Starting phenix.real_space_refine on Wed Aug 5 00:12:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgi_40456/08_2026/8sgi_40456.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgi_40456/08_2026/8sgi_40456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sgi_40456/08_2026/8sgi_40456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgi_40456/08_2026/8sgi_40456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sgi_40456/08_2026/8sgi_40456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgi_40456/08_2026/8sgi_40456.map" } resolution = 2.9 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= 0.002 sd= 0.071 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: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 S 31 5.16 5 Na 3 4.78 5 C 4969 2.51 5 N 1243 2.21 5 O 1440 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 7694 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5900 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 724} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 37 Unusual residues: {' CA': 6, ' NA': 3, 'EKY': 1} Classifications: {'undetermined': 10, 'water': 1} Link IDs: {None: 10} Time building chain proxies: 1.55, per 1000 atoms: 0.20 Number of scatterers: 7694 At special positions: 0 Unit cell: (136.12, 87.15, 137.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 6 19.99 S 31 16.00 Na 3 11.00 F 2 9.00 O 1440 8.00 N 1243 7.00 C 4969 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 413.4 milliseconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.8% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 36 through 72 removed outlier: 3.565A pdb=" N ILE A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.637A pdb=" N LEU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 124 Processing helix chain 'A' and resid 130 through 145 Processing helix chain 'A' and resid 145 through 155 removed outlier: 4.033A pdb=" N VAL A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 189 removed outlier: 3.785A pdb=" N TYR A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.978A pdb=" N ILE A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.641A pdb=" N VAL A 227 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 608 Processing helix chain 'A' and resid 656 through 666 Processing helix chain 'A' and resid 684 through 697 removed outlier: 3.605A pdb=" N LYS A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.596A pdb=" N PHE A 713 " --> pdb=" O TRP A 709 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 754 removed outlier: 5.177A pdb=" N PHE A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TRP A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 761 through 764 removed outlier: 3.697A pdb=" N ASN A 764 " --> pdb=" O GLU A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 764' Processing helix chain 'A' and resid 765 through 795 removed outlier: 3.617A pdb=" N VAL A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 828 through 845 removed outlier: 3.710A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 843 " --> pdb=" O ASN A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 861 removed outlier: 3.704A pdb=" N ALA A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 893 removed outlier: 4.585A pdb=" N LEU A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 932 removed outlier: 3.577A pdb=" N LEU A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.715A pdb=" N GLU L 84 " --> pdb=" O THR L 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.531A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.525A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 79 removed outlier: 8.344A pdb=" N ILE A 240 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG A 93 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU A 242 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TRP A 95 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N GLU A 244 " --> pdb=" O TRP A 95 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR A 228 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 195 removed outlier: 4.175A pdb=" N PHE A 865 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 443 Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.880A pdb=" N TYR A 381 " --> pdb=" O THR A 495 