Starting phenix.real_space_refine on Thu Jul 2 02:47:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7urc_26708/07_2026/7urc_26708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urc_26708/07_2026/7urc_26708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7urc_26708/07_2026/7urc_26708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urc_26708/07_2026/7urc_26708.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7urc_26708/07_2026/7urc_26708.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7urc_26708/07_2026/7urc_26708.cif" model { file = "/net/cci-nas-00/data/ceres_data/7urc_26708/07_2026/7urc_26708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urc_26708/07_2026/7urc_26708.cif" } resolution = 3.14 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= 0.008 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 31 5.16 5 C 3718 2.51 5 N 868 2.21 5 O 943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 5561 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3449 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 357 Unusual residues: {' ZN': 1, 'AJP': 1, 'CLR': 9, 'O50': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2833 SG CYS A 370 54.567 29.769 19.702 1.00119.07 S ATOM 2880 SG CYS A 376 53.579 28.925 23.636 1.00124.43 S ATOM 2908 SG CYS A 380 57.213 30.122 21.402 1.00134.93 S Time building chain proxies: 1.58, per 1000 atoms: 0.28 Number of scatterers: 5561 At special positions: 0 Unit cell: (97.11, 73.04, 93.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 31 16.00 O 943 8.00 N 868 7.00 C 3718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 209 " distance=2.02 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 164.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 512 " pdb="ZN ZN A 512 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 512 " - pdb=" SG CYS A 380 " pdb="ZN ZN A 512 " - pdb=" SG CYS A 370 " pdb="ZN ZN A 512 " - pdb=" SG CYS A 376 " Number of angles added : 3 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 7 sheets defined 52.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 removed outlier: 3.988A pdb=" N GLN A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 43 removed outlier: 3.744A pdb=" N ALA A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 34 " --> pdb=" O TRP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 68 Processing helix chain 'A' and resid 72 through 89 removed outlier: 4.400A pdb=" N LEU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 116 through 141 removed outlier: 4.567A pdb=" N LYS A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 124 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ALA A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 172 through 181 removed outlier: 4.017A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.926A pdb=" N LEU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.833A pdb=" N TYR A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 264 removed outlier: 3.531A pdb=" N ALA A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.661A pdb=" N ASN A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.661A pdb=" N VAL A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 368 removed outlier: 3.961A pdb=" N ALA A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 409 Processing helix chain 'A' and resid 410 through 413 removed outlier: 4.061A pdb=" N ASP A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 455 removed outlier: 3.886A pdb=" N PHE A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 removed outlier: 3.663A pdb=" N THR H 84 " --> pdb=" O GLN H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.975A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AA3, first strand: chain 'L' and resid 30 through 32 removed outlier: 6.970A pdb=" N LEU L 31 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP L 55 