Starting phenix.real_space_refine on Tue Aug 4 18:28:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iv8_60921/08_2026/9iv8_60921.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iv8_60921/08_2026/9iv8_60921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iv8_60921/08_2026/9iv8_60921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iv8_60921/08_2026/9iv8_60921.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iv8_60921/08_2026/9iv8_60921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iv8_60921/08_2026/9iv8_60921.map" } resolution = 3.5 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= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 3 5.49 5 S 24 5.16 5 C 3860 2.51 5 N 945 2.21 5 O 1110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 5947 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5895 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 724} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {' CA': 5, 'PIO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.30, per 1000 atoms: 0.22 Number of scatterers: 5947 At special positions: 0 Unit cell: (115.92, 89.04, 148.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 24 16.00 P 3 15.00 O 1110 8.00 N 945 7.00 C 3860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " 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: 0.50 Conformation dependent library (CDL) restraints added in 336.2 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 9 sheets defined 48.0% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 37 through 72 removed outlier: 3.516A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 56 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 57 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.676A pdb=" N ILE A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 155 removed outlier: 3.505A pdb=" N ILE A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 removed outlier: 3.767A pdb=" N TYR A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 225 removed outlier: 3.754A pdb=" N LEU A 202 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'A' and resid 656 through 666 removed outlier: 3.585A pdb=" N MET A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 698 Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 738 through 755 removed outlier: 4.848A pdb=" N PHE A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TRP A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 764 removed outlier: 3.712A 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: 3.607A pdb=" N ILE A 773 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 779 " --> pdb=" O MET A 775 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 811 through 825 removed outlier: 3.517A pdb=" N THR A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 816 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 817 " --> pdb=" O PRO A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 862 removed outlier: 4.227A pdb=" N ILE A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 843 " --> pdb=" O ASN A 839 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 848 " --> pdb=" O PHE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 893 removed outlier: 3.952A pdb=" N PHE A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 893 " --> pdb=" O VAL A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 932 removed outlier: 3.537A pdb=" N TYR A 932 " --> pdb=" O SER A 928 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 80 removed outlier: 3.754A pdb=" N GLN A 74 " --> pdb=" O ILE A 94 " (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 229 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 443 removed outlier: 5.789A pdb=" N SER A 372 " --> pdb=" O CYS A 485 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 384 removed outlier: 3.897A pdb=" N TYR A 381 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 497 " --> pdb=" O CYS A 383 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 463 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE A 406 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL A 465 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR A 404 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 405 " --> pdb=" O PHE A 431 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 574 removed outlier: 3.744A pdb=" N LYS A 569 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.567A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.045A 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: 6.567A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 598 through 599 removed outlier: 6.711A pdb=" N GLN A 623 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS A 618 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 625 " --> pdb=" O