Starting phenix.real_space_refine on Wed Mar 12 04:52:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rox_19406/03_2025/8rox_19406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rox_19406/03_2025/8rox_19406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rox_19406/03_2025/8rox_19406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rox_19406/03_2025/8rox_19406.map" model { file = "/net/cci-nas-00/data/ceres_data/8rox_19406/03_2025/8rox_19406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rox_19406/03_2025/8rox_19406.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 22 5.16 5 Cl 2 4.86 5 C 4651 2.51 5 N 1244 2.21 5 O 1330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7249 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2101 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 548 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 15, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 324 Chain: "B" Number of atoms: 4783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 4783 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 348} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 736} Chain breaks: 9 Unresolved non-hydrogen bonds: 1212 Unresolved non-hydrogen angles: 1500 Unresolved non-hydrogen dihedrals: 939 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 18, 'ASP:plan': 35, 'PHE:plan': 2, 'GLU:plan': 64, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 672 Chain: "D" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 339 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'A1H17': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.41, per 1000 atoms: 0.75 Number of scatterers: 7249 At special positions: 0 Unit cell: (90.522, 98.226, 105.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 22 16.00 O 1330 8.00 N 1244 7.00 C 4651 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 313 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 20 sheets defined 14.0% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.974A pdb=" N HIS A 466 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.050A pdb=" N LYS B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN B 255 " --> pdb=" O PRO B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 255' Processing helix chain 'B' and resid 381 through 384 Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'B' and resid 987 through 990 Processing helix chain 'B' and resid 1044 through 1062 Processing helix chain 'B' and resid 1064 through 1068 removed outlier: 3.946A pdb=" N ILE B1068 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1091 through 1100 removed outlier: 3.910A pdb=" N LEU B1098 " --> pdb=" O ILE B1094 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B1099 " --> pdb=" O GLU B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1110 Processing helix chain 'B' and resid 1127 through 1137 Processing helix chain 'D' and resid 53 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 83 removed outlier: 7.333A pdb=" N LEU A 91 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE A 83 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR A 89 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 109 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A 125 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TRP A 111 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.625A pdb=" N THR A 184 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 224 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 178 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP A 179 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN A 158 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.647A pdb=" N LEU A 251 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 448 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 482 removed outlier: 6.698A pdb=" N LEU A 489 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A 481 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN A 487 " --> pdb=" O VAL A 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1004 through 1009 removed outlier: 3.778A pdb=" N VAL B1006 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.583A pdb=" N TYR B 42 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU B 39 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU B 54 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 41 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER D 33 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 67 removed outlier: 3.637A pdb=" N ASN B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 