Starting phenix.real_space_refine on Wed Aug 5 12:22:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mc7_63791/08_2026/9mc7_63791_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mc7_63791/08_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_63791/08_2026/9mc7_63791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mc7_63791/08_2026/9mc7_63791.map" model { file = "/net/cci-nas-00/data/ceres_data/9mc7_63791/08_2026/9mc7_63791_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mc7_63791/08_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-2.2rc3-6140/lib/python3.11/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: 1.46, per 1000 atoms: 0.15 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: 0.54 Conformation dependent library (CDL) restraints added in 201.0 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: 0.21 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: 1.35 Time building geometry restraints manager: 0.69 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 - 1.90: 11137 1.90 - 3.80: 1643 3.80 - 5.70: 244 5.70 - 7.59: 35 7.59 - 9.49: 4 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=" CA CYS A1039 " pdb=" C CYS A1039 " pdb=" N CYS A1040 " pdb=" CA CYS A1040 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1054 0.072 - 0.144: 287 0.144 - 0.216: 74 0.216 - 0.288: 22 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: 4.480 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 1.356 9.493 13063 Z= 0.888 Chirality : 0.075 0.360 1439 Planarity : 0.012 0.213 1706 Dihedral : 14.587 131.155 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/Z covalent geometry : bond 0.00939 / 0.58 ( 9643) covalent geometry : angle 1.35550 / 0.89 (13063) hydrogen bonds : bond 0.16385 / 11.30 ( 427) hydrogen bonds : angle 7.60083 / 5.46 ( 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 : 0.209 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: 0.0713 time to fit residues: 15.1434 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 : 0.200 ------------------------------------------------------------------------------- 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... 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 = 0.194637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.143804 restraints weight = 18280.930| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 4.58 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9643 Z= 0.132 Angle : 0.633 7.777 13063 Z= 0.325 Chirality : 0.042 0.155 1439 Planarity : 0.005 0.047 1706 Dihedral : 6.906 120.913 1295 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.65 % Allowed : 10.80 % Favored : 87.55 % 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: -0.03 (0.24), residues: 1175 helix: 0.59 (0.24), residues: 462 sheet: -0.03 (0.35), residues: 185 loop : -0.45 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.017 0.001 TYR B1002 PHE 0.032 0.002 PHE B 934 TRP 0.014 0.002 TRP A 952 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9643) covalent geometry : angle 0.63334 / 0.33 (13063) hydrogen bonds : bond 0.04591 / 3.11 ( 427) hydrogen bonds : angle 5.46023 / 3.87 ( 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 135 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ILE cc_start: 0.8295 (tt) cc_final: 0.7904 (mp) REVERT: A 584 MET cc_start: 0.8372 (mpp) cc_final: 0.8040 (mmm) REVERT: A 647 TRP cc_start: 0.8843 (t60) cc_final: 0.8360 (t60) REVERT: A 714 TRP cc_start: 0.7131 (m100) cc_final: 0.6657 (t-100) REVERT: A 1013 GLN cc_start: 0.7015 (mt0) cc_final: 0.6637 (tt0) REVERT: B 976 LYS cc_start: 0.7221 (tptt) cc_final: 0.6801 (tptt) REVERT: B 985 PHE cc_start: 0.4257 (OUTLIER) cc_final: 0.3930 (t80) REVERT: B 1123 PHE cc_start: 0.8306 (m-80) cc_final: 0.8026 (m-80) REVERT: C 24 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7981 (mm-30) outliers start: 17 outliers final: 6 residues processed: 133 average time/residue: 0.0753 time to fit residues: 14.3402 Evaluate side-chains 114 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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: 1.9990 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1032 ASN B1080 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.188796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.136166 restraints weight = 18155.895| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 4.33 r_work: 0.3659 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9643 Z= 0.231 Angle : 0.679 9.399 13063 Z= 0.349 Chirality : 0.045 0.164 1439 Planarity : 0.005 0.060 1706 Dihedral : 6.697 113.884 1291 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.63 % Allowed : 11.96 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.24), residues: 1175 helix: 0.46 (0.23), residues: 468 sheet: -0.01 (0.38), residues: 176 loop : -0.47 (0.28), residues: 531 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 0.027 0.002 PHE A 564 TRP 0.016 0.002 TRP A 955 HIS 0.007 