Starting phenix.real_space_refine on Thu Jul 2 02:38:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iv8_60921/07_2026/9iv8_60921.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iv8_60921/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9iv8_60921/07_2026/9iv8_60921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iv8_60921/07_2026/9iv8_60921.map" model { file = "/net/cci-nas-00/data/ceres_data/9iv8_60921/07_2026/9iv8_60921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iv8_60921/07_2026/9iv8_60921.cif" } 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-dev-6108/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, 47 Ad-hoc single atom residues: {' CA': 5} Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain breaks: 5 Time building chain proxies: 1.14, per 1000 atoms: 0.19 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: 0.36 Conformation dependent library (CDL) restraints added in 213.1 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: 0.17 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: 0.87 Time building geometry restraints manager: 0.47 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 3.250 nonbonded pdb=" OD2 ASP A 421 " pdb="CA CA A1004 " model vdw 2.282 3.250 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 3.250 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: 2.500 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.380 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.050 ------------------------------------------------------------------------------- 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 : 0.145 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: 0.0575 time to fit residues: 5.2421 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 : 0.176 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.164719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130495 restraints weight = 8135.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128937 restraints weight = 9366.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129412 restraints weight = 10294.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129779 restraints weight = 8900.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129786 restraints weight = 8423.012| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6078 Z= 0.145 Angle : 0.534 7.277 8248 Z= 0.289 Chirality : 0.043 0.238 953 Planarity : 0.004 0.035 1024 Dihedral : 6.018 58.432 814 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.09 % Allowed : 11.70 % Favored : 87.21 % 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: 0.39 (0.31), residues: 738 helix: 1.15 (0.28), residues: 345 sheet: -0.30 (0.39), residues: 179 loop : -0.52 (0.41), residues: 214 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 0.012 0.001 PHE A 865 TRP 0.010 0.001 TRP A 709 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 6077) covalent geometry : angle 0.53369 / 0.29 ( 8246) SS BOND : bond 0.00156 / 0.08 ( 1) SS BOND : angle 0.41225 / 0.22 ( 2) hydrogen bonds : bond 0.04700 / 3.10 ( 320) hydrogen bonds : angle 5.11767 / 3.57 ( 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 79 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.231 Fit side-chains REVERT: A 204 PHE cc_start: 0.8464 (t80) cc_final: 0.8169 (t80) REVERT: A 665 GLU cc_start: 0.7557 (tp30) cc_final: 0.7120 (tt0) REVERT: A 775 MET cc_start: 0.7779 (tpp) cc_final: 0.7377 (ttm) outliers start: 7 outliers final: 4 residues processed: 79 average time/residue: 0.0777 time to fit residues: 8.2826 Evaluate side-chains 69 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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: 4.9990 chunk 39 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.157603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118914 restraints weight = 8207.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119289 restraints weight = 6145.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119631 restraints weight = 5649.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120130 restraints weight = 5423.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120221 restraints weight = 5235.226| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 6078 Z= 0.216 Angle : 0.581 7.784 8248 Z= 0.315 Chirality : 0.045 0.166 953 Planarity : 0.004 0.042 1024 Dihedral : 5.800 55.591 814 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.50 % Allowed : 13.88 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.30), residues: 738 helix: 1.04 (0.28), residues: 341 sheet: -0.52 (0.38), residues: 178 loop : -0.70 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.017 0.002 TYR A 228 PHE 0.014 0.002 PHE A 865 TRP 0.017 0.002 TRP A 709 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 ( 6077) covalent geometry : angle 0.58091 / 0.31 ( 8246) SS BOND : bond 0.00362 / 0.19 ( 1) SS BOND : angle 0.76210 / 0.41 ( 2) hydrogen bonds : bond 0.05006 / 3.31 ( 320) hydrogen bonds : angle 5.06950 / 3.53 ( 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 79 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 170 PHE cc_start: 0.6383 (t80) cc_final: 0.6154 (t80) REVERT: A 204 PHE cc_start: 0.8546 (t80) cc_final: 0.8319 (t80) REVERT: A 665 GLU cc_start: 0.7647 (tp30) cc_final: 0.6957 (tt0) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.0756 time to fit residues: 8.0149 Evaluate side-chains 73 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 196 GLU 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 779 LEU 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: 3.