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.417A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET H 53 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.417A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 834 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: 0.64 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.19: 5 1.19 - 1.39: 2276 1.39 - 1.58: 3413 1.58 - 1.78: 8 1.78 - 1.98: 48 Bond restraints: 5750 Sorted by residual: bond pdb=" C07 AJP A 511 " pdb=" C08 AJP A 511 " ideal model delta sigma weight residual 1.550 1.978 -0.428 2.00e-02 2.50e+03 4.59e+02 bond pdb=" C01 AJP A 511 " pdb=" C02 AJP A 511 " ideal model delta sigma weight residual 1.521 1.943 -0.422 2.00e-02 2.50e+03 4.46e+02 bond pdb=" C08 AJP A 511 " pdb=" O09 AJP A 511 " ideal model delta sigma weight residual 1.410 0.995 0.415 2.00e-02 2.50e+03 4.31e+02 bond pdb=" C02 AJP A 511 " pdb=" C03 AJP A 511 " ideal model delta sigma weight residual 1.525 1.136 0.389 2.00e-02 2.50e+03 3.78e+02 bond pdb=" C05 AJP A 511 " pdb=" O09 AJP A 511 " ideal model delta sigma weight residual 1.407 1.794 -0.387 2.00e-02 2.50e+03 3.74e+02 ... (remaining 5745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 7603 2.49 - 4.98: 217 4.98 - 7.47: 50 7.47 - 9.96: 11 9.96 - 12.44: 5 Bond angle restraints: 7886 Sorted by residual: angle pdb=" C03 AJP A 511 " pdb=" C02 AJP A 511 " pdb=" C85 AJP A 511 " ideal model delta sigma weight residual 109.14 121.58 -12.44 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C07 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C13 AJP A 511 " ideal model delta sigma weight residual 114.18 126.51 -12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C10 AJP A 511 " pdb=" C08 AJP A 511 " pdb=" O09 AJP A 511 " ideal model delta sigma weight residual 114.16 124.94 -10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C11 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C13 AJP A 511 " ideal model delta sigma weight residual 106.34 116.70 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C11 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C81 AJP A 511 " ideal model delta sigma weight residual 114.35 104.10 10.25 3.00e+00 1.11e-01 1.17e+01 ... (remaining 7881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.38: 2999 24.38 - 48.75: 144 48.75 - 73.13: 9 73.13 - 97.50: 3 97.50 - 121.87: 3 Dihedral angle restraints: 3158 sinusoidal: 1251 harmonic: 1907 Sorted by residual: dihedral pdb=" CB CYS A 17 " pdb=" SG CYS A 17 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual -86.00 -158.72 72.72 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CA TYR H 74 " pdb=" C TYR H 74 " pdb=" N VAL H 75 " pdb=" CA VAL H 75 " ideal model delta harmonic sigma weight residual -180.00 -151.87 -28.13 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" C12 AJP A 511 " pdb=" C13 AJP A 511 " pdb=" C14 AJP A 511 " pdb=" C15 AJP A 511 " ideal model delta sinusoidal sigma weight residual -53.33 68.54 -121.87 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 3155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.097: 883 1.097 - 2.193: 0 2.193 - 3.290: 0 3.290 - 4.386: 2 4.386 - 5.483: 27 Chirality restraints: 912 Sorted by residual: chirality pdb=" C20 AJP A 511 " pdb=" C15 AJP A 511 " pdb=" C19 AJP A 511 " pdb=" C21 AJP A 511 " both_signs ideal model delta sigma weight residual False 2.96 -2.53 5.48 2.00e-01 2.50e+01 7.52e+02 chirality pdb=" C16 AJP A 511 " pdb=" C11 AJP A 511 " pdb=" C15 AJP A 511 " pdb=" C17 AJP A 511 " both_signs ideal model delta sigma weight residual False -2.70 2.76 -5.46 2.00e-01 2.50e+01 7.47e+02 chirality pdb=" C15 AJP A 511 " pdb=" C14 AJP A 511 " pdb=" C16 AJP A 511 " pdb=" C20 AJP A 511 " both_signs ideal model delta sigma weight residual False -2.42 2.85 -5.27 2.00e-01 2.50e+01 6.95e+02 ... (remaining 909 not shown) Planarity restraints: 