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE A 497 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS A 383 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL A 463 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE A 406 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 574 Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.844A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.844A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A 534 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A 597 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLN A 623 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LYS A 618 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 625 " --> pdb=" O THR A 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'L' and resid 8 through 11 removed outlier: 6.466A pdb=" N LEU L 9 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU L 44 " --> pdb=" O LYS L 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 11 removed outlier: 6.466A pdb=" N LEU L 9 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.377A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1176 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: 1.58 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1243 1.31 - 1.44: 2226 1.44 - 1.56: 4351 1.56 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 7865 Sorted by residual: bond pdb=" C ALA A 931 " pdb=" O ALA A 931 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.26e-02 6.30e+03 1.40e+01 bond pdb=" CA ALA A 931 " pdb=" C ALA A 931 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.35e-02 5.49e+03 8.19e+00 bond pdb=" CA CYS A 933 " pdb=" C CYS A 933 " ideal model delta sigma weight residual 1.527 1.490 0.037 1.30e-02 5.92e+03 8.10e+00 bond pdb=" CA TYR A 932 " pdb=" CB TYR A 932 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.46e-02 4.69e+03 5.74e+00 bond pdb=" C TYR A 932 " pdb=" O TYR A 932 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.28e-02 6.10e+03 4.30e+00 ... (remaining 7860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10283 1.64 - 3.28: 321 3.28 - 4.91: 56 4.91 - 6.55: 10 6.55 - 8.19: 7 Bond angle restraints: 10677 Sorted by residual: angle pdb=" C ILE A 643 " pdb=" N ALA A 644 " pdb=" CA ALA A 644 " ideal model delta sigma weight residual 121.70 128.73 -7.03 1.80e+00 3.09e-01 1.52e+01 angle pdb=" C GLY L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 128.57 -7.03 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N THR H 61 " pdb=" CA THR H 61 " pdb=" C THR H 61 " ideal model delta sigma weight residual 110.52 105.40 5.12 1.48e+00 4.57e-01 1.20e+01 angle pdb=" N LEU A 637 " pdb=" CA LEU A 637 " pdb=" CB LEU A 637 " ideal model delta sigma weight residual 114.17 110.44 3.73 1.14e+00 7.69e-01 1.07e+01 angle pdb=" C TYR H 60 " pdb=" CA TYR H 60 " pdb=" CB TYR H 60 " ideal model delta sigma weight residual 110.67 103.71 6.96 2.23e+00 2.01e-01 9.73e+00 ... (remaining 10672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 4204 17.08 - 34.16: 299 34.16 - 51.24: 43 51.24 - 68.32: 8 68.32 - 85.41: 12 Dihedral angle restraints: 4566 sinusoidal: 1758 harmonic: 2808 Sorted by residual: dihedral pdb=" CA LEU A 637 " pdb=" C LEU A 637 " pdb=" N SER A 638 " pdb=" CA SER A 638 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C ILE A 935 " pdb=" N ILE A 935 " pdb=" CA ILE A 935 " pdb=" CB ILE A 935 " ideal model delta harmonic sigma weight residual -122.00 -131.13 9.13 0 2.50e+00 1.60e-01 1.33e+01 dihedral pdb=" CA GLY A 549 " pdb=" C GLY A 549 " pdb=" N GLY A 550 " pdb=" CA GLY A 550 " ideal model delta harmonic sigma weight residual -180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 4563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 989 0.062 - 0.123: 206 0.123 - 0.185: 17 0.185 - 0.246: 1 0.246 - 0.308: 2 Chirality restraints: 1215 Sorted by residual: chirality pdb=" CA CYS A 933 " pdb=" N CYS A 933 " pdb=" C CYS A 933 " pdb=" CB CYS A 933 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA ILE A 935 " pdb=" N ILE A 935 " pdb=" C ILE A 935 " pdb=" CB ILE A 935 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE A 615 " pdb=" CA ILE A 615 " pdb=" CG1 ILE A 615 " pdb=" CG2 ILE A 615 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1212 