104 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU B 90 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR B 102 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS B 92 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE B 100 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N GLN D 45 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG B 103 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 47 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS B 105 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N THR D 49 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N ASN B 107 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU B 152 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS B 153 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.955A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 178 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 193 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 201 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.955A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 178 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 193 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 221 Processing sheet with id=AB2, first strand: chain 'B' and resid 258 through 263 removed outlier: 6.310A pdb=" N GLY B 274 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS B 261 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 272 " --> pdb=" O HIS B 261 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ARG B 263 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG B 270 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 316 through 317 removed outlier: 3.681A pdb=" N VAL B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 332 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER B 331 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR B 352 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 333 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.832A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 376 " --> pdb=" O CYS B 363 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.227A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 742 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 750 " --> pdb=" O VAL B 742 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.227A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N HIS B 789 " --> pdb=" O GLN B 806 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN B 806 " --> pdb=" O HIS B 789 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU B 791 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 804 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 793 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 811 through 819 removed outlier: 6.258A pdb=" N GLY B 832 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 816 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE B 830 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER B 818 " --> pdb=" O TYR B 828 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR B 828 " --> pdb=" O SER B 818 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLN B 845 " --> pdb=" O MET B 835 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN B 852 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR B 860 " --> pdb=" O GLN B 852 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER B 854 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 874 through 876 Processing sheet with id=AB9, first strand: chain 'B' and resid 911 through 917 Processing sheet with id=AC1, first strand: chain 'B' and resid 956 through 961 removed outlier: 3.529A pdb=" N ALA B 956 " --> pdb=" O ALA B 968 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN B 964 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1076 through 1077 330 hydrogen bonds defined for protein. 