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 0.0010 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.161509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123682 restraints weight = 8227.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123819 restraints weight = 6949.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124306 restraints weight = 6098.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124591 restraints weight = 5749.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124767 restraints weight = 5634.750| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6078 Z= 0.115 Angle : 0.481 7.319 8248 Z= 0.259 Chirality : 0.042 0.162 953 Planarity : 0.004 0.055 1024 Dihedral : 5.199 53.641 814 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.56 % Allowed : 15.91 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.31), residues: 738 helix: 1.49 (0.28), residues: 337 sheet: -0.47 (0.39), residues: 177 loop : -0.73 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.011 0.001 TYR A 180 PHE 0.010 0.001 PHE A 865 TRP 0.008 0.001 TRP A 198 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 6077) covalent geometry : angle 0.48090 / 0.26 ( 8246) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.56934 / 0.31 ( 2) hydrogen bonds : bond 0.04106 / 2.73 ( 320) hydrogen bonds : angle 4.76726 / 3.33 ( 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 82 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 170 PHE cc_start: 0.6334 (t80) cc_final: 0.6114 (t80) REVERT: A 204 PHE cc_start: 0.8438 (t80) cc_final: 0.8183 (t80) REVERT: A 220 ARG cc_start: 0.7006 (ttp80) cc_final: 0.6430 (mmp80) REVERT: A 665 GLU cc_start: 0.7555 (tp30) cc_final: 0.6921 (tt0) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.0671 time to fit residues: 7.4169 Evaluate side-chains 70 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 242 GLU 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: 1.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.156758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117504 restraints weight = 8484.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118413 restraints weight = 7285.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118691 restraints weight = 6029.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119163 restraints weight = 5791.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119319 restraints weight = 5536.888| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 0.051 6078 Z= 0.214 Angle : 0.558 6.960 8248 Z= 0.302 Chirality : 0.045 0.166 953 Planarity : 0.004 0.037 1024 Dihedral : 5.121 52.146 814 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.59 % Allowed : 15.29 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.31), residues: 738 helix: 1.22 (0.28), residues: 337 sheet: -0.59 (0.38), residues: 179 loop : -0.86 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.015 0.002 TYR A 228 PHE 0.012 0.002 PHE A 865 TRP 0.010 0.001 TRP A 709 HIS 0.003 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.21 ( 6077) covalent geometry : angle 0.55825 / 0.30 ( 8246) SS BOND : bond 0.00378 / 0.20 ( 1) SS BOND : angle 0.81896 / 0.45 ( 2) hydrogen bonds : bond 0.04675 / 3.08 ( 320) hydrogen bonds : angle 4.91563 / 3.42 ( 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 87 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8552 (t80) cc_final: 0.8314 (t80) REVERT: A 421 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6001 (t0) REVERT: A 589 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8621 (tt) REVERT: A 665 GLU cc_start: 0.7600 (tp30) cc_final: 0.6935 (tt0) outliers start: 23 outliers final: 14 residues processed: 82 average time/residue: 0.0618 time to fit residues: 7.1505 Evaluate side-chains 78 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 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 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 752 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.159038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120625 restraints weight = 8344.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121330 restraints weight = 7366.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122068 restraints weight = 6088.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122701 restraints weight = 5760.