898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 376 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C CYS A 376 " -0.056 2.00e-02 2.50e+03 pdb=" O CYS A 376 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO A 377 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 219 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 220 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 375 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C ARG A 375 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG A 375 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 376 " -0.010 2.00e-02 2.50e+03 ... (remaining 895 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1288 2.78 - 3.31: 5100 3.31 - 3.84: 9015 3.84 - 4.37: 10719 4.37 - 4.90: 18577 Nonbonded interactions: 44699 Sorted by model distance: nonbonded pdb=" O62 AJP A 511 " pdb=" O63 AJP A 511 " model vdw 2.248 3.040 nonbonded pdb=" O42 AJP A 511 " pdb=" O43 AJP A 511 " model vdw 2.263 3.040 nonbonded pdb=" NH1 ARG A 183 " pdb=" OE1 GLU A 270 " model vdw 2.306 3.120 nonbonded pdb=" NH1 ARG A 360 " pdb=" O LEU A 372 " model vdw 2.334 3.120 nonbonded pdb=" O SER H 138 " pdb=" OG SER H 138 " model vdw 2.350 3.040 ... (remaining 44694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.540 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 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 : 0.021 0.880 5758 Z= 1.453 Angle : 1.081 26.669 7895 Z= 0.420 Chirality : 0.881 5.483 912 Planarity : 0.005 0.047 898 Dihedral : 13.636 121.875 1931 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -3.02 (0.29), residues: 648 helix: -1.25 (0.26), residues: 324 sheet: -2.18 (0.43), residues: 105 loop : -2.85 (0.35), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 318 TYR 0.013 0.001 TYR A 83 PHE 0.012 0.001 PHE A 167 TRP 0.008 0.001 TRP A 300 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.01752 / 0.87 ( 5750) covalent geometry : angle 1.00065 / 0.41 ( 7886) SS BOND : bond 0.00505 / 0.26 ( 3) SS BOND : angle 2.40252 / 1.31 ( 6) hydrogen bonds : bond 0.11577 / 6.72 ( 289) hydrogen bonds : angle 6.50840 / 4.76 ( 834) metal coordination : bond 0.08087 / 3.87 ( 4) metal coordination : angle 20.72802 / 11.85 ( 3) Misc. bond : bond 0.88006 / 46.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.202 Fit side-chains REVERT: A 191 GLN cc_start: 0.7938 (tt0) cc_final: 0.7545 (mt0) REVERT: A 235 ARG cc_start: 0.6878 (mmt180) cc_final: 0.5742 (mtm-85) REVERT: A 386 LEU cc_start: 0.9003 (pt) cc_final: 0.8725 (mp) REVERT: A 453 ARG cc_start: 0.7685 (ttt90) cc_final: 0.7377 (ttt180) REVERT: L 65 GLN cc_start: 0.7427 (mt0) cc_final: 0.6843 (mm-40) REVERT: L 72 LYS cc_start: 0.9082 (ptpt) cc_final: 0.8712 (ptmm) REVERT: L 81 ARG cc_start: 0.8592 (ptt-90) cc_final: 0.8042 (ptt-90) REVERT: H 38 LYS cc_start: 0.9157 (tttt) cc_final: 0.8893 (tttp) REVERT: H 62 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8261 (mmmm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1025 time to fit residues: 14.5064 Evaluate side-chains 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 24 GLN A 121 HIS A 247 HIS L 111 HIS H 24 GLN H 52 ASN H 78 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087852 restraints weight = 7657.138| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.50 r_work: 0.2915 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5758 Z= 0.132 Angle : 1.134 32.784 7895 Z= 0.424 Chirality : 0.125 2.294 912 Planarity : 0.004 0.045 898 Dihedral : 6.538 53.739 808 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.43 % Allowed : 8.94 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.32), residues: 648 helix: 0.34 (0.29), residues: 331 sheet: -1.94 (0.44), residues: 110 loop : -2.05 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.020 0.001 TYR A 83 PHE 0.011 0.001 PHE A 68 TRP 0.008 0.001 TRP A 120 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 