882 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: 3.26 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1991 1.33 - 1.45: 1462 1.45 - 1.57: 3922 1.57 - 1.69: 2 1.69 - 1.81: 25 Bond restraints: 7402 Sorted by residual: bond pdb=" C3 A1H17 A 701 " pdb=" S A1H17 A 701 " ideal model delta sigma weight residual 1.750 1.644 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta sigma weight residual 1.456 1.494 -0.038 9.50e-03 1.11e+04 1.60e+01 bond pdb=" N VAL B 957 " pdb=" CA VAL B 957 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.22e+01 bond pdb=" N VAL B 322 " pdb=" CA VAL B 322 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.14e-02 7.69e+03 1.17e+01 bond pdb=" N VAL B 212 " pdb=" CA VAL B 212 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.10e+01 ... (remaining 7397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 9472 1.97 - 3.94: 705 3.94 - 5.91: 32 5.91 - 7.89: 3 7.89 - 9.86: 4 Bond angle restraints: 10216 Sorted by residual: angle pdb=" N SER B 955 " pdb=" CA SER B 955 " pdb=" C SER B 955 " ideal model delta sigma weight residual 113.97 108.48 5.49 1.28e+00 6.10e-01 1.84e+01 angle pdb=" C ASN B 885 " pdb=" CA ASN B 885 " pdb=" CB ASN B 885 " ideal model delta sigma weight residual 116.54 111.96 4.58 1.15e+00 7.56e-01 1.59e+01 angle pdb=" N LEU B 717 " pdb=" CA LEU B 717 " pdb=" C LEU B 717 " ideal model delta sigma weight residual 114.31 109.18 5.13 1.29e+00 6.01e-01 1.58e+01 angle pdb=" CA VAL A 126 " pdb=" C VAL A 126 " pdb=" O VAL A 126 " ideal model delta sigma weight residual 121.63 117.75 3.88 9.90e-01 1.02e+00 1.54e+01 angle pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" C VAL A 123 " ideal model delta sigma weight residual 113.53 109.84 3.69 9.80e-01 1.04e+00 1.42e+01 ... (remaining 10211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 3856 15.78 - 31.56: 237 31.56 - 47.33: 59 47.33 - 63.11: 21 63.11 - 78.89: 2 Dihedral angle restraints: 4175 sinusoidal: 890 harmonic: 3285 Sorted by residual: dihedral pdb=" CB CYS B 18 " pdb=" SG CYS B 18 " pdb=" SG CYS B 313 " pdb=" CB CYS B 313 " ideal model delta sinusoidal sigma weight residual 93.00 157.91 -64.91 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CA THR A 447 " pdb=" C THR A 447 " pdb=" N LEU A 448 " pdb=" CA LEU A 448 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LEU A 53 " pdb=" C LEU A 53 " pdb=" N PHE A 54 " pdb=" CA PHE A 54 " ideal model delta harmonic sigma weight residual 180.00 163.42 16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 4172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 814 0.054 - 0.107: 282 0.107 - 0.161: 122 0.161 - 0.215: 49 0.215 - 0.268: 1 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA ILE B 848 " pdb=" N ILE B 848 " pdb=" C ILE B 848 " pdb=" CB ILE B 848 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE B 41 " pdb=" N ILE B 41 " pdb=" C ILE B 41 " pdb=" CB ILE B 41 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA VAL B 850 " pdb=" N VAL B 850 " pdb=" C VAL B 850 " pdb=" CB VAL B 850 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1265 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 134 " -0.434 9.50e-02 1.11e+02 1.95e-01 2.33e+01 pdb=" NE ARG B 134 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 134 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 134 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 134 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 117 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C GLU B 117 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU B 117 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B 118 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 132 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C GLY B 132 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY B 132 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 133 " -0.011 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2481 2.83 - 3.35: 6380 3.35 - 3.87: 11245 3.87 - 4.38: 11631 4.38 - 4.90: 20853 Nonbonded interactions: 52590 Sorted by model distance: nonbonded pdb=" O SER A 96 " pdb=" N TYR A 107 " model vdw 2.316 3.120 nonbonded pdb=" OG1 THR A 247 " pdb=" O SER A 250 " model vdw 2.403 3.040 nonbonded pdb=" N LEU A 109 " pdb=" O VAL A 126 " model vdw 2.410 3.120 nonbonded pdb=" OG SER A 250 " pdb=" O LEU A 448 " model vdw 2.414 3.040 nonbonded pdb=" N SER B 955 " pdb=" O ALA B 968 " model vdw 2.443 3.120 ... (remaining 52585 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.650 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.008 0.106 7402 Z= 0.576 Angle : 1.015 9.856 10216 Z= 0.716 Chirality : 0.070 0.268 1268 Planarity : 0.006 0.195 1319 Dihedral : 12.768 78.888 2040 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.59 % Allowed : 20.28 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.25), residues: 1088 helix: 0.06 (0.44), residues: 142 sheet: -1.26 (0.24), residues: 449 loop : -1.44 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 464 HIS 0.005 0.001 HIS A 259 PHE 0.021 0.002 PHE D 19 TYR 0.024 0.001 TYR B 913 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.7598 (m100) cc_final: 0.7303 (m100) REVERT: A 114 PHE cc_start: 0.8289 (t80) cc_final: 