Starting phenix.real_space_refine on Sun Apr 5 10:30:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mc7_63791/04_2026/9mc7_63791_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mc7_63791/04_2026/9mc7_63791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mc7_63791/04_2026/9mc7_63791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mc7_63791/04_2026/9mc7_63791.map" model { file = "/net/cci-nas-00/data/ceres_data/9mc7_63791/04_2026/9mc7_63791_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mc7_63791/04_2026/9mc7_63791_neut.cif" } resolution = 3.34 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= 0.007 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 P 1 5.49 5 S 46 5.16 5 C 6006 2.51 5 N 1617 2.21 5 O 1764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9434 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 855, 6735 Classifications: {'peptide': 855} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 811} Chain breaks: 3 Chain: "B" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2074 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 1 Chain: "C" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.53, per 1000 atoms: 0.27 Number of scatterers: 9434 At special positions: 0 Unit cell: (79.704, 102.384, 124.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 1 15.00 O 1764 8.00 N 1617 7.00 C 6006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 559.2 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2214 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 10 sheets defined 45.4% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 126 through 136 Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.840A pdb=" N ALA A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.803A pdb=" N PHE A 323 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 344 removed outlier: 3.759A pdb=" N GLN A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.885A pdb=" N LEU A 445 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 removed outlier: 3.629A pdb=" N VAL A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.576A pdb=" N LYS A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.605A pdb=" N ASN A 514 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.618A pdb=" N VAL A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 561 through 568 removed outlier: 3.537A pdb=" N PHE A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 591 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 640 through 657 removed outlier: 3.595A pdb=" N THR A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP A 647 " --> pdb=" O HIS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 719 Processing helix chain 'A' and resid 719 through 729 Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.521A pdb=" N ASP A 763 " --> pdb=" O PRO A 759 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A 765 " --> pdb=" O HIS A 761 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 879 through 888 Processing helix chain 'A' and resid 894 through 914 removed outlier: 3.625A pdb=" N THR A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 914 " --> pdb=" O TYR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'A' and resid 971 through 983 removed outlier: 3.735A pdb=" N PHE A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1011 Processing helix chain 'A' and resid 1014 through 1024 Processing helix chain 'B' and resid 950 through 969 removed outlier: 3.798A pdb=" N THR B 967 " --> pdb=" O ALA B 963 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1015 removed outlier: 3.568A pdb=" N VAL B1015 " --> pdb=" O TYR B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1045 Processing helix chain 'B' and resid 1050 through 1054 Processing helix chain 'B' and resid 1061 through 1072 Processing helix chain 'B' and resid 1076 through 1081 removed outlier: 3.507A pdb=" N TYR B1079 " --> pdb=" O GLU B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1088 Processing helix chain 'B' and resid 1090 through 1118 Processing helix chain 'B' and resid 1123 through 1151 removed outlier: 4.432A pdb=" N THR B1133 " --> pdb=" O GLN B1129 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N TRP B1136 " --> pdb=" O SER B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1262 through 1284 removed outlier: 4.064A pdb=" N GLY B1271 " --> pdb=" O LYS B1267 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B1284 " --> pdb=" O LEU B1280 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 147 removed outlier: 6.852A pdb=" N VAL A 75 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N HIS A 102 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 77 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER A 74 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL A 163 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU A 76 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR A 165 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N SER A 78 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 162 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA A 189 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU A 164 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N THR A 191 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR A 425 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 266 removed outlier: 7.072A pdb=" N THR A 233 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 224 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL A 231 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 548 removed outlier: 6.589A pdb=" N ILE A 500 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N HIS A 548 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 502 " --> pdb=" O HIS A 548 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 503 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS A 470 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA A 572 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE A 472 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 571 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N SER A 598 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A 573 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N THR A 600 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 933 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 944 through 947 Processing sheet with id=AA6, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.721A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU A1037 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU A 990 " --> pdb=" O GLU A1037 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS A1039 " --> pdb=" O THR A 988 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.721A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS A1040 " --> pdb=" O VAL A1048 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 973 through 977 Processing sheet with id=AA9, first strand: chain 'B' and resid 1033 through 1034 removed outlier: 3.557A pdb=" N LYS B1038 " --> pdb=" O TYR B1034 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 12 through 16 removed outlier: 8.744A pdb=" N LEU C 67 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE C 4 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU C 69 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS C 6 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG C 42 " --> pdb=" O VAL C 70 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1161 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: 1.90 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2306 1.33 - 1.45: 1913 1.45 - 1.58: 5351 1.58 - 1.70: 1 1.70 - 1.82: 72 Bond restraints: 9643 Sorted by residual: bond pdb=" C4 AMP A1101 " pdb=" C5 AMP A1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C5 AMP A1101 " pdb=" C6 AMP A1101 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N VAL B 975 " pdb=" CA VAL B 975 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.14e-02 7.69e+03 1.49e+01 bond pdb=" CA ILE A 611 " pdb=" C ILE A 611 " ideal model delta sigma weight residual 1.524 1.561 -0.036 1.05e-02 9.07e+03 1.18e+01 bond pdb=" N VAL A1048 " pdb=" CA VAL A1048 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.12e+01 ... (remaining 9638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11781 2.39 - 4.78: 1173 4.78 - 7.17: 99 7.17 - 9.56: 9 9.56 - 11.95: 1 Bond angle restraints: 13063 Sorted by residual: angle pdb=" CA GLY A 230 " pdb=" C GLY A 230 " pdb=" O GLY A 230 " ideal model delta sigma weight residual 122.24 117.26 4.98 8.70e-01 1.32e+00 3.28e+01 angle pdb=" C THR B 977 " pdb=" N PHE B 978 " pdb=" CA PHE B 978 " ideal model delta sigma weight residual 122.53 114.99 7.54 1.61e+00 3.86e-01 2.19e+01 angle pdb=" CA GLU A 616 " pdb=" C GLU A 616 " pdb=" O GLU A 616 " ideal model delta sigma weight residual 121.94 116.66 5.28 1.15e+00 7.56e-01 2.10e+01 angle pdb=" N LEU B1061 " pdb=" CA LEU B1061 " pdb=" C LEU B1061 " ideal model delta sigma weight residual 113.18 107.98 5.20 1.21e+00 6.83e-01 1.85e+01 angle pdb=" CA LYS A 416 " pdb=" C LYS A 416 " pdb=" O LYS A 416 " ideal model delta sigma weight residual 121.87 117.04 4.83 1.16e+00 7.43e-01 1.73e+01 ... (remaining 13058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.23: 5528 26.23 - 52.46: 232 52.46 - 78.69: 38 78.69 - 104.92: 4 104.92 - 131.15: 1 Dihedral angle restraints: 5803 sinusoidal: 2371 harmonic: 3432 Sorted by residual: dihedral