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.049 5.00e-02 4.00e+02 7.37e-02 8.69e+00 pdb=" N PRO A 133 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 933 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C CYS A 933 " -0.039 2.00e-02 2.50e+03 pdb=" O CYS A 933 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS A 934 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 812 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 813 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 813 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 813 " 0.029 5.00e-02 4.00e+02 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 330 2.72 - 3.26: 7422 3.26 - 3.81: 12368 3.81 - 4.35: 16050 4.35 - 4.90: 27651 Nonbonded interactions: 63821 Sorted by model distance: nonbonded pdb=" O SER A 109 " pdb="NA NA A1008 " model vdw 2.175 2.470 nonbonded pdb=" OD1 ASP A 421 " pdb="CA CA A1004 " model vdw 2.199 2.510 nonbonded pdb=" OD2 ASP A 421 " pdb="CA CA A1004 " model vdw 2.212 2.510 nonbonded pdb=" OE1 GLN H 35 " pdb=" NE1 TRP H 47 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU A 451 " pdb="CA CA A1004 " model vdw 2.252 2.510 ... (remaining 63816 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.030 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7868 Z= 0.218 Angle : 0.704 8.188 10683 Z= 0.375 Chirality : 0.050 0.308 1215 Planarity : 0.006 0.074 1335 Dihedral : 12.690 85.406 2759 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.60 (0.25), residues: 966 helix: -0.96 (0.23), residues: 336 sheet: 0.54 (0.29), residues: 308 loop : -0.44 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 62 TYR 0.027 0.002 TYR H 60 PHE 0.023 0.002 PHE A 925 TRP 0.022 0.002 TRP A 215 HIS 0.005 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 ( 7865) covalent geometry : angle 0.70360 / 0.38 (10677) SS BOND : bond 0.00334 / 0.16 ( 3) SS BOND : angle 1.19764 / 0.51 ( 6) hydrogen bonds : bond 0.22613 / 15.40 ( 402) hydrogen bonds : angle 8.21122 / 5.83 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.288 Fit side-chains REVERT: A 395 ILE cc_start: 0.8522 (mt) cc_final: 0.8301 (mp) REVERT: A 410 ARG cc_start: 0.7010 (ttp-170) cc_final: 0.6699 (pmm-80) REVERT: A 437 GLN cc_start: 0.7296 (pt0) cc_final: 0.6951 (pp30) REVERT: A 438 LYS cc_start: 0.6275 (mmmt) cc_final: 0.5861 (mmtm) REVERT: A 910 LEU cc_start: 0.8098 (mt) cc_final: 0.7854 (mt) REVERT: A 914 CYS cc_start: 0.7862 (m) cc_final: 0.7648 (m) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.5694 time to fit residues: 75.7061 Evaluate side-chains 96 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0060 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 124 HIS A 630 HIS A 764 ASN ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN H 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.152281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117517 restraints weight = 9169.177| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.21 r_work: 0.3307 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7868 Z= 0.121 Angle : 0.529 8.095 10683 Z= 0.291 Chirality : 0.043 0.153 1215 Planarity : 0.004 0.047 1335 Dihedral : 6.594 78.123 1059 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.09 % Allowed : 6.90 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.67 (0.26), residues: 966 helix: 1.12 (0.26), residues: 344 sheet: 0.46 (0.29), residues: 295 loop : -0.12 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 62 TYR 0.014 0.001 TYR L 93 PHE 0.020 0.001 PHE A 925 TRP 0.018 0.001 TRP A 215 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 7865) covalent geometry : angle 0.52861 / 0.29 (10677) SS BOND : bond 0.00222 / 0.11 ( 3) SS BOND : angle 0.89971 / 0.39 ( 6) hydrogen bonds : bond 0.04905 / 3.48 ( 402) hydrogen bonds : angle 5.11230 / 3.64 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.296 Fit side-chains REVERT: A 410 ARG cc_start: 0.7120 (ttp-170) cc_final: 0.6228 (pmm-80) REVERT: A 437 GLN cc_start: 0.7600 (pt0) cc_final: 0.6972 (pp30) REVERT: A 547 ARG cc_start: 0.7554 (mmm160) cc_final: 0.7295 (mmm160) REVERT: A 657 GLU cc_start: 0.6569 (tm-30) cc_final: 0.6260 (tm-30) outliers start: 9 outliers final: 2 residues processed: 104 average time/residue: 0.6454 