0.8076 (t80) REVERT: B 990 GLN cc_start: 0.9265 (mt0) cc_final: 0.9057 (mp10) outliers start: 8 outliers final: 1 residues processed: 133 average time/residue: 0.1514 time to fit residues: 28.9376 Evaluate side-chains 103 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083196 restraints weight = 25832.137| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.83 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7402 Z= 0.147 Angle : 0.520 8.110 10216 Z= 0.273 Chirality : 0.044 0.139 1268 Planarity : 0.003 0.028 1319 Dihedral : 5.537 53.695 1172 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.38 % Allowed : 21.27 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.25), residues: 1088 helix: 1.28 (0.46), residues: 143 sheet: -0.91 (0.24), residues: 463 loop : -1.09 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 112 HIS 0.004 0.001 HIS A 514 PHE 0.018 0.001 PHE B 323 TYR 0.020 0.001 TYR A 226 ARG 0.002 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 473 ASP cc_start: 0.7922 (p0) cc_final: 0.7587 (p0) REVERT: A 548 TRP cc_start: 0.8239 (m100) cc_final: 0.7096 (m100) REVERT: B 326 SER cc_start: 0.8825 (t) cc_final: 0.8084 (p) REVERT: B 732 CYS cc_start: 0.8705 (m) cc_final: 0.8417 (t) REVERT: B 733 PHE cc_start: 0.8874 (m-80) cc_final: 0.8472 (m-80) outliers start: 17 outliers final: 11 residues processed: 121 average time/residue: 0.1492 time to fit residues: 27.6480 Evaluate side-chains 110 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 866 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079108 restraints weight = 26394.291| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.65 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7402 Z= 0.303 Angle : 0.561 8.418 10216 Z= 0.299 Chirality : 0.045 0.130 1268 Planarity : 0.003 0.033 1319 Dihedral : 5.775 52.852 1172 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 6.96 % Allowed : 19.28 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1088 helix: 1.98 (0.47), residues: 134 sheet: -0.86 (0.24), residues: 464 loop : -0.90 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 562 HIS 0.005 0.001 HIS B 905 PHE 0.017 0.002 PHE B1097 TYR 0.015 0.002 TYR B 193 ARG 0.004 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 473 ASP cc_start: 0.8398 (p0) cc_final: 0.8005 (p0) REVERT: A 548 TRP cc_start: 0.8293 (m100) cc_final: 0.7250 (m100) REVERT: B 170 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8655 (mt) REVERT: B 1093 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8681 (tt) REVERT: B 1096 SER cc_start: 0.9482 (m) cc_final: 0.9270 (p) outliers start: 35 outliers final: 24 residues processed: 120 average time/residue: 0.1320 time to fit residues: 25.2530 Evaluate side-chains 116 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.095395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.079176 restraints weight = 26869.358| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.90 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7402 Z= 0.228 Angle : 0.505 8.341 10216 Z= 0.266 Chirality : 0.044 0.135 1268 Planarity : 0.003 0.058 1319 Dihedral : 5.422 48.142 1172 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.77 % Allowed : 21.07 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1088 helix: 2.22 (0.47), residues: 134 sheet: -0.62 (0.25), residues: 446 loop : -0.91 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 464 HIS 0.009 0.001 HIS A 514 PHE 0.010 0.001 PHE B1030 TYR 0.016 0.001 TYR A 226 ARG 0.002 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 1.164 Fit side-chains REVERT: A 473 ASP cc_start: 0.8343 (p0) cc_final: 0.7892 (p0) REVERT: A 548 TRP cc_start: 0.8297 (m100) cc_final: 0.7155 (m100) REVERT: B 183 GLN cc_start: 0.7848 (pp30) cc_final: 0.7480 (pm20) REVERT: B 207 TRP cc_start: 0.8953 (OUTLIER) cc_final: 0.8670 (p-90) REVERT: B 732 CYS cc_start: 0.9016 (m) cc_final: 0.8479 (t) outliers start: 29 outliers final: 23 residues processed: 121 average time/residue: 0.2106 time to fit residues: 39.2657 Evaluate side-chains 114 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 0.0040 chunk 11 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.096129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081062 restraints weight = 26093.312| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 4.64 r_work: 0.3251 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7402 Z= 0.171 Angle : 0.479 7.056 10216 Z= 0.250 Chirality : 0.044 0.158 1268 Planarity : 0.003 0.031 1319 Dihedral : 5.142 44.557 1172 