5750) covalent geometry : angle 1.13219 / 0.42 ( 7886) SS BOND : bond 0.00473 / 0.25 ( 3) SS BOND : angle 1.34435 / 0.82 ( 6) hydrogen bonds : bond 0.03093 / 1.99 ( 289) hydrogen bonds : angle 4.47072 / 3.29 ( 834) metal coordination : bond 0.00936 / 0.47 ( 4) metal coordination : angle 3.15082 / 2.07 ( 3) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.189 Fit side-chains REVERT: A 112 MET cc_start: 0.8220 (ptp) cc_final: 0.7848 (ptt) REVERT: A 188 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7121 (mtp85) REVERT: A 191 GLN cc_start: 0.8045 (tt0) cc_final: 0.7684 (mt0) REVERT: A 235 ARG cc_start: 0.7280 (mmt180) cc_final: 0.6647 (ptt-90) REVERT: A 386 LEU cc_start: 0.9016 (pt) cc_final: 0.8604 (mp) REVERT: A 453 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7178 (ttt180) REVERT: L 72 LYS cc_start: 0.9027 (ptpt) cc_final: 0.8588 (ptmm) REVERT: L 81 ARG cc_start: 0.8499 (ptt-90) cc_final: 0.8130 (ptt-90) REVERT: L 98 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7111 (mp) REVERT: H 38 LYS cc_start: 0.9011 (tttt) cc_final: 0.8654 (tttp) REVERT: H 62 LYS cc_start: 0.8531 (mmtm) cc_final: 0.8040 (mmmm) outliers start: 8 outliers final: 3 residues processed: 97 average time/residue: 0.0994 time to fit residues: 12.0842 Evaluate side-chains 94 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 ASN H 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.085757 restraints weight = 7579.919| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.52 r_work: 0.2921 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5758 Z= 0.181 Angle : 1.109 31.958 7895 Z= 0.420 Chirality : 0.123 2.206 912 Planarity : 0.004 0.044 898 Dihedral : 6.535 55.127 808 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.43 % Allowed : 10.55 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.33), residues: 648 helix: 0.96 (0.30), residues: 329 sheet: -1.76 (0.44), residues: 111 loop : -1.67 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 318 TYR 0.019 0.001 TYR A 83 PHE 0.011 0.001 PHE A 167 TRP 0.011 0.001 TRP A 300 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 5750) covalent geometry : angle 1.10817 / 0.42 ( 7886) SS BOND : bond 0.00562 / 0.29 ( 3) SS BOND : angle 1.61521 / 1.00 ( 6) hydrogen bonds : bond 0.03211 / 2.09 ( 289) hydrogen bonds : angle 4.27813 / 3.16 ( 834) metal coordination : bond 0.01169 / 0.59 ( 4) metal coordination : angle 2.36686 / 1.42 ( 3) Misc. bond : bond 0.00107 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.138 Fit side-chains REVERT: A 112 MET cc_start: 0.8345 (ptp) cc_final: 0.7907 (ptt) REVERT: A 188 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7303 (mtp85) REVERT: A 191 GLN cc_start: 0.8189 (tt0) cc_final: 0.7737 (mt0) REVERT: A 235 ARG cc_start: 0.7394 (mmt180) cc_final: 0.6750 (ptt-90) REVERT: A 386 LEU cc_start: 0.9025 (pt) cc_final: 0.8611 (mp) REVERT: A 436 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8494 (mm-30) REVERT: A 453 ARG cc_start: 0.7980 (ttt90) cc_final: 0.7315 (ttp-170) REVERT: L 56 TYR cc_start: 0.9429 (m-80) cc_final: 0.9218 (m-80) REVERT: L 72 LYS cc_start: 0.9048 (ptpt) cc_final: 0.8692 (ptmm) REVERT: L 81 ARG cc_start: 0.8633 (ptt-90) cc_final: 0.8151 (ptt-90) REVERT: H 38 LYS cc_start: 0.9005 (tttt) cc_final: 0.8686 (tttp) REVERT: H 62 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8026 (mmmm) outliers start: 8 outliers final: 2 residues processed: 96 average time/residue: 0.0903 time to fit residues: 10.9038 Evaluate side-chains 94 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain L residue 25 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 52 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.118997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089492 restraints weight = 7595.310| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.58 r_work: 0.2878 