time to fit residues: 70.7082 Evaluate side-chains 84 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 824 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110462 restraints weight = 9182.408| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.21 r_work: 0.3215 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7868 Z= 0.226 Angle : 0.602 9.684 10683 Z= 0.325 Chirality : 0.046 0.158 1215 Planarity : 0.005 0.047 1335 Dihedral : 6.534 75.404 1059 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.21 % Allowed : 9.81 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.58 (0.26), residues: 966 helix: 1.22 (0.26), residues: 343 sheet: 0.27 (0.29), residues: 295 loop : -0.23 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 247 TYR 0.019 0.002 TYR A 180 PHE 0.017 0.002 PHE A 587 TRP 0.014 0.002 TRP A 198 HIS 0.005 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 ( 7865) covalent geometry : angle 0.59327 / 0.32 (10677) SS BOND : bond 0.00872 / 0.45 ( 3) SS BOND : angle 4.24238 / 2.46 ( 6) hydrogen bonds : bond 0.05484 / 3.85 ( 402) hydrogen bonds : angle 5.01172 / 3.58 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.300 Fit side-chains REVERT: A 410 ARG cc_start: 0.7161 (ttp-170) cc_final: 0.6147 (pmm-80) REVERT: A 437 GLN cc_start: 0.7588 (pt0) cc_final: 0.6917 (pp30) REVERT: A 547 ARG cc_start: 0.7673 (mmm160) cc_final: 0.7294 (mmm160) REVERT: A 632 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7213 (ptp90) REVERT: A 657 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6462 (tm-30) REVERT: A 711 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7720 (mm-30) REVERT: A 895 ARG cc_start: 0.5938 (ptm160) cc_final: 0.5651 (ptm-80) REVERT: A 914 CYS cc_start: 0.8511 (m) cc_final: 0.8228 (m) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.6228 time to fit residues: 66.3026 Evaluate side-chains 97 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain H residue 34 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.147652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112153 restraints weight = 9290.124| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.23 r_work: 0.3237 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7868 Z= 0.163 Angle : 0.529 8.527 10683 Z= 0.289 Chirality : 0.043 0.146 1215 Planarity : 0.004 0.057 1335 Dihedral : 6.432 74.804 1059 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.69 % Allowed : 10.29 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.72 (0.26), residues: 966 helix: 1.43 (0.26), residues: 343 sheet: 0.29 (0.30), residues: 294 loop : -0.22 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 247 TYR 0.017 0.001 TYR A 180 PHE 0.015 0.001 PHE A 587 TRP 0.011 0.002 TRP A 198 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 7865) covalent geometry : angle 0.52403 / 0.29 (10677) SS BOND : bond 0.00224 / 0.11 ( 3) SS BOND : angle 3.09864 / 1.80 ( 6) hydrogen bonds : bond 0.04602 / 3.25 ( 402) hydrogen bonds : angle 4.82044 / 3.43 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.180 Fit side-chains REVERT: A 21 LYS cc_start: 0.8056 (ptmt) cc_final: 0.7561 (ptmm) REVERT: A 382 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7301 (mt0) REVERT: A 410 ARG cc_start: 0.7139 (ttp-170) cc_final: 0.6165 (pmm-80) REVERT: A 437 GLN cc_start: 0.7583 (pt0) cc_final: 0.6918 (pp30) REVERT: A 441 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.7744 (mtt180) REVERT: A 554 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8592 (mt-10) REVERT: A 657 GLU cc_start: 0.6704 (tm-30) cc_final: 0.6329 (tm-30) REVERT: A 711 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 764 ASN cc_start: 0.7715 (t0) cc_final: 0.7438 (t0) outliers start: 14 outliers final: 7 residues processed: 106 average time/residue: 0.6556 time to fit residues: 73.0085 Evaluate side-chains 100 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111868 restraints weight = 9283.921| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.22 r_work: 0.3233 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7868 Z= 0.154 Angle : 0.507 9.882 10683 Z= 0.278 Chirality : 0.043 0.163 1215 Planarity : 0.004 0.042 1335 Dihedral : 6.308 74.225 1059 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.69 % Allowed : 