THR A 616 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 963 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: 1.08 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1023 1.32 - 1.45: 1615 1.45 - 1.57: 3399 1.57 - 1.69: 5 1.69 - 1.81: 35 Bond restraints: 6077 Sorted by residual: bond pdb=" O4 PIO A1002 " pdb=" P4 PIO A1002 " ideal model delta sigma weight residual 1.710 1.626 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O5 PIO A1002 " pdb=" P5 PIO A1002 " ideal model delta sigma weight residual 1.699 1.629 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N VAL A 211 " pdb=" CA VAL A 211 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.87e+00 bond pdb=" N ILE A 163 " pdb=" CA ILE A 163 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.08e-02 8.57e+03 8.71e+00 bond pdb=" C5 PIO A1002 " pdb=" O5 PIO A1002 " ideal model delta sigma weight residual 1.388 1.447 -0.059 2.00e-02 2.50e+03 8.61e+00 ... (remaining 6072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 7819 1.57 - 3.14: 353 3.14 - 4.71: 60 4.71 - 6.28: 9 6.28 - 7.85: 5 Bond angle restraints: 8246 Sorted by residual: angle pdb=" CA GLU A 930 " pdb=" CB GLU A 930 " pdb=" CG GLU A 930 " ideal model delta sigma weight residual 114.10 121.66 -7.56 2.00e+00 2.50e-01 1.43e+01 angle pdb=" N LEU A 107 " pdb=" CA LEU A 107 " pdb=" C LEU A 107 " ideal model delta sigma weight residual 111.28 107.24 4.04 1.09e+00 8.42e-01 1.37e+01 angle pdb=" CA THR A 98 " pdb=" C THR A 98 " pdb=" O THR A 98 " ideal model delta sigma weight residual 121.40 117.32 4.08 1.13e+00 7.83e-01 1.30e+01 angle pdb=" CB GLU A 930 " pdb=" CG GLU A 930 " pdb=" CD GLU A 930 " ideal model delta sigma weight residual 112.60 118.66 -6.06 1.70e+00 3.46e-01 1.27e+01 angle pdb=" C VAL A 803 " pdb=" N VAL A 804 " pdb=" CA VAL A 804 " ideal model delta sigma weight residual 122.35 118.36 3.99 1.18e+00 7.18e-01 1.15e+01 ... (remaining 8241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 3164 17.67 - 35.34: 298 35.34 - 53.01: 57 53.01 - 70.69: 9 70.69 - 88.36: 4 Dihedral angle restraints: 3532 sinusoidal: 1380 harmonic: 2152 Sorted by residual: dihedral pdb=" C TYR A 827 " pdb=" N TYR A 827 " pdb=" CA TYR A 827 " pdb=" CB TYR A 827 " ideal model delta harmonic sigma weight residual -122.60 -113.67 -8.93 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" CA THR A 506 " pdb=" C THR A 506 " pdb=" N PHE A 507 " pdb=" CA PHE A 507 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 761 " pdb=" CG GLU A 761 " pdb=" CD GLU A 761 " pdb=" OE1 GLU A 761 " ideal model delta sinusoidal sigma weight residual 0.00 88.36 -88.36 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 750 0.060 - 0.120: 157 0.120 - 0.179: 35 0.179 - 0.239: 7 0.239 - 0.299: 4 Chirality restraints: 953 Sorted by residual: chirality pdb=" CA TYR A 827 " pdb=" N TYR A 827 " pdb=" C TYR A 827 " pdb=" CB TYR A 827 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA LEU A 107 " pdb=" N LEU A 107 " pdb=" C LEU A 107 " pdb=" CB LEU A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2C PIO A1002 " pdb=" C1C PIO A1002 " pdb=" C3C PIO A1002 " pdb=" O2C PIO A1002 " both_signs ideal model delta sigma weight residual False -2.56 -2.30 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 950 not shown) Planarity restraints: 1024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 30 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO A 31 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 784 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C GLY A 784 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY A 784 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 785 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 29 " 0.013 2.00e-02 2.50e+03 1.05e-02 2.78e+00 pdb=" CG TRP A 29 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 29 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 29 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 29 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 29 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 29 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 29 " 0.002 2.00e-02 2.50e+03 ... (remaining 1021 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1353 2.79 - 3.32: 5590 3.32 - 3.85: 9415 3.85 - 4.37: 10417 4.37 - 4.90: 18967 Nonbonded interactions: 45742 Sorted by model distance: nonbonded pdb=" OE2 GLU A 385 " pdb="CA CA A1004 " model vdw 2.266 2.510 nonbonded pdb=" OD2 ASP A 421 " pdb="CA CA A1004 " model vdw 2.282 2.510 nonbonded pdb=" NH1 ARG A 161 " pdb=" O ASP A 825 " model vdw 2.314 3.120 nonbonded pdb=" OE2 GLU A 385 " pdb="CA CA A1006 " model vdw 2.318 2.510 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 814 " model vdw 2.325 3.040 ... (remaining 