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.57 % Allowed : 22.07 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1088 helix: 2.29 (0.48), residues: 134 sheet: -0.47 (0.26), residues: 435 loop : -0.83 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 464 HIS 0.006 0.001 HIS A 514 PHE 0.013 0.001 PHE B1030 TYR 0.020 0.001 TYR A 226 ARG 0.002 0.000 ARG B 739 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.578 Fit side-chains REVERT: A 226 TYR cc_start: 0.8745 (t80) cc_final: 0.8408 (t80) REVERT: A 473 ASP cc_start: 0.8513 (p0) cc_final: 0.8001 (p0) REVERT: A 548 TRP cc_start: 0.8125 (m100) cc_final: 0.6968 (m100) REVERT: B 183 GLN cc_start: 0.7962 (pp30) cc_final: 0.7735 (pm20) REVERT: B 727 GLN cc_start: 0.9012 (tt0) cc_final: 0.8744 (tt0) REVERT: B 732 CYS cc_start: 0.9270 (m) cc_final: 0.8685 (t) REVERT: B 990 GLN cc_start: 0.8868 (mp10) cc_final: 0.8666 (mp10) outliers start: 28 outliers final: 24 residues processed: 119 average time/residue: 0.1623 time to fit residues: 30.7980 Evaluate side-chains 118 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.073435 restraints weight = 27644.114| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 4.73 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 7402 Z= 0.480 Angle : 0.631 7.020 10216 Z= 0.344 Chirality : 0.046 0.160 1268 Planarity : 0.004 0.053 1319 Dihedral : 6.034 51.387 1172 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 7.75 % Allowed : 21.07 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1088 helix: 2.04 (0.47), residues: 133 sheet: -0.64 (0.26), residues: 432 loop : -1.10 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 562 HIS 0.008 0.001 HIS A 514 PHE 0.019 0.002 PHE B1097 TYR 0.014 0.002 TYR B 812 ARG 0.004 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 1.873 Fit side-chains REVERT: A 473 ASP cc_start: 0.8400 (p0) cc_final: 0.7896 (p0) REVERT: A 548 TRP cc_start: 0.8288 (m100) cc_final: 0.7328 (m100) REVERT: B 207 TRP cc_start: 0.9014 (OUTLIER) cc_final: 0.8669 (p-90) outliers start: 39 outliers final: 30 residues processed: 109 average time/residue: 0.2775 time to fit residues: 48.4299 Evaluate side-chains 110 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.077998 restraints weight = 26689.819| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 4.82 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7402 Z= 0.147 Angle : 0.499 6.755 10216 Z= 0.257 Chirality : 0.045 0.133 1268 Planarity : 0.003 0.042 1319 Dihedral : 5.192 43.603 1172 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.98 % Allowed : 25.25 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1088 helix: 2.13 (0.48), residues: 135 sheet: -0.46 (0.26), residues: 430 loop : -0.98 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 464 HIS 0.005 0.001 HIS A 514 PHE 0.013 0.001 PHE B1030 TYR 0.029 0.001 TYR A 226 ARG 0.001 0.000 ARG B 739 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.799 Fit side-chains REVERT: A 231 PHE cc_start: 0.8010 (t80) cc_final: 0.7544 (t80) REVERT: A 267 CYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7468 (p) REVERT: A 473 ASP cc_start: 0.8475 (p0) cc_final: 0.7968 (p0) REVERT: A 548 TRP cc_start: 0.8230 (m100) cc_final: 0.7134 (m100) REVERT: A 558 MET cc_start: 0.8983 (tpp) cc_final: 0.8550 (tpt) REVERT: B 207 TRP cc_start: 0.9010 (OUTLIER) cc_final: 0.8686 (p-90) REVERT: B 732 CYS cc_start: 0.8975 (m) cc_final: 0.8496 (t) REVERT: B 990 GLN cc_start: 0.8879 (mp10) cc_final: 0.8575 (mp10) outliers start: 20 outliers final: 16 residues processed: 108 average time/residue: 0.1194 time to fit residues: 20.5699 Evaluate side-chains 106 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1082 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 4 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076416 restraints weight = 27543.510| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.81 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7402 Z= 0.296 Angle : 0.532 6.366 10216 Z= 0.282 Chirality : 0.045 0.147 1268 Planarity : 0.003 0.030 1319 Dihedral : 5.405 45.660 1172 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.37 % Allowed : 23.86 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1088 helix: 2.21 (0.48), residues: 134 sheet: -0.50 (0.26), residues: 428 loop : -1.04 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 562 HIS 0.006 0.001 HIS A 514 PHE 0.011 0.001 PHE B1097 TYR 0.020 0.001 TYR A 226 ARG 0.003 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 1.034 Fit side-chains REVERT: A 226 TYR cc_start: 0.8661 (t80) cc_final: 