pdb=" C5' AMP A1101 " pdb=" O5' AMP A1101 " pdb=" P AMP A1101 " pdb=" O3P AMP A1101 " ideal model delta sinusoidal sigma weight residual 300.00 168.85 131.15 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" C2' AMP A1101 " pdb=" C1' AMP A1101 " pdb=" N9 AMP A1101 " pdb=" C4 AMP A1101 " ideal model delta sinusoidal sigma weight residual 91.55 163.19 -71.64 1 2.00e+01 2.50e-03 1.64e+01 dihedral pdb=" C4' AMP A1101 " pdb=" C5' AMP A1101 " pdb=" O5' AMP A1101 " pdb=" P AMP A1101 " ideal model delta sinusoidal sigma weight residual 180.00 111.47 68.53 1 2.00e+01 2.50e-03 1.52e+01 ... (remaining 5800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1053 0.072 - 0.144: 287 0.144 - 0.216: 74 0.216 - 0.288: 23 0.288 - 0.360: 2 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CA PHE A 613 " pdb=" N PHE A 613 " pdb=" C PHE A 613 " pdb=" CB PHE A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CG LEU A 963 " pdb=" CB LEU A 963 " pdb=" CD1 LEU A 963 " pdb=" CD2 LEU A 963 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA PRO B1077 " pdb=" N PRO B1077 " pdb=" C PRO B1077 " pdb=" CB PRO B1077 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 1436 not shown) Planarity restraints: 1706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1002 " 0.191 2.00e-02 2.50e+03 1.02e-01 2.08e+02 pdb=" CG TYR B1002 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR B1002 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 TYR B1002 " -0.089 2.00e-02 2.50e+03 pdb=" CE1 TYR B1002 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR B1002 " -0.047 2.00e-02 2.50e+03 pdb=" CZ TYR B1002 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B1002 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1100 " 0.160 2.00e-02 2.50e+03 8.80e-02 1.55e+02 pdb=" CG TYR B1100 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B1100 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR B1100 " -0.076 2.00e-02 2.50e+03 pdb=" CE1 TYR B1100 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR B1100 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR B1100 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR B1100 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 273 " 0.114 2.00e-02 2.50e+03 6.43e-02 8.26e+01 pdb=" CG TYR A 273 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 273 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 273 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 273 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 273 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR A 273 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 273 " 0.105 2.00e-02 2.50e+03 ... (remaining 1703 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 2 2.52 - 3.11: 6916 3.11 - 3.71: 14355 3.71 - 4.30: 20552 4.30 - 4.90: 34053 Nonbonded interactions: 75878 Sorted by model distance: nonbonded pdb=" OG SER A 113 " pdb=" OD2 ASP A 393 " model vdw 1.924 3.040 nonbonded pdb=" N THR B 977 " pdb=" O THR B 977 " model vdw 2.498 2.496 nonbonded pdb=" OD1 ASP C 21 " pdb=" O THR C 22 " model vdw 2.521 3.040 nonbonded pdb=" N GLU C 18 " pdb=" OE1 GLU C 18 " model vdw 2.545 3.120 nonbonded pdb=" O GLY A 82 " pdb=" N GLY A 84 " model vdw 2.566 3.120 ... (remaining 75873 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: 8.100 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.009 0.109 9643 Z= 0.581 Angle : 1.365 11.948 13063 Z= 0.888 Chirality : 0.075 0.360 1439 Planarity : 0.012 0.213 1706 Dihedral : 14.602 131.155 3589 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.29 % Allowed : 10.80 % Favored : 88.91 % 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: -0.87 (0.23), residues: 1175 helix: -0.49 (0.22), residues: 454 sheet: -0.09 (0.36), residues: 178 loop : -0.68 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 72 TYR 0.191 0.018 TYR B1002 PHE 0.063 0.008 PHE A 320 TRP 0.084 0.007 TRP A 952 HIS 0.008 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00940 ( 9643) covalent geometry : angle 1.36537 (13063) hydrogen bonds : bond 0.16385 ( 427) hydrogen bonds : angle 7.60083 ( 1161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.7527 (mt0) cc_final: 0.7180 (mt0) REVERT: A 291 ILE cc_start: 0.8397 (tt) cc_final: 0.8121 (mp) REVERT: A 584 MET cc_start: 0.8570 (mpp) cc_final: 0.8219 (mmt) REVERT: A 647 TRP cc_start: 0.8845 (t60) cc_final: 0.8241 (t60) REVERT: A 714 TRP cc_start: 0.6744 (m100) cc_final: 0.6388 (t-100) REVERT: C 23 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7183 (mp) REVERT: C 27 LYS cc_start: 0.8447 (mttm) cc_final: 0.8202 (mttm) REVERT: C 51 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6116 (mm-30) REVERT: C 60 ASN cc_start: 0.8980 (t0) cc_final: 0.8767 (t0) outliers start: 3 outliers final: 1 residues processed: 145 average time/residue: 0.0958 time to fit residues: 19.9556 Evaluate side-chains 112 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain C residue 23 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0470 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B1024 GLN C 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.194663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.144067 restraints weight = 18276.315| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 4.49 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9643 Z= 0.131 Angle : 0.635 7.712 13063 Z= 0.323 Chirality : 0.043 0.152 1439 Planarity : 0.005 0.046 1706 Dihedral : 6.941 132.966 1295 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.56 % Allowed : 10.99 % Favored : 87.45 % 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: -0.00 (0.24), residues: 1175 helix: 0.62 (0.24), residues: 462 sheet: -0.03 (0.35), residues: 185 loop : -0.44 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 981 TYR 0.013 0.002 TYR B1002 PHE 0.030 0.002 PHE B 934 TRP 0.014 0.002 TRP A 952 HIS 0.002 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9643) covalent geometry : angle 0.63490 (13063) hydrogen bonds : bond 0.04455 ( 427) hydrogen bonds : angle 5.39822 ( 1161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ILE cc_start: 0.8303 (tt) cc_final: 0.7927 (mp) REVERT: A 584 MET cc_start: 0.8380 (mpp) cc_final: 0.8062 (mmm) REVERT: A 647 TRP cc_start: 0.8818 (t60) cc_final: 0.8351 (t60) REVERT: A 714 TRP cc_start: 0.7158 (m100) cc_final: 0.6659 (t-100) REVERT: A 1013 GLN cc_start: 0.7019 (mt0) cc_final: 0.6667 (tt0) REVERT: B 976 LYS cc_start: 0.7239 (tptt) cc_final: 0.6772 (tptt) REVERT: B 985 PHE cc_start: 0.4261 (OUTLIER) cc_final: 0.3920 (t80) REVERT: B 1123 PHE cc_start: 0.8280 (m-80) cc_final: 0.7997 (m-80) outliers start: 16 outliers final: 6 residues processed: 134 average time/residue: 0.0956 time to fit residues: 18.2428 Evaluate side-chains 113 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain B residue 985 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 94 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B1032 ASN B1080 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.192550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.141268 restraints weight = 18147.726| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 4.44 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9643 Z= 0.147 Angle : 0.608 9.419 13063 Z= 0.306 Chirality : 0.042 0.143 1439 Planarity : 0.004 0.052 1706 Dihedral : 6.487 132.417 1291 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.85 % Allowed : 12.55 % Favored : 85.60 % 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: 0.16 (0.24), residues: 1175 helix: 0.80 (0.24), residues: 469 sheet: -0.00 (0.37), residues: 171 loop : -0.38 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1270 TYR 0.011 0.001 TYR A 978 PHE 0.021 0.002 PHE B 934 TRP 0.014 0.002 TRP A 952 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9643) covalent geometry : angle 0.60845 (13063) hydrogen bonds : bond 0.04251 ( 427) hydrogen bonds : angle 5.07158 ( 1161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ILE cc_start: 0.8283 (tt) cc_final: 0.7837 (mp) REVERT: A 377 ASN cc_start: 0.8019 (t0) cc_final: 0.7771 (t0) REVERT: A 463 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.6792 (tm130) REVERT: A 584 MET cc_start: 0.8438 (mpp) cc_final: 0.8056 (mmm) REVERT: A 647 TRP cc_start: 0.8805 (t60) cc_final: 0.8330 (t60) REVERT: A 714 TRP cc_start: 0.7112 (m100) cc_final: 0.6585 (t-100) REVERT: A 1013 GLN cc_start: 0.7071 (mt0) cc_final: 0.6682 (tt0) REVERT: B 1123 PHE cc_start: 0.8167 (m-80) cc_final: 0.7947 (m-80) REVERT: C 18 GLU cc_start: 0.7745 (mp0) cc_final: 0.7490 (mp0) outliers start: 19 outliers final: 11 residues processed: 128 average time/residue: 0.0825 time to fit residues: 15.8773 Evaluate side-chains 117 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain B residue 1131 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 ASN A 643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.191716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.140675 restraints weight = 18376.369| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 4.45 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9643 Z= 0.155 Angle : 0.591 8.816 13063 Z= 0.299 Chirality : 0.042 0.159 1439 Planarity : 0.004 0.052 1706 Dihedral : 6.422 134.352 1291 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.92 % Allowed : 12.65 % Favored : 84.44 % 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: 0.29 (0.25), residues: 1175 helix: 0.83 (0.24), residues: 474 sheet: 0.21 (0.37), residues: 190 loop : -0.30 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1270 TYR 0.011 0.001 TYR A 978 PHE 0.027 0.002 PHE B1259 TRP 0.013 0.002 TRP A 952 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9643) covalent geometry : angle 0.59061 (13063) hydrogen bonds : bond 0.04041 ( 427) hydrogen bonds : angle 4.94459 ( 1161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 ILE cc_start: 0.8247 (tt) cc_final: 0.7833 (mp) REVERT: A 377 ASN cc_start: 0.8085 (t0) cc_final: 0.7847 (t0) REVERT: A 463 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.6877 (tm130) REVERT: A 584 MET cc_start: 0.8397 (mpp) cc_final: 0.7997 (mmm) REVERT: A 647 TRP cc_start: 0.8805 (t60) cc_final: 0.8300 (t60) REVERT: A 714 TRP cc_start: 0.7070 (m100) cc_final: 0.6517 (t-100) REVERT: A 1013 GLN cc_start: 0.7105 (mt0) cc_final: 0.6425 (mp10) REVERT: B 976 LYS cc_start: 0.7658 (tptp) cc_final: 0.7274 (tptt) REVERT: B 1123 PHE cc_start: 0.8225 (m-80) cc_final: 0.7990 (m-80) REVERT: C 18 GLU cc_start: 0.7812 (mp0) cc_final: 0.7477 (mp0) REVERT: C 31 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.6896 (tp40) outliers start: 30 outliers final: 17 residues processed: 128 average time/residue: 0.0802 time to fit residues: 15.5855 Evaluate side-chains 119 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 112 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.191871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.140862 restraints weight = 17985.600| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 4.16 r_work: 0.3707 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9643 Z= 0.130 Angle : 0.579 8.062 13063 Z= 0.291 Chirality : 0.041 0.154 1439 Planarity : 0.004 0.051 1706 Dihedral : 6.307 133.626 1291 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.33 % Allowed : 13.33 % Favored : 84.34 % 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: 0.42 (0.25), residues: 1175 helix: 1.01 (0.24), residues: 468 sheet: 0.16 (0.39), residues: 176 loop : -0.24 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.012 0.001 TYR A 471 PHE 0.031 0.002 PHE A 517 TRP 0.012 0.001 TRP A 952 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9643) covalent geometry : angle 0.57891 (13063) hydrogen bonds : bond 0.03867 ( 427) hydrogen bonds : angle 4.82479 ( 1161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8252 (ppp) cc_final: 0.7947 (ppp) REVERT: A 291 ILE cc_start: 0.8257 (tt) cc_final: 0.7769 (mp) REVERT: A 463 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7051 (tm130) REVERT: A 584 MET cc_start: 0.8452 (mpp) cc_final: 0.8128 (mmm) REVERT: A 647 TRP cc_start: 0.8807 (t60) cc_final: 0.8184 (t60) REVERT: A 714 TRP cc_start: 0.6669 (m100) cc_final: 0.6163 (t-100) REVERT: A 1013 GLN cc_start: 0.7100 (mt0) cc_final: 0.6564 (mp10) REVERT: B 976 LYS cc_start: 0.7763 (tptp) cc_final: 0.7208 (tptt) REVERT: B 1123 PHE cc_start: 0.8103 (m-80) cc_final: 0.7803 (m-80) REVERT: C 31 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7031 (tp40) outliers start: 24 outliers final: 17 residues processed: 124 average time/residue: 0.0775 time to fit residues: 14.7212 Evaluate side-chains 120 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 102 optimal weight: 30.0000 chunk 1 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.191029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.139826 restraints weight = 18398.975| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 4.36 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9643 Z= 0.158 Angle : 0.605 10.167 13063 Z= 0.302 Chirality : 0.042 0.156 1439 Planarity : 0.004 0.053 1706 Dihedral : 6.263 131.456 1291 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.31 % Allowed : 13.13 % Favored : 83.56 % 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: 0.34 (0.25), residues: 1175 helix: 0.93 (0.24), residues: 474 sheet: 0.11 (0.39), residues: 176 loop : -0.27 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.011 0.001 TYR A 978 PHE 0.028 0.002 PHE B1259 TRP 0.012 0.002 TRP A 952 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9643) covalent geometry : angle 0.60524 (13063) hydrogen bonds : bond 0.03945 ( 427) hydrogen bonds : angle 4.83051 ( 1161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6950 (t-90) REVERT: A 206 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6665 (tmm) REVERT: A 256 MET cc_start: 0.4589 (ttm) cc_final: 0.4308 (ttm) REVERT: A 291 ILE cc_start: 0.8255 (tt) cc_final: 0.7812 (mp) REVERT: A 463 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.6852 (tm130) REVERT: A 584 MET cc_start: 0.8413 (mpp) cc_final: 0.8028 (mmm) REVERT: A 714 TRP cc_start: 0.7078 (m100) cc_final: 0.6252 (t-100) REVERT: A 1013 GLN cc_start: 0.7120 (mt0) cc_final: 0.6570 (mp10) REVERT: B 976 LYS cc_start: 0.7642 (tptp) cc_final: 0.7199 (tptt) REVERT: C 31 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.6873 (tp40) outliers start: 34 outliers final: 22 residues processed: 124 average time/residue: 0.0754 time to fit residues: 14.3237 Evaluate side-chains 123 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.190994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.140061 restraints weight = 18371.592| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 4.30 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9643 Z= 0.151 Angle : 0.601 9.274 13063 Z= 0.300 Chirality : 0.042 0.151 1439 Planarity : 0.004 0.052 1706 Dihedral : 6.176 128.554 1291 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.60 % Allowed : 13.04 % Favored : 83.37 % 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: 0.34 (0.25), residues: 1175 helix: 0.91 (0.24), residues: 476 sheet: 0.09 (0.39), residues: 168 loop : -0.25 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.011 0.001 TYR A 978 PHE 0.029 0.002 PHE B1259 TRP 0.013 0.002 TRP A 423 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9643) covalent geometry : angle 0.60139 (13063) hydrogen bonds : bond 0.03877 ( 427) hydrogen bonds : angle 4.81653 ( 1161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.6598 (tmm) REVERT: A 256 MET cc_start: 0.4658 (ttm) cc_final: 0.4253 (ttm) REVERT: A 291 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 463 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.6832 (tm130) REVERT: A 584 MET cc_start: 0.8418 (mpp) cc_final: 0.8049 (mmm) REVERT: A 714 TRP cc_start: 0.7078 (m100) cc_final: 0.6196 (t-100) REVERT: C 31 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6824 (tp40) outliers start: 37 outliers final: 23 residues processed: 120 average time/residue: 0.0788 time to fit residues: 14.4985 Evaluate side-chains 121 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 113 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.192459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.140802 restraints weight = 18381.221| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 4.33 r_work: 0.3727 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9643 Z= 0.118 Angle : 0.591 9.441 13063 Z= 0.291 Chirality : 0.041 0.173 1439 Planarity : 0.004 0.048 1706 Dihedral : 6.029 125.559 1291 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.82 % Allowed : 13.81 % Favored : 83.37 % 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: 0.40 (0.25), residues: 1175 helix: 1.00 (0.24), residues: 476 sheet: 0.07 (0.39), residues: 172 loop : -0.24 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.010 0.001 TYR A1052 PHE 0.039 0.002 PHE B1259 TRP 0.012 0.001 TRP A 522 HIS 0.003 0.000 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9643) covalent geometry : angle 0.59074 (13063) hydrogen bonds : bond 0.03653 ( 427) hydrogen bonds : angle 4.70849 ( 1161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6554 (tmm) REVERT: A 256 MET cc_start: 0.5073 (ttm) cc_final: 0.4690 (ttm) REVERT: A 291 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7728 (mp) REVERT: A 463 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7017 (tm130) REVERT: A 473 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8160 (mm) REVERT: A 584 MET cc_start: 0.8422 (mpp) cc_final: 0.8126 (mmm) REVERT: A 714 TRP cc_start: 0.6623 (m100) cc_final: 0.5831 (t-100) REVERT: B 1256 PHE cc_start: -0.2691 (OUTLIER) cc_final: -0.3596 (p90) REVERT: B 1259 PHE cc_start: 0.4956 (p90) cc_final: 0.4673 (p90) REVERT: C 31 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.6895 (tp40) outliers start: 29 outliers final: 19 residues processed: 121 average time/residue: 0.0835 time to fit residues: 15.1606 Evaluate side-chains 119 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain B residue 1256 PHE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 76 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 30.0000 chunk 83 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 5 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.187883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.136734 restraints weight = 18333.035| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 4.49 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9643 Z= 0.227 Angle : 0.686 8.298 13063 Z= 0.346 Chirality : 0.045 0.233 1439 Planarity : 0.005 0.058 1706 Dihedral : 6.187 117.659 1291 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.72 % Allowed : 14.40 % Favored : 82.88 % 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: 0.13 (0.24), residues: 1175 helix: 0.68 (0.23), residues: 