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5758 Z= 0.110 Angle : 1.066 31.141 7895 Z= 0.396 Chirality : 0.120 2.152 912 Planarity : 0.004 0.043 898 Dihedral : 6.348 54.786 808 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.72 % Allowed : 12.34 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.34), residues: 648 helix: 1.43 (0.30), residues: 329 sheet: -1.49 (0.46), residues: 110 loop : -1.46 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 117 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 167 TRP 0.008 0.001 TRP A 300 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 5750) covalent geometry : angle 1.06613 / 0.40 ( 7886) SS BOND : bond 0.00591 / 0.31 ( 3) SS BOND : angle 1.19002 / 0.72 ( 6) hydrogen bonds : bond 0.02649 / 1.72 ( 289) hydrogen bonds : angle 3.91535 / 2.89 ( 834) metal coordination : bond 0.00357 / 0.18 ( 4) metal coordination : angle 1.52438 / 0.89 ( 3) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.200 Fit side-chains REVERT: A 112 MET cc_start: 0.8126 (ptp) cc_final: 0.7767 (ptt) REVERT: A 188 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7052 (mtp85) REVERT: A 191 GLN cc_start: 0.7932 (tt0) cc_final: 0.7564 (mt0) REVERT: A 235 ARG cc_start: 0.7232 (mmt180) cc_final: 0.5936 (mtm110) REVERT: A 386 LEU cc_start: 0.9056 (pt) cc_final: 0.8675 (mp) REVERT: A 436 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8023 (tt0) REVERT: A 453 ARG cc_start: 0.7795 (ttt90) cc_final: 0.7199 (ttp-170) REVERT: H 38 LYS cc_start: 0.8906 (tttt) cc_final: 0.8605 (tttp) REVERT: H 62 LYS cc_start: 0.8358 (mmtm) cc_final: 0.7815 (mmmm) REVERT: H 92 ASP cc_start: 0.7019 (t70) cc_final: 0.6787 (t70) REVERT: H 127 TYR cc_start: 0.8769 (m-80) cc_final: 0.8269 (m-80) outliers start: 4 outliers final: 1 residues processed: 97 average time/residue: 0.0946 time to fit residues: 11.5937 Evaluate side-chains 88 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.089780 restraints weight = 7650.120| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.42 r_work: 0.2885 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 0.027 5758 Z= 0.115 Angle : 1.064 31.197 7895 Z= 0.394 Chirality : 0.120 2.145 912 Planarity : 0.004 0.041 898 Dihedral : 6.326 55.070 808 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.25 % Allowed : 12.88 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.23 (0.34), residues: 648 helix: 1.61 (0.30), residues: 329 sheet: -1.38 (0.47), residues: 111 loop : -1.27 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.018 0.001 TYR A 83 PHE 0.009 0.001 PHE A 340 TRP 0.008 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 5750) covalent geometry : angle 1.06406 / 0.39 ( 7886) SS BOND : bond 0.00462 / 0.24 ( 3) SS BOND : angle 1.25294 / 0.76 ( 6) hydrogen bonds : bond 0.02651 / 1.72 ( 289) hydrogen bonds : angle 3.84667 / 2.83 ( 834) metal coordination : bond 0.00412 / 0.21 ( 4) metal coordination : angle 1.49848 / 0.87 ( 3) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.202 Fit side-chains REVERT: A 112 MET cc_start: 0.8179 (ptp) cc_final: 0.7814 (ptt) REVERT: A 132 MET cc_start: 0.8257 (mtp) cc_final: 0.7853 (mtm) REVERT: A 188 ARG cc_start: 0.7621 (mtt180) cc_final: 0.6988 (mmt-90) REVERT: A 191 GLN cc_start: 0.7991 (tt0) cc_final: 0.7623 (mt0) REVERT: A 235 ARG cc_start: 0.7311 (mmt180) cc_final: 0.5976 (mtm110) REVERT: A 436 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8085 (tt0) REVERT: A 453 ARG cc_start: 0.7754 (ttt90) cc_final: 0.7065 (ttp-170) REVERT: H 38 LYS cc_start: 0.8830 (tttt) cc_final: 0.8519 (tttp) REVERT: H 62 LYS cc_start: 0.8369 (mmtm) cc_final: 0.7781 (mmmm) REVERT: H 127 TYR cc_start: 0.8801 (m-80) cc_final: 0.8322 (m-80) outliers start: 7 outliers final: 4 residues processed: 95 average time/residue: 0.0889 time to fit residues: 10.7807 Evaluate side-chains 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain H residue 