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122773 restraints weight = 5194.797| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1878 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= 0.135 Angle : 0.496 7.697 8248 Z= 0.268 Chirality : 0.042 0.151 953 Planarity : 0.004 0.037 1024 Dihedral : 5.003 52.643 814 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.59 % Allowed : 15.29 % Favored : 81.12 % 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: 0.39 (0.31), residues: 738 helix: 1.43 (0.28), residues: 338 sheet: -0.46 (0.38), residues: 179 loop : -0.82 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.011 0.001 TYR A 180 PHE 0.009 0.001 PHE A 587 TRP 0.008 0.001 TRP A 198 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6077) covalent geometry : angle 0.49597 / 0.27 ( 8246) SS BOND : bond 0.00213 / 0.11 ( 1) SS BOND : angle 0.67074 / 0.37 ( 2) hydrogen bonds : bond 0.04160 / 2.76 ( 320) hydrogen bonds : angle 4.76568 / 3.33 ( 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: 23 poor density : 63 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8458 (t80) cc_final: 0.8146 (t80) REVERT: A 589 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8631 (tt) REVERT: A 665 GLU cc_start: 0.7579 (tp30) cc_final: 0.6935 (tt0) outliers start: 23 outliers final: 12 residues processed: 81 average time/residue: 0.0694 time to fit residues: 7.9179 Evaluate side-chains 75 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE 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 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 589 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 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: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.156524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117697 restraints weight = 8391.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118553 restraints weight = 7347.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118809 restraints weight = 6130.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119174 restraints weight = 5855.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119278 restraints weight = 5645.603| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6078 Z= 0.213 Angle : 0.559 7.298 8248 Z= 0.301 Chirality : 0.044 0.150 953 Planarity : 0.004 0.036 1024 Dihedral : 5.115 53.664 814 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.12 % Allowed : 15.44 % 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: 0.14 (0.31), residues: 738 helix: 1.22 (0.28), residues: 338 sheet: -0.59 (0.38), residues: 179 loop : -0.92 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 527 TYR 0.014 0.002 TYR A 180 PHE 0.012 0.002 PHE A 450 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 0.00522 / 0.21 ( 6077) covalent geometry : angle 0.55841 / 0.30 ( 8246) SS BOND : bond 0.00335 / 0.18 ( 1) SS BOND : angle 0.88937 / 0.49 ( 2) hydrogen bonds : bond 0.04588 / 3.02 ( 320) hydrogen bonds : angle 4.90471 / 3.41 ( 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 81 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8552 (t80) cc_final: 0.8319 (t80) REVERT: A 421 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6026 (t0) REVERT: A 665 GLU cc_start: 0.7597 (tp30) cc_final: 0.6934 (tt0) outliers start: 20 outliers final: 17 residues processed: 78 average time/residue: 0.0650 time to fit residues: 7.1493 Evaluate side-chains 77 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 556 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 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: 2.9990 chunk 16 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 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 = 0.3869 r_free = 0.3869 target = 0.159366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121435 restraints weight = 8298.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121785 restraints weight = 7049.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122658 restraints weight = 6324.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122795 restraints weight = 5647.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123017 restraints weight = 5381.295| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6078 Z= 0.122 Angle : 0.491 7.625 8248 Z= 0.263 Chirality : 0.042 0.149 953 Planarity : 0.003 0.037 1024 Dihedral : 4.985 54.157 814 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.65 % Allowed : 16.54 % 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: 0.42 (0.31), residues: 738 helix: 1.53 (0.28), residues: 338 sheet: -0.51 (0.38), residues: 179 loop : -0.86 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.011 0.001 TYR A 180 PHE 0.008 0.001 PHE A 587 TRP 0.008 0.001 TRP A 198 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 6077) covalent geometry : angle 0.49096 / 0.26 ( 8246) SS BOND : bond 0.00182 / 0.10 ( 1) SS BOND : angle 0.66411 / 0.36 ( 2) hydrogen bonds : bond 0.04032 / 2.67 ( 320) hydrogen bonds : angle 4.73267 / 3.30 ( 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 81 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8415 (t80) cc_final: 0.7915 (t80) REVERT: A 421 ASP cc_start: 0.6460 (OUTLIER) cc_final: 0.5559 (t0) REVERT: A 665 GLU cc_start: 0.7580 (tp30) cc_final: 0.6937 (tt0) outliers start: 17 outliers final: 14 residues processed: 77 average time/residue: 0.0773 time to fit residues: 8.2009 Evaluate side-chains 75 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE 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 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 615 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=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: 0.6980 chunk 35 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.159440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121469 restraints weight = 8357.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121644 restraints weight = 7105.