: 0.3893 (tmm) REVERT: F 50 LEU cc_start: 0.7508 (tp) cc_final: 0.7176 (mt) outliers start: 81 outliers final: 65 residues processed: 279 average time/residue: 0.1202 time to fit residues: 54.8595 Evaluate side-chains 278 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 208 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 508 TRP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 694 ARG Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 147 optimal weight: 40.0000 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 156 optimal weight: 0.3980 chunk 179 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.134122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.113803 restraints weight = 67578.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.113641 restraints weight = 80182.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.114581 restraints weight = 64772.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.114893 restraints weight = 42850.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.115753 restraints weight = 38500.276| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 20091 Z= 0.146 Angle : 0.699 11.188 27024 Z= 0.352 Chirality : 0.043 0.244 2912 Planarity : 0.004 0.042 3513 Dihedral : 6.711 98.064 2668 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.17 % Allowed : 23.75 % Favored : 73.08 % 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: -0.74 (0.17), residues: 2424 helix: 0.52 (0.14), residues: 1362 sheet: -2.38 (0.50), residues: 92 loop : -1.74 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 51 TYR 0.028 0.002 TYR E 153 PHE 0.022 0.002 PHE B 494 TRP 0.015 0.002 TRP B 827 HIS 0.016 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00329 (20090) covalent geometry : angle 0.69859 (27024) hydrogen bonds : bond 0.04195 ( 1054) hydrogen bonds : angle 5.28534 ( 3093) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6952 (mmt) cc_final: 0.6307 (mmt) REVERT: A 465 PHE cc_start: 0.7866 (t80) cc_final: 0.7620 (m-80) REVERT: A 563 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.5709 (t80) REVERT: A 679 LYS cc_start: 0.7254 (tttt) cc_final: 0.7010 (mttm) REVERT: A 922 MET cc_start: 0.0434 (tmm) cc_final: 0.0076 (ttp) REVERT: B 113 MET cc_start: 0.5098 (mmp) cc_final: 0.4750 (mmp) REVERT: B 240 ASN cc_start: 0.6322 (OUTLIER) cc_final: 0.5568 (m-40) REVERT: B 388 MET cc_start: 0.3932 (ppp) cc_final: 0.3638 (ppp) REVERT: B 422 TYR cc_start: 0.6616 (t80) cc_final: 0.6393 (t80) REVERT: B 599 ASP cc_start: -0.1264 (OUTLIER) cc_final: -0.2128 (p0) REVERT: B 709 PHE cc_start: 0.0597 (OUTLIER) cc_final: -0.0641 (p90) REVERT: B 932 MET cc_start: 0.4163 (ppp) cc_final: 0.2765 (tpt) REVERT: C 71 ASP cc_start: 0.5881 (m-30) cc_final: 0.5468 (m-30) REVERT: C 94 ASN cc_start: 0.4485 (p0) cc_final: 0.3528 (m-40) REVERT: C 110 MET cc_start: 0.1056 (tpp) cc_final: 0.0822 (tpp) REVERT: C 157 MET cc_start: 0.5459 (mmt) cc_final: 0.4955 (mmp) REVERT: D 142 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.6349 (ptt) REVERT: E 70 MET cc_start: 0.6668 (pmm) cc_final: 0.5016 (mmp) REVERT: E 123 LEU cc_start: 0.7948 (mt) cc_final: 0.7709 (pp) REVERT: E 139 MET cc_start: 0.4462 (tmm) cc_final: 0.4242 (tmm) outliers start: 67 outliers final: 55 residues processed: 276 average time/residue: 0.1247 time to fit residues: 56.2883 Evaluate side-chains 272 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 694 ARG Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 29 optimal weight: 0.1980 chunk 215 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.132599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.111879 restraints weight = 67717.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.112486 restraints weight = 80997.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.113537 restraints weight = 64460.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.113486 restraints weight = 45516.