30 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.117975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.090364 restraints weight = 7535.180| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.41 r_work: 0.2949 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5758 Z= 0.109 Angle : 1.055 31.089 7895 Z= 0.389 Chirality : 0.120 2.134 912 Planarity : 0.004 0.041 898 Dihedral : 6.266 55.227 808 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.25 % Allowed : 14.67 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.51 (0.34), residues: 648 helix: 1.80 (0.30), residues: 330 sheet: -1.19 (0.48), residues: 111 loop : -1.14 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.021 0.001 TYR A 452 PHE 0.009 0.001 PHE A 340 TRP 0.010 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 5750) covalent geometry : angle 1.05457 / 0.39 ( 7886) SS BOND : bond 0.00428 / 0.22 ( 3) SS BOND : angle 1.18124 / 0.72 ( 6) hydrogen bonds : bond 0.02531 / 1.64 ( 289) hydrogen bonds : angle 3.76990 / 2.78 ( 834) metal coordination : bond 0.00327 / 0.16 ( 4) metal coordination : angle 1.39099 / 0.83 ( 3) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 112 MET cc_start: 0.8253 (ptp) cc_final: 0.7907 (ptt) REVERT: A 132 MET cc_start: 0.8306 (mtp) cc_final: 0.8031 (mtp) REVERT: A 188 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7045 (mmt-90) REVERT: A 191 GLN cc_start: 0.8036 (tt0) cc_final: 0.7667 (mt0) REVERT: A 235 ARG cc_start: 0.7324 (mmt180) cc_final: 0.5987 (mtm110) REVERT: A 436 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8133 (tt0) REVERT: A 453 ARG cc_start: 0.7778 (ttt90) cc_final: 0.7114 (ttp-170) REVERT: L 81 ARG cc_start: 0.8466 (ptt-90) cc_final: 0.8178 (ptt-90) REVERT: H 38 LYS cc_start: 0.8886 (tttt) cc_final: 0.8588 (tttp) REVERT: H 62 LYS cc_start: 0.8422 (mmtm) cc_final: 0.7825 (mmmm) REVERT: H 127 TYR cc_start: 0.8854 (m-80) cc_final: 0.8327 (m-80) outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 0.0775 time to fit residues: 9.2218 Evaluate side-chains 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 0.0170 chunk 2 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.119809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.090420 restraints weight = 7692.521| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.58 r_work: 0.2895 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5758 Z= 0.107 Angle : 1.052 31.164 7895 Z= 0.388 Chirality : 0.120 2.128 912 Planarity : 0.004 0.040 898 Dihedral : 6.236 56.190 808 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.43 % Allowed : 15.21 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.71 (0.35), residues: 648 helix: 1.95 (0.30), residues: 330 sheet: -1.07 (0.49), residues: 111 loop : -1.03 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 81 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 340 TRP 0.010 0.001 TRP A 120 HIS 0.003 0.000 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 5750) covalent geometry : angle 1.05207 / 0.39 ( 7886) SS BOND : bond 0.00325 / 0.17 ( 3) SS BOND : angle 1.13581 / 0.72 ( 6) hydrogen bonds : bond 0.02507 / 1.63 ( 289) hydrogen bonds : angle 3.71491 / 2.73 ( 834) metal coordination : bond 0.00318 / 0.16 ( 4) metal coordination : angle 1.31748 / 0.78 ( 3) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.193 Fit side-chains REVERT: A 112 MET cc_start: 0.8137 (ptp) cc_final: 0.7797 (ptt) REVERT: A 132 MET cc_start: 0.7997 (mtp) cc_final: 0.7725 (mtp) REVERT: A 191 GLN cc_start: 0.7904 (tt0) cc_final: 0.7552 (mt0) REVERT: A 235 ARG cc_start: 0.7190 (mmt180) cc_final: 0.5832 (mtm110) REVERT: A 427 MET cc_start: 0.7293 (ttp) cc_final: 0.6962 (tmm) REVERT: A 436 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8048 (tt0) REVERT: A 452 TYR cc_start: 0.8275 (t80) cc_final: 0.8015 (t80) REVERT: A 453 ARG cc_start: 0.7645 (ttt90) cc_final: 0.6987 (ttp-170) REVERT: L 81 ARG cc_start: 0.8420 (ptt-90) cc_final: 0.8160 (ptt-90) REVERT: L 98 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7121 (mp) REVERT: H 38 LYS cc_start: 0.8821 (tttt) cc_final: 0.8522 (tttp) REVERT: H 62 LYS cc_start: 0.8390 (mmtm) cc_final: 0.7777 (mmmm) REVERT: H 127 TYR cc_start: 0.8766 (m-80) cc_final: 0.8224 (m-80) outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.0900 time to fit residues: 10.6961 Evaluate side-chains 91 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 37 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.118561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.091413 restraints weight = 7451.350| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.38 r_work: 0.2911 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5758 Z= 0.104 Angle : 1.049 31.194 7895 Z= 0.387 Chirality : 0.120 2.126 912 Planarity : 0.004 0.039 898 Dihedral : 6.209 57.369 808 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.25 % Allowed : 15.21 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.81 (0.35), residues: 648 helix: 2.00 (0.30), residues: 332 sheet: -0.90 (0.50), residues: 111 loop : -1.03 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 81 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 340 TRP 0.010 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 5750) covalent geometry : angle 1.04928 / 0.39 ( 7886) SS BOND : bond 0.00238 / 0.12 ( 3) SS BOND : angle 1.16738 / 0.74 ( 6) hydrogen bonds : bond 0.02477 / 1.61 ( 289) hydrogen bonds : angle 3.68232 / 2.71 ( 834) metal coordination : bond 0.00279 / 0.14 ( 4) metal coordination : angle 1.28093 / 0.77 ( 3) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.221 Fit side-chains REVERT: A 112 MET cc_start: 0.8181 (ptp) cc_final: 0.7846 (ptt) REVERT: A 128 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8018 (ttp) REVERT: A 132 MET cc_start: 0.8150 (mtp) cc_final: 0.7757 (mtm) REVERT: A 191 GLN cc_start: 0.7956 (tt0) cc_final: 0.7595 (mt0) REVERT: A 235 ARG cc_start: 0.7266 (mmt180) cc_final: 0.5832 (mtm110) REVERT: A 375 ARG cc_start: 0.5616 (mmt180) cc_final: 0.5368 (mmt180) REVERT: A 427 MET cc_start: 0.7322 (ttp) cc_final: 0.7009 (tmm) REVERT: A 436 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8080 (tt0) REVERT: A 452 TYR cc_start: 0.8418 (t80) cc_final: 0.8163 (t80) REVERT: A 453 ARG cc_start: 0.7656 (ttt90) cc_final: 0.6952 (ttp-170) REVERT: L 81 ARG cc_start: 0.8343 (ptt-90) cc_final: 0.8134 (ptt-90) REVERT: L 98 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7056 (mp) REVERT: H 38 LYS cc_start: 0.8795 (tttt) cc_final: 0.8488 (tttp) REVERT: H 62 LYS cc_start: 0.8362 (mmtm) cc_final: 0.7739 (mmmm) REVERT: H 127 TYR cc_start: 0.8787 (m-80) cc_final: 0.8252 (m-80) outliers start: 7 outliers final: 4 residues processed: 95 average time/residue: 0.0992 time to fit residues: 11.9068 Evaluate side-chains 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 chunk 49 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 2 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092563 restraints weight = 7521.998| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.43 r_work: 0.2935 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5758 Z= 0.091 Angle : 1.044 31.111 7895 Z= 0.384 Chirality : 0.119 2.117 912 Planarity : 0.004 0.038 898 Dihedral : 6.169 58.912 808 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.25 % Allowed : 15.56 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.35), residues: 648 helix: 2.14 (0.30), residues: 331 sheet: -0.51 (0.54), residues: 101 loop : -1.11 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 340 TRP 0.018 0.001 TRP A 120 HIS 0.003 0.000 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 5750) covalent geometry : angle 1.04351 / 0.38 ( 7886) SS BOND : bond 0.00250 / 0.13 ( 3) SS BOND : angle 1.02344 / 0.65 ( 6) hydrogen