11.62 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.82 (0.27), residues: 966 helix: 1.56 (0.27), residues: 343 sheet: 0.34 (0.30), residues: 293 loop : -0.20 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 247 TYR 0.017 0.001 TYR A 180 PHE 0.015 0.001 PHE A 587 TRP 0.011 0.001 TRP A 198 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 7865) covalent geometry : angle 0.50674 / 0.28 (10677) SS BOND : bond 0.00489 / 0.25 ( 3) SS BOND : angle 1.05654 / 0.59 ( 6) hydrogen bonds : bond 0.04431 / 3.13 ( 402) hydrogen bonds : angle 4.74383 / 3.38 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8529 (t0) cc_final: 0.8277 (t0) REVERT: A 382 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7312 (mt0) REVERT: A 410 ARG cc_start: 0.7123 (ttp-170) cc_final: 0.6156 (pmm-80) REVERT: A 437 GLN cc_start: 0.7571 (pt0) cc_final: 0.6896 (pp30) REVERT: A 547 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7332 (mmm160) REVERT: A 554 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8582 (mt-10) REVERT: A 632 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7517 (ptp90) REVERT: A 657 GLU cc_start: 0.6788 (tm-30) cc_final: 0.6383 (tm-30) REVERT: A 711 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7733 (mt-10) REVERT: A 764 ASN cc_start: 0.7739 (t0) cc_final: 0.7413 (t0) REVERT: H 5 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7812 (tm-30) outliers start: 14 outliers final: 7 residues processed: 95 average time/residue: 0.6212 time to fit residues: 62.3246 Evaluate side-chains 94 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 34 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 1 optimal weight: 0.0270 chunk 80 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 78 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.8899 > 50:) chunk 24 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114686 restraints weight = 9203.376| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.23 r_work: 0.3274 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7868 Z= 0.107 Angle : 0.464 9.529 10683 Z= 0.255 Chirality : 0.041 0.140 1215 Planarity : 0.004 0.036 1335 Dihedral : 6.085 72.553 1059 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.21 % Allowed : 12.95 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.27), residues: 966 helix: 1.80 (0.27), residues: 341 sheet: 0.43 (0.30), residues: 293 loop : -0.15 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 247 TYR 0.013 0.001 TYR A 180 PHE 0.012 0.001 PHE A 587 TRP 0.011 0.001 TRP A 182 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7865) covalent geometry : angle 0.46391 / 0.25 (10677) SS BOND : bond 0.00250 / 0.13 ( 3) SS BOND : angle 0.54925 / 0.28 ( 6) hydrogen bonds : bond 0.03838 / 2.70 ( 402) hydrogen bonds : angle 4.53919 / 3.22 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 382 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7238 (mt0) REVERT: A 410 ARG cc_start: 0.7098 (ttp-170) cc_final: 0.6149 (pmm-80) REVERT: A 437 GLN cc_start: 0.7615 (pt0) cc_final: 0.6940 (pp30) REVERT: A 547 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7211 (mmm160) REVERT: A 554 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8560 (mt-10) REVERT: A 657 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6459 (tm-30) REVERT: A 711 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7708 (mt-10) REVERT: A 764 ASN cc_start: 0.7702 (t0) cc_final: 0.7331 (t0) outliers start: 10 outliers final: 4 residues processed: 94 average time/residue: 0.6406 time to fit residues: 63.6296 Evaluate side-chains 89 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 76 optimal weight: 0.0370 chunk 87 optimal weight: 0.4980 chunk 53 optimal weight: 0.0870 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115462 restraints weight = 9221.836| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.23 r_work: 0.3285 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7868 Z= 0.102 Angle : 0.464 9.535 10683 Z= 0.251 Chirality : 0.041 0.140 1215 Planarity : 0.004 0.040 1335 Dihedral : 5.891 71.041 1059 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.57 % Allowed : 12.95 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.27), residues: 966 helix: 1.92 (0.27), residues: 341 sheet: 