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 ( 9643) covalent geometry : angle 0.67855 / 0.35 (13063) hydrogen bonds : bond 0.04830 / 3.29 ( 427) hydrogen bonds : angle 5.40803 / 3.84 ( 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 140 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ILE cc_start: 0.8298 (tt) cc_final: 0.7822 (mp) REVERT: A 377 ASN cc_start: 0.8342 (t0) cc_final: 0.8098 (t0) REVERT: A 463 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.6799 (tm130) REVERT: A 584 MET cc_start: 0.8446 (mpp) cc_final: 0.8044 (mmm) REVERT: A 647 TRP cc_start: 0.8854 (t60) cc_final: 0.8245 (t60) REVERT: A 714 TRP cc_start: 0.6744 (m100) cc_final: 0.6325 (t-100) REVERT: B 1123 PHE cc_start: 0.8171 (m-80) cc_final: 0.7910 (m-80) REVERT: C 18 GLU cc_start: 0.7918 (mp0) cc_final: 0.7669 (mp0) outliers start: 27 outliers final: 16 residues processed: 130 average time/residue: 0.0739 time to fit residues: 13.9751 Evaluate side-chains 117 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 578 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 0.0010 chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.192379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.141306 restraints weight = 18353.514| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 4.60 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2121 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= 0.121 Angle : 0.581 8.672 13063 Z= 0.295 Chirality : 0.041 0.162 1439 Planarity : 0.004 0.047 1706 Dihedral : 6.405 115.273 1291 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.02 % Allowed : 12.45 % Favored : 84.53 % 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: 0.21 (0.25), residues: 1175 helix: 0.79 (0.24), residues: 474 sheet: 0.00 (0.38), residues: 171 loop : -0.30 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1270 TYR 0.009 0.001 TYR B1002 PHE 0.028 0.002 PHE B1259 TRP 0.012 0.001 TRP A 952 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9643) covalent geometry : angle 0.58144 / 0.30 (13063) hydrogen bonds : bond 0.03955 / 2.67 ( 427) hydrogen bonds : angle 4.96598 / 3.52 ( 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 149 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.4261 (ttm) cc_final: 0.3820 (ttm) REVERT: A 291 ILE cc_start: 0.8230 (tt) cc_final: 0.7812 (mp) REVERT: A 300 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8376 (ttpp) REVERT: A 377 ASN cc_start: 0.8055 (t0) cc_final: 0.7816 (t0) REVERT: A 463 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.6769 (tm130) REVERT: A 584 MET cc_start: 0.8315 (mpp) cc_final: 0.8021 (mmm) REVERT: A 647 TRP cc_start: 0.8851 (t60) cc_final: 0.8308 (t60) REVERT: A 714 TRP cc_start: 0.7009 (m100) cc_final: 0.6481 (t-100) REVERT: A 1013 GLN cc_start: 0.7078 (mt0) cc_final: 0.6422 (mp10) REVERT: B 1123 PHE cc_start: 0.8218 (m-80) cc_final: 0.8008 (m-80) REVERT: C 18 GLU cc_start: 0.7743 (mp0) cc_final: 0.7409 (mp0) REVERT: C 24 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7962 (mm-30) REVERT: C 31 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.6832 (tp40) outliers start: 31 outliers final: 13 residues processed: 140 average time/residue: 0.0738 time to fit residues: 15.0993 Evaluate side-chains 127 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 463 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 556 THR 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 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: 3.9990 chunk 7 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 ASN A 622 GLN A 643 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.190126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.138909 restraints weight = 18359.759| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 4.45 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9643 Z= 0.174 Angle : 0.613 10.758 13063 Z= 0.310 Chirality : 0.043 0.162 1439 Planarity : 0.005 0.054 1706 Dihedral : 6.394 112.207 1291 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.21 % Allowed : 12.94 % Favored : 83.85 % 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: 0.27 (0.25), residues: 1175 helix: 0.82 (0.24), residues: 468 sheet: 0.10 (0.38), residues: 185 loop : -0.25 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 944 TYR 0.013 0.002 TYR A 978 PHE 0.028 0.002 PHE B1259 TRP 0.013 0.002 TRP A 952 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 9643) covalent geometry : angle 0.61272 / 0.31 (13063) hydrogen bonds : bond 0.04165 / 2.85 ( 427) hydrogen bonds : angle 5.00738 / 3.56 ( 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 141 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.6685 (tmm) REVERT: A 208 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7122 (mt) REVERT: A 256 MET cc_start: 0.4577 (ttm) cc_final: 0.4264 (ttm) REVERT: A 291 ILE cc_start: 0.8240 (tt) cc_final: 0.7803 (mp) REVERT: A 377 ASN cc_start: 0.8072 (t0) cc_final: 0.7859 (t0) REVERT: A 463 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.6732 (tm130) REVERT: A 584 MET cc_start: 0.8381 (mpp) cc_final: 0.7945 (mmm) REVERT: A 647 TRP cc_start: 0.8804 (t60) cc_final: 0.8302 (t60) REVERT: A 714 TRP cc_start: 0.7059 (m100) cc_final: 0.6279 (t-100) REVERT: A 1013 GLN cc_start: 0.7148 (mt0) cc_final: 0.6558 (mp10) REVERT: B 976 LYS cc_start: 0.7639 (tptp) cc_final: 0.7195 (tptt) REVERT: B 1123 PHE cc_start: 0.8160 (m-80) cc_final: 0.7930 (m-80) REVERT: C 31 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.6867 (tp40) outliers start: 33 outliers final: 21 residues processed: 131 average time/residue: 0.0737 time to fit residues: 14.1309 Evaluate side-chains 126 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 208 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 280 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 615 THR Chi-restraints excluded: chain A residue 912 VAL 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: 8.9990 chunk 1 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 992 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.188897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.137829 restraints weight = 18466.793| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 4.49 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9643 Z= 0.194 Angle : 0.629 8.854 13063 Z= 0.320 Chirality : 0.043 0.153 1439 Planarity : 0.005 0.056 1706 Dihedral : 6.406 110.026 1291 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.31 % Allowed : 13.62 % 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: 0.07 (0.25), residues: 1175 helix: 0.63 (0.23), residues: 475 sheet: 0.02 (0.38), residues: 185 loop : -0.37 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 944 TYR 0.014 0.002 TYR A 978 PHE 0.027 0.002 PHE B1259 TRP 0.014 0.002 TRP A 952 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 9643) covalent geometry : angle 0.62895 / 0.32 (13063) hydrogen bonds : bond 0.04298 / 2.93 ( 427) hydrogen bonds : angle 5.06704 / 3.62 ( 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 132 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6733 (tmm) REVERT: A 208 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7050 (mt) REVERT: A 291 ILE cc_start: 0.8238 (tt) cc_final: 0.7784 (mp) REVERT: A 463 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.6668 (tm130) REVERT: A 584 MET cc_start: 0.8425 (mpp) cc_final: 0.8078 (mmm) REVERT: A 714 TRP cc_start: 0.7064 (m100) cc_final: 0.6238 (t-100) REVERT: A 1013 GLN cc_start: 0.7107 (mt0) cc_final: 0.6519 (mp10) REVERT: B 976 LYS cc_start: 0.7707 (tptp) cc_final: 0.7274 (tptt) REVERT: B 1123 PHE cc_start: 0.8142 (m-80) cc_final: 0.7936 (m-80) REVERT: C 31 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.6902 (tp40) outliers start: 34 outliers final: 22 residues processed: 119 average time/residue: 0.0619 time to fit residues: 11.1905 Evaluate side-chains 121 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 235 LEU 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 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 989 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4566 r_free = 0.4566 target = 0.192197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.141296 restraints weight = 18213.351| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 4.17 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2724 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= 0.117 Angle : 0.584 9.066 13063 Z= 0.290 Chirality : 0.041 0.153 1439 Planarity : 0.004 0.047 1706 Dihedral : 6.147 105.046 1291 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.14 % Allowed : 15.47 % Favored : 82.39 % 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: 0.30 (0.25), residues: 1175 helix: 0.95 (0.24), residues: 473 sheet: 0.02 (0.39), residues: 170 loop : -0.33 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.011 0.001 TYR A 471 PHE 0.029 0.001 PHE B1259 TRP 0.014 0.001 TRP A 522 HIS 0.002 0.000 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9643) covalent geometry : angle 0.58360 / 0.29 (13063) hydrogen bonds : bond 0.03730 / 2.52 ( 427) hydrogen bonds : angle 4.79317 / 3.42 ( 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 126 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6776 (tmm) REVERT: A 256 MET cc_start: 0.4352 (ttm) cc_final: 0.3822 (ttm) REVERT: A 291 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7785 (mp) REVERT: A 300 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8222 (ptmt) REVERT: A 435 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7330 (p0) REVERT: A 584 MET cc_start: 0.8282 (mpp) cc_final: 0.8036 (mmm) REVERT: A 647 TRP cc_start: 0.8819 (t60) cc_final: 0.8273 (t60) REVERT: A 714 TRP cc_start: 0.6952 (m100) cc_final: 0.6092 (t-100) REVERT: A 1013 GLN cc_start: 0.7139 (mt0) cc_final: 0.6618 (mp10) REVERT: B 976 LYS cc_start: 0.7776 (tptp) cc_final: 0.7335 (tptt) REVERT: B 1256 PHE cc_start: -0.2692 (OUTLIER) cc_final: -0.3167 (p90) REVERT: C 24 