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.114314 restraints weight = 39754.301| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 20091 Z= 0.203 Angle : 0.733 12.167 27024 Z= 0.370 Chirality : 0.044 0.255 2912 Planarity : 0.004 0.042 3513 Dihedral : 6.736 97.101 2668 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.45 % Allowed : 23.65 % Favored : 72.89 % 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: -0.77 (0.17), residues: 2424 helix: 0.49 (0.14), residues: 1358 sheet: -2.13 (0.60), residues: 73 loop : -1.79 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 51 TYR 0.029 0.002 TYR A 109 PHE 0.023 0.002 PHE B 46 TRP 0.015 0.002 TRP B 827 HIS 0.015 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00465 (20090) covalent geometry : angle 0.73254 (27024) hydrogen bonds : bond 0.04440 ( 1054) hydrogen bonds : angle 5.33450 ( 3093) Misc. bond : bond 0.00035 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 221 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7727 (mtp) cc_final: 0.7432 (mtp) REVERT: A 113 MET cc_start: 0.7124 (mmt) cc_final: 0.6336 (mmt) REVERT: A 465 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: A 563 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.5735 (t80) REVERT: A 723 ARG cc_start: 0.4024 (ptt90) cc_final: 0.3791 (ptt90) REVERT: B 240 ASN cc_start: 0.6583 (OUTLIER) cc_final: 0.5947 (m110) REVERT: B 388 MET cc_start: 0.4037 (ppp) cc_final: 0.3734 (ppp) REVERT: B 422 TYR cc_start: 0.6683 (t80) cc_final: 0.6452 (t80) REVERT: B 599 ASP cc_start: -0.1127 (OUTLIER) cc_final: -0.2047 (p0) REVERT: B 690 MET cc_start: 0.6182 (tpp) cc_final: 0.5821 (tpp) REVERT: B 709 PHE cc_start: 0.0804 (OUTLIER) cc_final: -0.0515 (p90) REVERT: B 932 MET cc_start: 0.4110 (ppp) cc_final: 0.2702 (tpt) REVERT: C 71 ASP cc_start: 0.5942 (m-30) cc_final: 0.5527 (m-30) REVERT: C 94 ASN cc_start: 0.4676 (p0) cc_final: 0.3717 (m-40) REVERT: C 110 MET cc_start: 0.0932 (tpp) cc_final: 0.0731 (tpp) REVERT: C 157 MET cc_start: 0.5685 (mmt) cc_final: 0.5203 (mmp) REVERT: D 142 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6459 (ptt) REVERT: E 70 MET cc_start: 0.6665 (pmm) cc_final: 0.4707 (mmt) REVERT: E 123 LEU cc_start: 0.7991 (mt) cc_final: 0.7728 (pp) REVERT: E 139 MET cc_start: 0.4435 (tmm) cc_final: 0.4171 (tmm) REVERT: F 51 ARG cc_start: 0.8152 (mmp80) cc_final: 0.7782 (mmp80) outliers start: 73 outliers final: 60 residues processed: 274 average time/residue: 0.1225 time to fit residues: 55.4264 Evaluate side-chains 274 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 694 ARG Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 145 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 123 optimal weight: 0.3980 chunk 239 optimal weight: 0.8980 chunk 176 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.134143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.114326 restraints weight = 68450.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.114678 restraints weight = 82029.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.115430 restraints weight = 63959.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.115817 restraints weight = 44234.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.116711 restraints weight = 38773.313| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20091 Z= 0.146 Angle : 0.711 11.757 27024 Z= 0.355 Chirality : 0.043 0.258 2912 Planarity : 0.004 0.042 3513 Dihedral : 6.715 99.193 2668 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.03 % Allowed : 23.98 % Favored : 72.99 % 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: -0.63 (0.17), residues: 2424 helix: 0.60 (0.14), residues: 1347 sheet: -1.99 (0.57), residues: 78 loop : -1.71 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 51 TYR 0.028 0.002 TYR A 109 PHE 0.020 0.002 PHE B 540 TRP 0.016 0.002 TRP B 827 HIS 0.016 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00330 (20090) covalent geometry : angle 0.71094 (27024) hydrogen bonds : bond 0.04131 ( 1054) hydrogen bonds : angle 5.28613 ( 3093) Misc. bond : bond 0.00033 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.06 seconds wall clock time: 52 minutes 4.82 seconds (3124.82 seconds total)