45737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.440 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 0.084 6078 Z= 0.290 Angle : 0.761 7.847 8248 Z= 0.469 Chirality : 0.056 0.299 953 Planarity : 0.005 0.052 1024 Dihedral : 14.252 88.357 2145 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.30), residues: 738 helix: 0.68 (0.27), residues: 338 sheet: -0.28 (0.38), residues: 182 loop : -0.57 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 42 TYR 0.017 0.002 TYR A 827 PHE 0.017 0.002 PHE A 865 TRP 0.028 0.002 TRP A 29 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.29 ( 6077) covalent geometry : angle 0.76067 / 0.47 ( 8246) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.43724 / 0.24 ( 2) hydrogen bonds : bond 0.13521 / 8.83 ( 320) hydrogen bonds : angle 6.37544 / 4.45 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.260 Fit side-chains REVERT: A 204 PHE cc_start: 0.8482 (t80) cc_final: 0.8207 (t80) REVERT: A 665 GLU cc_start: 0.7628 (tp30) cc_final: 0.7154 (tt0) REVERT: A 775 MET cc_start: 0.7702 (tpp) cc_final: 0.7205 (mtt) REVERT: A 861 ASN cc_start: 0.7530 (t0) cc_final: 0.7179 (t0) REVERT: A 925 PHE cc_start: 0.6809 (t80) cc_final: 0.6572 (t80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0759 time to fit residues: 6.9812 Evaluate side-chains 60 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.163501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127863 restraints weight = 8102.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128379 restraints weight = 7810.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128379 restraints weight = 7558.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128378 restraints weight = 7558.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128378 restraints weight = 7558.527| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6078 Z= 0.140 Angle : 0.526 7.145 8248 Z= 0.284 Chirality : 0.043 0.228 953 Planarity : 0.004 0.036 1024 Dihedral : 5.962 58.270 814 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.09 % Allowed : 11.86 % Favored : 87.05 % 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: 0.45 (0.30), residues: 738 helix: 1.23 (0.28), residues: 339 sheet: -0.29 (0.39), residues: 177 loop : -0.47 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 219 TYR 0.011 0.001 TYR A 180 PHE 0.013 0.001 PHE A 865 TRP 0.010 0.001 TRP A 709 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 6077) covalent geometry : angle 0.52590 / 0.28 ( 8246) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.42979 / 0.23 ( 2) hydrogen bonds : bond 0.04732 / 3.11 ( 320) hydrogen bonds : angle 5.10308 / 3.56 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.282 Fit side-chains REVERT: A 665 GLU cc_start: 0.7567 (tp30) cc_final: 0.7095 (tt0) REVERT: A 775 MET cc_start: 0.7815 (tpp) cc_final: 0.7421 (ttm) REVERT: A 925 PHE cc_start: 0.6930 (t80) cc_final: 0.6718 (t80) outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 0.0802 time to fit residues: 8.4278 Evaluate side-chains 67 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 242 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 0.0040 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 overall best weight: 1.8596 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.156676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117146 restraints weight = 8200.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117721 restraints weight = 7134.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117760 restraints weight = 6156.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118069 restraints weight = 6024.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118259 restraints weight = 5850.237| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 6078 Z= 0.227 Angle : 0.579 7.624 8248 Z= 0.314 Chirality : 0.045 0.168 953 Planarity : 0.004 0.043 1024 Dihedral : 5.803 56.623 814 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.18 % Allowed : 14.66 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.30), residues: 738 helix: 1.08 (0.28), residues: 338 sheet: -0.51 (0.38), residues: 177 loop : -0.67 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.016 0.002 TYR A 228 PHE 0.013 0.002 PHE A 865 TRP 0.016 0.001 TRP A 709 HIS 0.004 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.23 ( 6077) covalent geometry : angle 0.57881 / 0.31 ( 8246) SS BOND : bond 0.00380 / 0.20 ( 1) SS BOND : angle 0.73690 / 0.40 ( 2) hydrogen bonds : bond 0.05016 / 3.31 ( 320) hydrogen bonds : angle 5.09217 / 3.54 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.215 Fit side-chains REVERT: A 170 PHE cc_start: 0.6387 (t80) cc_final: 0.6144 (t80) REVERT: A 665 GLU cc_start: 0.7779 (tp30) cc_final: 0.7077 (tt0) REVERT: A 775 MET cc_start: 0.7980 (tpp) cc_final: 0.7452 (mtt) REVERT: A 925 PHE cc_start: 0.7231 (t80) cc_final: 0.6954 (t80) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.0744 time to fit residues: 7.8111 Evaluate side-chains 77 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 841 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.159299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120229 restraints weight = 8195.