471 sheet: 0.15 (0.40), residues: 168 loop : -0.35 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 944 TYR 0.017 0.002 TYR A 978 PHE 0.037 0.002 PHE B1259 TRP 0.013 0.002 TRP B1055 HIS 0.007 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 9643) covalent geometry : angle 0.68583 (13063) hydrogen bonds : bond 0.04455 ( 427) hydrogen bonds : angle 5.05019 ( 1161) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6644 (tmm) REVERT: A 256 MET cc_start: 0.4385 (ttm) cc_final: 0.4003 (ttm) REVERT: A 291 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7788 (mp) REVERT: A 435 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7339 (p0) REVERT: A 463 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.6756 (tm130) REVERT: A 584 MET cc_start: 0.8413 (mpp) cc_final: 0.8026 (mmm) REVERT: A 714 TRP cc_start: 0.6975 (m100) cc_final: 0.6648 (t-100) REVERT: B 1256 PHE cc_start: -0.2499 (OUTLIER) cc_final: -0.3309 (p90) REVERT: B 1259 PHE cc_start: 0.4763 (p90) cc_final: 0.4502 (p90) REVERT: C 18 GLU cc_start: 0.7607 (mp0) cc_final: 0.7364 (mp0) REVERT: C 31 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.6914 (tp40) outliers start: 28 outliers final: 17 residues processed: 111 average time/residue: 0.0848 time to fit residues: 14.2365 Evaluate side-chains 114 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain B residue 1256 PHE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 55 optimal weight: 0.4980 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.190989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.140993 restraints weight = 17937.952| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.90 r_work: 0.3706 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9643 Z= 0.132 Angle : 0.656 16.980 13063 Z= 0.321 Chirality : 0.043 0.209 1439 Planarity : 0.004 0.048 1706 Dihedral : 6.032 115.421 1291 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.53 % Allowed : 14.30 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.25), residues: 1175 helix: 0.86 (0.24), residues: 477 sheet: 0.11 (0.40), residues: 166 loop : -0.35 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.010 0.001 TYR A 471 PHE 0.037 0.002 PHE B1259 TRP 0.014 0.001 TRP A 522 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9643) covalent geometry : angle 0.65614 (13063) hydrogen bonds : bond 0.03819 ( 427) hydrogen bonds : angle 4.81513 ( 1161) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.6600 (tmm) REVERT: A 256 MET cc_start: 0.4998 (ttm) cc_final: 0.4646 (ttm) REVERT: A 291 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 435 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7401 (p0) REVERT: A 463 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.6933 (tm130) REVERT: A 473 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8161 (mm) REVERT: A 584 MET cc_start: 0.8434 (mpp) cc_final: 0.8123 (mmm) REVERT: A 647 TRP cc_start: 0.8743 (t60) cc_final: 0.8146 (t60) REVERT: A 1013 GLN cc_start: 0.7093 (mt0) cc_final: 0.6567 (mp10) REVERT: B 1256 PHE cc_start: -0.2686 (OUTLIER) cc_final: -0.3593 (p90) REVERT: B 1259 PHE cc_start: 0.5201 (p90) cc_final: 0.4929 (p90) REVERT: C 18 GLU cc_start: 0.7771 (mp0) cc_final: 0.7517 (mp0) REVERT: C 31 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6879 (tp40) outliers start: 26 outliers final: 18 residues processed: 117 average time/residue: 0.0800 time to fit residues: 14.2808 Evaluate side-chains 123 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain B residue 1256 PHE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 57 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 ASN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.189605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.139189 restraints weight = 18206.927| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 4.52 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9643 Z= 0.166 Angle : 0.667 16.168 13063 Z= 0.327 Chirality : 0.043 0.162 1439 Planarity : 0.004 0.053 1706 Dihedral : 5.978 109.482 1291 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.72 % Allowed : 14.20 % Favored : 83.07 % 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: 0.17 (0.25), residues: 1175 helix: 0.83 (0.24), residues: 476 sheet: -0.05 (0.40), residues: 170 loop : -0.39 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.012 0.001 TYR A 978 PHE 0.036 0.002 PHE B1259 TRP 0.020 0.002 TRP A 714 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9643) covalent geometry : angle 0.66710 (13063) hydrogen bonds : bond 0.03951 ( 427) hydrogen bonds : angle 4.88569 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.91 seconds wall clock time: 41 minutes 34.64 seconds (2494.64 seconds total)