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122290 restraints weight = 6647.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122426 restraints weight = 5899.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123322 restraints weight = 5544.487| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6078 Z= 0.136 Angle : 0.495 7.372 8248 Z= 0.266 Chirality : 0.042 0.146 953 Planarity : 0.004 0.058 1024 Dihedral : 4.960 55.279 814 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.50 % Allowed : 16.85 % Favored : 80.66 % 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: 1.56 (0.28), residues: 338 sheet: -0.47 (0.38), residues: 179 loop : -0.90 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 220 TYR 0.011 0.001 TYR A 180 PHE 0.009 0.001 PHE A 865 TRP 0.008 0.001 TRP A 198 HIS 0.002 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6077) covalent geometry : angle 0.49504 / 0.27 ( 8246) SS BOND : bond 0.00175 / 0.09 ( 1) SS BOND : angle 0.73631 / 0.40 ( 2) hydrogen bonds : bond 0.04010 / 2.66 ( 320) hydrogen bonds : angle 4.69071 / 3.28 ( 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 76 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8399 (t80) cc_final: 0.7914 (t80) REVERT: A 421 ASP cc_start: 0.6628 (OUTLIER) cc_final: 0.5840 (t0) REVERT: A 665 GLU cc_start: 0.7569 (tp30) cc_final: 0.6977 (tt0) outliers start: 16 outliers final: 14 residues processed: 73 average time/residue: 0.0736 time to fit residues: 7.5107 Evaluate side-chains 74 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE 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 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 556 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: 0.9980 chunk 43 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.157971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119563 restraints weight = 8352.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119849 restraints weight = 7254.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120560 restraints weight = 6167.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120909 restraints weight = 5749.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121081 restraints weight = 5528.590| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6078 Z= 0.169 Angle : 0.519 7.494 8248 Z= 0.279 Chirality : 0.043 0.145 953 Planarity : 0.004 0.045 1024 Dihedral : 5.021 56.073 814 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.65 % Allowed : 16.22 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.31), residues: 738 helix: 1.47 (0.28), residues: 338 sheet: -0.53 (0.38), residues: 179 loop : -0.96 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 220 TYR 0.012 0.001 TYR A 180 PHE 0.010 0.001 PHE A 865 TRP 0.007 0.001 TRP A 709 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 6077) covalent geometry : angle 0.51875 / 0.28 ( 8246) SS BOND : bond 0.00290 / 0.15 ( 1) SS BOND : angle 0.88398 / 0.48 ( 2) hydrogen bonds : bond 0.04203 / 2.79 ( 320) hydrogen bonds : angle 4.74856 / 3.31 ( 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 76 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7502 (pttt) cc_final: 0.7265 (pttt) REVERT: A 204 PHE cc_start: 0.8455 (t80) cc_final: 0.7955 (t80) REVERT: A 421 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.5975 (t0) REVERT: A 665 GLU cc_start: 0.7599 (tp30) cc_final: 0.7000 (tt0) outliers start: 17 outliers final: 15 residues processed: 73 average time/residue: 0.0657 time to fit residues: 6.7034 Evaluate side-chains 76 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE 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 196 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 556 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 Chi-restraints excluded: chain A residue 911 LEU 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: 0.2980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.159443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121293 restraints weight = 8339.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122008 restraints weight = 7128.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122489 restraints weight = 6279.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122661 restraints weight = 5754.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123034 restraints weight = 5499.977| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6078 Z= 0.137 Angle : 0.500 7.294 8248 Z= 0.269 Chirality : 0.042 0.148 953 Planarity : 0.004 0.041 1024 Dihedral : 4.970 56.494 814 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.81 % Allowed : 16.38 % 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: 0.49 (0.31), residues: 738 helix: 1.63 (0.28), residues: 338 sheet: -0.46 (0.39), residues: 178 loop : -0.93 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 220 TYR 0.012 0.001 TYR A 180 PHE 0.009 0.001 PHE A 409 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 0.00326 / 0.14 ( 6077) covalent geometry : angle 0.49988 / 0.27 ( 8246) SS BOND : bond 0.00250 / 0.13 ( 1) SS BOND : angle 0.84640 / 0.46 ( 2) hydrogen bonds : bond 0.04000 / 2.66 ( 320) hydrogen bonds : angle 4.67035 / 3.26 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1184.00 seconds wall clock time: 21 minutes 11.91 seconds (1271.91 seconds total)