0.43 (0.30), residues: 293 loop : -0.10 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 247 TYR 0.013 0.001 TYR A 180 PHE 0.013 0.001 PHE A 587 TRP 0.010 0.001 TRP A 198 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7865) covalent geometry : angle 0.46429 / 0.25 (10677) SS BOND : bond 0.00255 / 0.13 ( 3) SS BOND : angle 0.49331 / 0.25 ( 6) hydrogen bonds : bond 0.03704 / 2.60 ( 402) hydrogen bonds : angle 4.41778 / 3.14 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7228 (mt0) REVERT: A 410 ARG cc_start: 0.7061 (ttp-170) cc_final: 0.6165 (pmm-80) REVERT: A 437 GLN cc_start: 0.7594 (pt0) cc_final: 0.6937 (pp30) REVERT: A 547 ARG cc_start: 0.7611 (mmm160) cc_final: 0.7343 (mmm160) REVERT: A 554 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8538 (mt-10) REVERT: A 657 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6390 (tm-30) REVERT: A 711 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7695 (mt-10) REVERT: A 764 ASN cc_start: 0.7677 (t0) cc_final: 0.7272 (t0) REVERT: A 906 ARG cc_start: 0.7126 (tpp-160) cc_final: 0.6639 (tpp-160) REVERT: H 5 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7698 (tm-30) outliers start: 13 outliers final: 6 residues processed: 97 average time/residue: 0.6155 time to fit residues: 63.1215 Evaluate side-chains 93 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 8.9990 chunk 81 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.0060 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114912 restraints weight = 9175.025| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.22 r_work: 0.3276 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7868 Z= 0.118 Angle : 0.468 8.649 10683 Z= 0.253 Chirality : 0.041 0.140 1215 Planarity : 0.004 0.052 1335 Dihedral : 5.863 70.780 1059 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.09 % Allowed : 13.92 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.27), residues: 966 helix: 1.88 (0.27), residues: 341 sheet: 0.46 (0.30), residues: 293 loop : -0.11 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 247 TYR 0.014 0.001 TYR A 180 PHE 0.013 0.001 PHE A 587 TRP 0.010 0.001 TRP A 198 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7865) covalent geometry : angle 0.46749 / 0.25 (10677) SS BOND : bond 0.00276 / 0.14 ( 3) SS BOND : angle 0.48073 / 0.25 ( 6) hydrogen bonds : bond 0.03795 / 2.68 ( 402) hydrogen bonds : angle 4.43612 / 3.16 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8482 (tt0) cc_final: 0.8234 (tp30) REVERT: A 244 GLU cc_start: 0.8648 (tt0) cc_final: 0.8366 (pt0) REVERT: A 382 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: A 410 ARG cc_start: 0.7077 (ttp-170) cc_final: 0.6134 (pmm-80) REVERT: A 437 GLN cc_start: 0.7614 (pt0) cc_final: 0.6972 (pp30) REVERT: A 547 ARG cc_start: 0.7661 (mmm160) cc_final: 0.7396 (mmm160) REVERT: A 554 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8513 (mt-10) REVERT: A 657 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6492 (tm-30) REVERT: A 711 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7730 (mt-10) REVERT: A 764 ASN cc_start: 0.7708 (t0) cc_final: 0.7286 (t0) REVERT: A 906 ARG cc_start: 0.7148 (tpp-160) cc_final: 0.6682 (tpp-160) REVERT: H 5 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7704 (tm-30) outliers start: 9 outliers final: 7 residues processed: 95 average time/residue: 0.4928 time to fit residues: 49.5839 Evaluate side-chains 94 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113423 restraints weight = 9225.665| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.22 r_work: 0.3255 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7868 Z= 0.139 Angle : 0.481 8.974 10683 Z= 0.261 Chirality : 0.042 0.155 1215 Planarity : 0.004 0.053 1335 Dihedral : 5.925 71.250 1059 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.21 % Allowed : 14.29 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 966 helix: 1.83 (0.27), residues: 341 sheet: 0.44 (0.30), residues: 293 loop : -0.14 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 247 TYR 0.016 0.001 TYR A 180 PHE 0.013 0.001 PHE A 587 TRP 0.010 0.001 TRP A 198 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 7865) covalent geometry : angle 0.48132 / 0.26 (10677) SS BOND : bond 0.00305 / 