0.8286 (t80) REVERT: A 231 PHE cc_start: 0.8087 (t80) cc_final: 0.7595 (t80) REVERT: A 473 ASP cc_start: 0.8499 (p0) cc_final: 0.8012 (p0) REVERT: A 548 TRP cc_start: 0.8236 (m100) cc_final: 0.7282 (m100) REVERT: B 207 TRP cc_start: 0.9023 (OUTLIER) cc_final: 0.8707 (p-90) REVERT: B 732 CYS cc_start: 0.8982 (m) cc_final: 0.8531 (t) REVERT: B 990 GLN cc_start: 0.8895 (mp10) cc_final: 0.8588 (mp10) outliers start: 27 outliers final: 22 residues processed: 106 average time/residue: 0.1350 time to fit residues: 23.9164 Evaluate side-chains 107 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1082 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.092902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.077186 restraints weight = 27463.110| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 4.84 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7402 Z= 0.201 Angle : 0.502 7.205 10216 Z= 0.260 Chirality : 0.044 0.144 1268 Planarity : 0.003 0.050 1319 Dihedral : 5.129 42.340 1172 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.37 % Allowed : 24.65 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1088 helix: 2.19 (0.48), residues: 135 sheet: -0.50 (0.26), residues: 427 loop : -1.06 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 562 HIS 0.005 0.001 HIS A 514 PHE 0.011 0.001 PHE B1030 TYR 0.018 0.001 TYR A 226 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 2.139 Fit side-chains REVERT: A 226 TYR cc_start: 0.8654 (t80) cc_final: 0.8282 (t80) REVERT: A 231 PHE cc_start: 0.8065 (t80) cc_final: 0.7548 (t80) REVERT: A 473 ASP cc_start: 0.8489 (p0) cc_final: 0.7999 (p0) REVERT: A 548 TRP cc_start: 0.8222 (m100) cc_final: 0.7242 (m100) REVERT: B 207 TRP cc_start: 0.9035 (OUTLIER) cc_final: 0.8722 (p-90) REVERT: B 732 CYS cc_start: 0.8945 (m) cc_final: 0.8502 (t) REVERT: B 990 GLN cc_start: 0.8910 (mp10) cc_final: 0.8578 (mp10) outliers start: 22 outliers final: 21 residues processed: 111 average time/residue: 0.1507 time to fit residues: 28.4192 Evaluate side-chains 112 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 95 optimal weight: 0.0370 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.0060 chunk 81 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.096260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081217 restraints weight = 26954.648| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 4.68 r_work: 0.3247 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7402 Z= 0.136 Angle : 0.488 7.180 10216 Z= 0.250 Chirality : 0.044 0.170 1268 Planarity : 0.003 0.030 1319 Dihedral : 4.775 37.704 1172 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.97 % Allowed : 24.45 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.26), residues: 1088 helix: 2.25 (0.48), residues: 135 sheet: -0.33 (0.26), residues: 420 loop : -1.05 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 562 HIS 0.004 0.001 HIS A 117 PHE 0.013 0.001 PHE B1030 TYR 0.019 0.001 TYR A 226 ARG 0.002 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.924 Fit side-chains REVERT: A 226 TYR cc_start: 0.8692 (t80) cc_final: 0.8324 (t80) REVERT: A 231 PHE cc_start: 0.7939 (t80) cc_final: 0.7399 (t80) REVERT: A 473 ASP cc_start: 0.8624 (p0) cc_final: 0.8116 (p0) REVERT: A 548 TRP cc_start: 0.8038 (m100) cc_final: 0.7078 (m100) REVERT: B 207 TRP cc_start: 0.9030 (OUTLIER) cc_final: 0.8740 (p-90) REVERT: B 732 CYS cc_start: 0.9212 (m) cc_final: 0.8684 (t) REVERT: B 990 GLN cc_start: 0.9042 (mp10) cc_final: 0.8717 (mp10) outliers start: 25 outliers final: 23 residues processed: 111 average time/residue: 0.1638 time to fit residues: 28.9677 Evaluate side-chains 115 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.093448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078481 restraints weight = 29060.187| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 4.54 r_work: 0.3134 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7402 Z= 0.455 Angle : 0.615 6.982 10216 Z= 0.332 Chirality : 0.046 0.206 1268 Planarity : 0.004 0.050 1319 Dihedral : 5.689 46.459 1172 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.96 % Allowed : 23.66 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1088 helix: 2.04 (0.48), residues: 133 sheet: -0.47 (0.26), residues: 416 loop : -1.21 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 562 HIS 0.007 0.001 HIS A 514 PHE 0.016 0.002 PHE B1097 TYR 0.018 0.002 TYR A 226 ARG 0.005 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3207.48 seconds wall clock time: 59 minutes 21.16 seconds (3561.16 seconds total)