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120877 restraints weight = 7210.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120881 restraints weight = 6099.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121635 restraints weight = 5952.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121780 restraints weight = 5503.769| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6078 Z= 0.128 Angle : 0.493 7.317 8248 Z= 0.266 Chirality : 0.042 0.194 953 Planarity : 0.004 0.058 1024 Dihedral : 5.294 54.281 814 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.03 % Allowed : 15.13 % Favored : 82.84 % 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: 0.44 (0.31), residues: 738 helix: 1.40 (0.28), residues: 338 sheet: -0.49 (0.38), residues: 178 loop : -0.61 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 220 TYR 0.011 0.001 TYR A 180 PHE 0.010 0.001 PHE A 865 TRP 0.008 0.001 TRP A 709 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6077) covalent geometry : angle 0.49333 / 0.27 ( 8246) SS BOND : bond 0.00159 / 0.08 ( 1) SS BOND : angle 0.65336 / 0.36 ( 2) hydrogen bonds : bond 0.04277 / 2.84 ( 320) hydrogen bonds : angle 4.85212 / 3.38 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 170 PHE cc_start: 0.6236 (t80) cc_final: 0.6026 (t80) REVERT: A 665 GLU cc_start: 0.7587 (tp30) cc_final: 0.6909 (tt0) REVERT: A 925 PHE cc_start: 0.7254 (t80) cc_final: 0.6970 (t80) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.0731 time to fit residues: 8.2397 Evaluate side-chains 75 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 812 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.161962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123135 restraints weight = 8376.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123500 restraints weight = 6528.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124170 restraints weight = 5804.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124541 restraints weight = 5411.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124783 restraints weight = 5213.807| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6078 Z= 0.102 Angle : 0.462 7.063 8248 Z= 0.247 Chirality : 0.041 0.159 953 Planarity : 0.003 0.039 1024 Dihedral : 4.828 51.677 814 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.12 % Allowed : 15.29 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.31), residues: 738 helix: 1.63 (0.28), residues: 339 sheet: -0.32 (0.39), residues: 178 loop : -0.57 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.010 0.001 TYR A 180 PHE 0.008 0.001 PHE A 865 TRP 0.007 0.001 TRP A 198 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 6077) covalent geometry : angle 0.46195 / 0.25 ( 8246) SS BOND : bond 0.00122 / 0.06 ( 1) SS BOND : angle 0.57981 / 0.31 ( 2) hydrogen bonds : bond 0.03848 / 2.56 ( 320) hydrogen bonds : angle 4.63426 / 3.24 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 170 PHE cc_start: 0.6377 (t80) cc_final: 0.6165 (t80) REVERT: A 204 PHE cc_start: 0.8428 (t80) cc_final: 0.8142 (t80) REVERT: A 220 ARG cc_start: 0.6886 (ttp80) cc_final: 0.6439 (mmp80) REVERT: A 665 GLU cc_start: 0.7586 (tp30) cc_final: 0.6925 (tt0) REVERT: A 925 PHE cc_start: 0.7254 (t80) cc_final: 0.6979 (t80) outliers start: 20 outliers final: 8 residues processed: 88 average time/residue: 0.0598 time to fit residues: 7.1929 Evaluate side-chains 75 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 812 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.157349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118267 restraints weight = 8367.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118989 restraints weight = 7425.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119227 restraints weight = 6359.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119757 restraints weight = 6051.