0.16 ( 3) SS BOND : angle 0.53805 / 0.28 ( 6) hydrogen bonds : bond 0.04010 / 2.84 ( 402) hydrogen bonds : angle 4.51608 / 3.21 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8469 (tt0) cc_final: 0.8183 (tp30) REVERT: A 244 GLU cc_start: 0.8702 (tt0) cc_final: 0.8418 (pt0) REVERT: A 382 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: A 410 ARG cc_start: 0.7076 (ttp-170) cc_final: 0.6083 (pmm-80) REVERT: A 437 GLN cc_start: 0.7592 (pt0) cc_final: 0.6929 (pp30) REVERT: A 547 ARG cc_start: 0.7667 (mmm160) cc_final: 0.7296 (mmm160) REVERT: A 657 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6534 (tm-30) REVERT: A 711 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7736 (mt-10) REVERT: A 764 ASN cc_start: 0.7798 (t0) cc_final: 0.7379 (t0) REVERT: A 906 ARG cc_start: 0.7138 (tpp-160) cc_final: 0.6625 (tpp-160) REVERT: H 5 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7723 (tm-30) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.5645 time to fit residues: 55.5541 Evaluate side-chains 93 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.149578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114606 restraints weight = 9168.779| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.22 r_work: 0.3271 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7868 Z= 0.113 Angle : 0.463 8.442 10683 Z= 0.251 Chirality : 0.041 0.141 1215 Planarity : 0.004 0.055 1335 Dihedral : 5.873 70.734 1059 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.85 % Allowed : 14.77 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.27), residues: 966 helix: 1.88 (0.27), residues: 341 sheet: 0.48 (0.31), residues: 293 loop : -0.08 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 247 TYR 0.014 0.001 TYR A 180 PHE 0.016 0.001 PHE A 613 TRP 0.010 0.001 TRP A 198 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7865) covalent geometry : angle 0.46320 / 0.25 (10677) SS BOND : bond 0.00256 / 0.13 ( 3) SS BOND : angle 0.48057 / 0.24 ( 6) hydrogen bonds : bond 0.03803 / 2.70 ( 402) hydrogen bonds : angle 4.44470 / 3.16 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.186 Fit side-chains REVERT: A 77 GLU cc_start: 0.8477 (tt0) cc_final: 0.8197 (tp30) REVERT: A 244 GLU cc_start: 0.8698 (tt0) cc_final: 0.8425 (pt0) REVERT: A 382 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7243 (mt0) REVERT: A 410 ARG cc_start: 0.7072 (ttp-170) cc_final: 0.6066 (pmm-80) REVERT: A 437 GLN cc_start: 0.7590 (pt0) cc_final: 0.6923 (pp30) REVERT: A 547 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7290 (mmm160) REVERT: A 632 ARG cc_start: 0.8078 (ptp90) cc_final: 0.7719 (ptp90) REVERT: A 657 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6531 (tm-30) REVERT: A 711 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7744 (mt-10) REVERT: A 764 ASN cc_start: 0.7779 (t0) cc_final: 0.7390 (t0) REVERT: A 906 ARG cc_start: 0.7155 (tpp-160) cc_final: 0.6644 (tpp-160) REVERT: H 5 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7705 (tm-30) outliers start: 7 outliers final: 4 residues processed: 88 average time/residue: 0.5666 time to fit residues: 52.7502 Evaluate side-chains 88 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113426 restraints weight = 9161.128| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.22 r_work: 0.3255 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7868 Z= 0.137 Angle : 0.481 8.693 10683 Z= 0.259 Chirality : 0.042 0.145 1215 Planarity : 0.004 0.045 1335 Dihedral : 5.903 71.058 1059 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.21 % Allowed : 14.29 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.27), residues: 966 helix: 1.82 (0.27), residues: 341 sheet: 0.47 (0.31), residues: 293 loop : -0.11 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 632 TYR 0.016 0.001 TYR A 180 PHE 0.014 0.001 PHE A 587 TRP 0.010 0.001 TRP A 198 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7865) covalent geometry : angle 0.48059 / 0.26 (10677) SS BOND : bond 0.00291 / 0.15 ( 3) SS BOND : angle 0.50767 / 0.26 ( 6) hydrogen bonds : bond 0.03986 / 2.83 ( 402) hydrogen bonds : angle 4.50361 / 3.20 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3015.21 seconds wall clock time: 52 minutes 3.32 seconds (3123.32 seconds total)