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7851 (mm-30) outliers start: 22 outliers final: 15 residues processed: 119 average time/residue: 0.0676 time to fit residues: 12.1878 Evaluate side-chains 118 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 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 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 985 LEU Chi-restraints excluded: chain A residue 987 ILE 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 B residue 1256 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4552 r_free = 0.4552 target = 0.191070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.140544 restraints weight = 18206.031| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 4.20 r_work: 0.3702 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9643 Z= 0.133 Angle : 0.603 9.006 13063 Z= 0.303 Chirality : 0.041 0.171 1439 Planarity : 0.004 0.049 1706 Dihedral : 6.067 99.675 1291 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.82 % Allowed : 15.56 % Favored : 81.61 % 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: 0.31 (0.25), residues: 1175 helix: 0.96 (0.24), residues: 476 sheet: 0.05 (0.40), residues: 170 loop : -0.35 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.010 0.001 TYR A 471 PHE 0.039 0.002 PHE B1259 TRP 0.012 0.001 TRP A 952 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 9643) covalent geometry : angle 0.60286 / 0.30 (13063) hydrogen bonds : bond 0.03783 / 2.57 ( 427) hydrogen bonds : angle 4.77564 / 3.40 ( 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 129 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.6805 (tmm) REVERT: A 208 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7193 (mt) REVERT: A 256 MET cc_start: 0.5019 (ttm) cc_final: 0.4773 (ttm) REVERT: A 291 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7659 (mt) REVERT: A 300 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8363 (ptmt) REVERT: A 435 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7388 (p0) REVERT: A 463 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.6937 (tm130) REVERT: A 584 MET cc_start: 0.8404 (mpp) cc_final: 0.8046 (mmm) REVERT: A 647 TRP cc_start: 0.8779 (t60) cc_final: 0.8166 (t60) REVERT: A 714 TRP cc_start: 0.6597 (m100) cc_final: 0.5794 (t-100) REVERT: B 976 LYS cc_start: 0.7808 (tptp) cc_final: 0.7363 (tptt) REVERT: B 1256 PHE cc_start: -0.2734 (OUTLIER) cc_final: -0.3611 (p90) REVERT: B 1259 PHE cc_start: 0.4941 (p90) cc_final: 0.4649 (p90) REVERT: C 31 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.6899 (tp40) outliers start: 29 outliers final: 17 residues processed: 121 average time/residue: 0.0645 time to fit residues: 11.9102 Evaluate side-chains 120 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 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 953 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 985 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 B residue 1256 PHE Chi-restraints excluded: chain C residue 31 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 76 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 30.0000 chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4561 r_free = 0.4561 target = 0.191373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.141540 restraints weight = 17781.980| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 3.93 r_work: 0.3708 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9643 Z= 0.134 Angle : 0.605 8.241 13063 Z= 0.302 Chirality : 0.042 0.166 1439 Planarity : 0.004 0.049 1706 Dihedral : 5.990 92.164 1291 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.11 % Allowed : 15.18 % Favored : 81.71 % 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: 0.33 (0.25), residues: 1175 helix: 1.02 (0.24), residues: 476 sheet: 0.05 (0.40), residues: 170 loop : -0.37 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.010 0.001 TYR A 978 PHE 0.037 0.002 PHE B1259 TRP 0.012 0.001 TRP A 952 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 9643) covalent geometry : angle 0.60464 / 0.30 (13063) hydrogen bonds : bond 0.03750 / 2.55 ( 427) hydrogen bonds : angle 4.75453 / 3.39 ( 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 134 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.6924 (tmm) REVERT: A 208 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7212 (mt) REVERT: A 256 MET cc_start: 0.4987 (ttm) cc_final: 0.4520 (ttm) REVERT: A 291 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 300 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8370 (ptmt) REVERT: A 435 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7394 (p0) REVERT: A 463 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.6924 (tm130) REVERT: A 473 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8161 (mm) REVERT: A 584 MET cc_start: 0.8418 (mpp) cc_final: 0.8081 (mmm) REVERT: A 647 TRP cc_start: 0.8710 (t60) cc_final: 0.8101 (t60) REVERT: A 1013 GLN cc_start: 0.7146 (mt0) cc_final: 0.6700 (mp10) REVERT: B 976 LYS cc_start: 0.7941 (tptp) cc_final: 0.7227 (tptt) REVERT: B 1256 PHE cc_start: -0.2653 (OUTLIER) cc_final: -0.3556 (p90) REVERT: B 1259 PHE cc_start: 0.5202 (p90) cc_final: 0.4924 (p90) REVERT: C 18 GLU cc_start: 0.7770 (mp0) cc_final: 0.7478 (mp0) REVERT: C 24 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8183 (mm-30) REVERT: C 31 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6836 (tp40) outliers start: 32 outliers final: 18 residues processed: 126 average time/residue: 0.0681 time to fit residues: 13.0114 Evaluate side-chains 121 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 208 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 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 615 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 987 ILE 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 B residue 1256 PHE Chi-restraints excluded: chain C residue 31 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 79 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.191747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.141952 restraints weight = 17805.652| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.92 r_work: 0.3719 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9643 Z= 0.125 Angle : 0.633 17.367 13063 Z= 0.312 Chirality : 0.042 0.185 1439 Planarity : 0.004 0.048 1706 Dihedral : 5.921 87.281 1291 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.72 % Allowed : 15.08 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1175 helix: 1.04 (0.24), residues: 474 sheet: 0.11 (0.40), residues: 170 loop : -0.40 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.012 0.001 TYR A 590 PHE 0.037 0.002 PHE B1259 TRP 0.031 0.002 TRP A 714 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 9643) covalent geometry : angle 0.63324 / 0.31 (13063) hydrogen bonds : bond 0.03663 / 2.48 ( 427) hydrogen bonds : angle 4.73905 / 3.38 ( 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: 28 poor density : 98 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.6933 (tmm) REVERT: A 256 MET cc_start: 0.4971 (ttm) cc_final: 0.4510 (ttm) REVERT: A 291 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7734 (mp) REVERT: A 300 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8359 (ptmt) REVERT: A 435 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7398 (p0) REVERT: A 463 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.6886 (tm130) REVERT: A 473 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8178 (mm) REVERT: A 584 MET cc_start: 0.8406 (mpp) cc_final: 0.8085 (mmm) REVERT: A 647 TRP cc_start: 0.8701 (t60) cc_final: 0.8097 (t60) REVERT: A 714 TRP cc_start: 0.5612 (t-100) cc_final: 0.5386 (t-100) REVERT: A 1013 GLN cc_start: 0.7132 (mt0) cc_final: 0.6740 (mp10) REVERT: B 1256 PHE cc_start: -0.2765 (OUTLIER) cc_final: -0.3661 (p90) REVERT: B 1259 PHE cc_start: 0.5178 (p90) cc_final: 0.4902 (p90) REVERT: C 18 GLU cc_start: 0.7775 (mp0) cc_final: 0.7500 (mp0) REVERT: C 24 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8161 (mm-30) REVERT: C 31 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6821 (tp40) outliers start: 28 outliers final: 19 residues processed: 118 average time/residue: 0.0690 time to fit residues: 12.1985 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 : 0.256 ------------------------------------------------------------------------------- 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 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 615 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 973 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 57 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 0.0170 chunk 107 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.0000 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 ASN ** 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 = 0.4580 r_free = 0.4580 target = 0.193491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.143399 restraints weight = 18083.472| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 4.53 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9643 Z= 0.108 Angle : 0.622 16.200 13063 Z= 0.303 Chirality : 0.041 0.164 1439 Planarity : 0.004 0.047 1706 Dihedral : 5.779 78.884 1291 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.53 % Allowed : 15.47 % Favored : 82.00 % 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: 0.46 (0.25), residues: 1175 helix: 1.10 (0.24), residues: 476 sheet: 0.25 (0.40), residues: 170 loop : -0.32 (0.28), residues: 529 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 0.036 0.002 PHE B1259 TRP 0.015 0.001 TRP A 522 HIS 0.002 0.000 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9643) covalent geometry : angle 0.62199 / 0.30 (13063) hydrogen bonds : bond 0.03493 / 2.35 ( 427) hydrogen bonds : angle 4.62545 / 3.31 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1946.70 seconds wall clock time: 34 minutes 1.07 seconds (2041.07 seconds total)