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120001 restraints weight = 5625.470| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6078 Z= 0.193 Angle : 0.536 6.556 8248 Z= 0.289 Chirality : 0.044 0.146 953 Planarity : 0.004 0.037 1024 Dihedral : 4.948 51.031 814 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.96 % Allowed : 15.60 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.31), residues: 738 helix: 1.34 (0.28), residues: 338 sheet: -0.45 (0.38), residues: 179 loop : -0.70 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.013 0.002 TYR A 180 PHE 0.011 0.001 PHE A 865 TRP 0.009 0.001 TRP A 709 HIS 0.003 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.19 ( 6077) covalent geometry : angle 0.53570 / 0.29 ( 8246) SS BOND : bond 0.00362 / 0.19 ( 1) SS BOND : angle 0.79350 / 0.43 ( 2) hydrogen bonds : bond 0.04357 / 2.88 ( 320) hydrogen bonds : angle 4.81679 / 3.35 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8537 (t80) cc_final: 0.8286 (t80) REVERT: A 665 GLU cc_start: 0.7602 (tp30) cc_final: 0.6931 (tt0) REVERT: A 925 PHE cc_start: 0.7285 (t80) cc_final: 0.7020 (t80) outliers start: 19 outliers final: 15 residues processed: 83 average time/residue: 0.0696 time to fit residues: 7.9753 Evaluate side-chains 80 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 841 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.157434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118611 restraints weight = 8312.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119148 restraints weight = 7161.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119553 restraints weight = 6189.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119903 restraints weight = 5970.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120097 restraints weight = 5709.088| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6078 Z= 0.179 Angle : 0.530 7.674 8248 Z= 0.285 Chirality : 0.043 0.143 953 Planarity : 0.004 0.037 1024 Dihedral : 4.989 52.368 814 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.28 % Allowed : 15.29 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.31), residues: 738 helix: 1.25 (0.28), residues: 338 sheet: -0.50 (0.38), residues: 179 loop : -0.78 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 220 TYR 0.013 0.001 TYR A 180 PHE 0.010 0.001 PHE A 456 TRP 0.008 0.001 TRP A 709 HIS 0.003 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 ( 6077) covalent geometry : angle 0.53023 / 0.29 ( 8246) SS BOND : bond 0.00337 / 0.18 ( 1) SS BOND : angle 0.72243 / 0.40 ( 2) hydrogen bonds : bond 0.04317 / 2.84 ( 320) hydrogen bonds : angle 4.82948 / 3.37 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8533 (t80) cc_final: 0.8266 (t80) REVERT: A 665 GLU cc_start: 0.7598 (tp30) cc_final: 0.6934 (tt0) REVERT: A 925 PHE cc_start: 0.7238 (t80) cc_final: 0.6974 (t80) outliers start: 21 outliers final: 15 residues processed: 85 average time/residue: 0.0668 time to fit residues: 7.7756 Evaluate side-chains 79 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 841 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 0.0040 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.159508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121354 restraints weight = 8241.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121749 restraints weight = 7124.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122373 restraints weight = 6264.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122654 restraints weight = 5701.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122833 restraints weight = 5545.042| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6078 Z= 0.124 Angle : 0.496 7.973 8248 Z= 0.263 Chirality : 0.042 0.150 953 Planarity : 0.003 0.037 1024 Dihedral : 4.846 51.572 814 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.50 % Allowed : 16.69 % Favored : 80.81 % 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: 0.48 (0.31), residues: 738 helix: 1.47 (0.28), residues: 339 sheet: -0.37 (0.39), residues: 177 loop : -0.75 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.011 0.001 TYR A 180 PHE 0.008 0.001 PHE A 865 TRP 0.008 0.001 TRP A 198 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 6077) covalent geometry : angle 0.49625 / 0.26 ( 8246) SS BOND : bond 0.00188 / 0.10 ( 1) SS BOND : angle 0.78952 / 0.43 ( 2) hydrogen bonds : bond 0.03944 / 2.61 ( 320) hydrogen bonds : angle 4.69305 / 3.28 ( 963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8492 (t80) cc_final: 0.8218 (t80) REVERT: A 665 GLU cc_start: 0.7596 (tp30) cc_final: 0.6969 (tt0) REVERT: A 925 PHE cc_start: 0.7239 (t80) cc_final: 0.6987 (t80) outliers start: 16 outliers final: 14 residues processed: 80 average time/residue: 0.0741 time to fit residues: 8.1685 Evaluate side-chains 80 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 812 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.158966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120547 restraints weight = 8330.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121726 restraints weight = 7243.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121366 restraints weight = 6393.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121889 restraints weight = 6612.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122111 restraints weight = 5867.097| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6078 Z= 0.143 Angle : 0.510 7.981 8248 Z= 0.271 Chirality : 0.043 0.147 953 Planarity : 0.003 0.037 1024 Dihedral : 4.841 52.109 814 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.34 % Allowed : 16.69 % Favored : 80.97 % 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: 0.45 (0.31), residues: 738 helix: 1.44 (0.28), residues: 339 sheet: -0.39 (0.39), residues: 178 loop : -0.77 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 220 TYR 0.011 0.001 TYR A 180 PHE 0.015 0.001 PHE A 170 TRP 0.007 0.001 TRP A 709 HIS 0.003 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 6077) covalent geometry : angle 0.51021 / 0.27 ( 8246) SS BOND : bond 0.00214 / 0.11 ( 1) SS BOND : angle 0.71264 / 0.39 ( 2) hydrogen bonds : bond 0.04028 / 2.67 ( 320) hydrogen bonds : angle 4.69267 / 3.29 ( 963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8510 (t80) cc_final: 0.8216 (t80) REVERT: A 665 GLU cc_start: 0.7620 (tp30) cc_final: 0.6984 (tt0) REVERT: A 925 PHE cc_start: 0.7237 (t80) cc_final: 0.6989 (t80) outliers start: 15 outliers final: 14 residues processed: 77 average time/residue: 0.0672 time to fit residues: 7.0582 Evaluate side-chains 78 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.159844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121658 restraints weight = 8281.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122735 restraints weight = 7176.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122509 restraints weight = 6651.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122858 restraints weight = 6128.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123073 restraints weight = 5833.078| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6078 Z= 0.127 Angle : 0.500 7.848 8248 Z= 0.265 Chirality : 0.042 0.148 953 Planarity : 0.003 0.037 1024 Dihedral : 4.796 51.844 814 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.50 % Allowed : 16.54 % Favored : 80.97 % 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: 0.55 (0.31), residues: 738 helix: 1.54 (0.28), residues: 339 sheet: -0.33 (0.39), residues: 178 loop : -0.76 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.011 0.001 TYR A 180 PHE 0.014 0.001 PHE A 170 TRP 0.007 0.001 TRP A 198 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6077) covalent geometry : angle 0.49992 / 0.27 ( 8246) SS BOND : bond 0.00194 / 0.10 ( 1) SS BOND : angle 0.90780 / 0.49 ( 2) hydrogen bonds : bond 0.03891 / 2.58 ( 320) hydrogen bonds : angle 4.65112 / 3.26 ( 963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6594 (tt) REVERT: A 204 PHE cc_start: 0.8471 (t80) cc_final: 0.8187 (t80) REVERT: A 665 GLU cc_start: 0.7620 (tp30) cc_final: 0.6959 (tt0) REVERT: A 925 PHE cc_start: 0.7247 (t80) cc_final: 0.6992 (t80) outliers start: 16 outliers final: 14 residues processed: 78 average time/residue: 0.0781 time to fit residues: 8.3121 Evaluate side-chains 80 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.0020 chunk 57 optimal weight: 0.0060 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 44 optimal weight: 0.0770 chunk 29 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.4364 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.162747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123187 restraints weight = 8231.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123800 restraints weight = 6845.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124219 restraints weight = 5981.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124772 restraints weight = 5632.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124878 restraints weight = 5256.784| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6078 Z= 0.102 Angle : 0.478 7.709 8248 Z= 0.253 Chirality : 0.042 0.151 953 Planarity : 0.003 0.037 1024 Dihedral : 4.680 52.078 814 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.72 % Allowed : 17.32 % Favored : 80.97 % 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: 0.79 (0.31), residues: 738 helix: 1.77 (0.28), residues: 339 sheet: -0.22 (0.39), residues: 178 loop : -0.69 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.010 0.001 TYR A 180 PHE 0.015 0.001 PHE A 170 TRP 0.007 0.001 TRP A 198 HIS 0.002 0.000 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 6077) covalent geometry : angle 0.47833 / 0.25 ( 8246) SS BOND : bond 0.00127 / 0.07 ( 1) SS BOND : angle 0.86063 / 0.46 ( 2) hydrogen bonds : bond 0.03589 / 2.39 ( 320) hydrogen bonds : angle 4.52426 / 3.18 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1168.85 seconds wall clock time: 20 minutes 45.63 seconds (1245.63 seconds total)