bonds : bond 0.02370 / 1.53 ( 289) hydrogen bonds : angle 3.61232 / 2.64 ( 834) metal coordination : bond 0.00250 / 0.12 ( 4) metal coordination : angle 1.31981 / 0.80 ( 3) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.200 Fit side-chains REVERT: A 112 MET cc_start: 0.8166 (ptp) cc_final: 0.7824 (ptt) REVERT: A 132 MET cc_start: 0.8039 (mtp) cc_final: 0.7727 (mtm) REVERT: A 191 GLN cc_start: 0.7927 (tt0) cc_final: 0.7544 (mt0) REVERT: A 235 ARG cc_start: 0.7269 (mmt180) cc_final: 0.5823 (mtm110) REVERT: A 427 MET cc_start: 0.7314 (ttp) cc_final: 0.7016 (tmm) REVERT: A 436 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8074 (tt0) REVERT: A 452 TYR cc_start: 0.8408 (t80) cc_final: 0.8163 (t80) REVERT: A 453 ARG cc_start: 0.7609 (ttt90) cc_final: 0.6882 (ttp-170) REVERT: L 98 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7031 (mp) REVERT: H 38 LYS cc_start: 0.8779 (tttt) cc_final: 0.8485 (tttp) REVERT: H 62 LYS cc_start: 0.8343 (mmtm) cc_final: 0.7711 (mmmm) REVERT: H 127 TYR cc_start: 0.8759 (m-80) cc_final: 0.8166 (m-80) outliers start: 7 outliers final: 4 residues processed: 96 average time/residue: 0.0874 time to fit residues: 10.8319 Evaluate side-chains 94 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.119300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.090073 restraints weight = 7689.733| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.60 r_work: 0.2883 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5758 Z= 0.118 Angle : 1.055 31.398 7895 Z= 0.391 Chirality : 0.120 2.133 912 Planarity : 0.004 0.039 898 Dihedral : 6.202 58.902 808 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.89 % Allowed : 15.92 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.96 (0.35), residues: 648 helix: 2.11 (0.29), residues: 331 sheet: -0.75 (0.51), residues: 111 loop : -0.98 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.018 0.001 TYR A 83 PHE 0.009 0.001 PHE A 167 TRP 0.017 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 5750) covalent geometry : angle 1.05459 / 0.39 ( 7886) SS BOND : bond 0.00354 / 0.18 ( 3) SS BOND : angle 1.27191 / 0.86 ( 6) hydrogen bonds : bond 0.02596 / 1.69 ( 289) hydrogen bonds : angle 3.68066 / 2.70 ( 834) metal coordination : bond 0.00360 / 0.18 ( 4) metal coordination : angle 1.56999 / 1.01 ( 3) Misc. bond : bond 0.00009 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.199 Fit side-chains REVERT: A 112 MET cc_start: 0.8184 (ptp) cc_final: 0.7838 (ptt) REVERT: A 191 GLN cc_start: 0.7900 (tt0) cc_final: 0.7527 (mt0) REVERT: A 235 ARG cc_start: 0.7195 (mmt180) cc_final: 0.5798 (mtm110) REVERT: A 375 ARG cc_start: 0.5673 (mmt180) cc_final: 0.5209 (mmt90) REVERT: A 427 MET cc_start: 0.7326 (ttp) cc_final: 0.7034 (tmm) REVERT: A 436 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8037 (tt0) REVERT: A 453 ARG cc_start: 0.7572 (ttt90) cc_final: 0.6947 (ttp-170) REVERT: L 98 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7116 (mp) REVERT: H 38 LYS cc_start: 0.8824 (tttt) cc_final: 0.8529 (tttp) REVERT: H 62 LYS cc_start: 0.8389 (mmtm) cc_final: 0.7771 (mmmm) REVERT: H 127 TYR cc_start: 0.8775 (m-80) cc_final: 0.8236 (m-80) outliers start: 5 outliers final: 4 residues processed: 93 average time/residue: 0.0894 time to fit residues: 10.6825 Evaluate side-chains 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.120442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.091153 restraints weight = 7607.923| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.61 r_work: 0.2905 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5758 Z= 0.103 Angle : 1.048 31.215 7895 Z= 0.387 Chirality : 0.120 2.129 912 Planarity : 0.004 0.039 898 Dihedral : 6.174 59.971 808 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.07 % Allowed : 16.10 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.35), residues: 648 helix: 2.15 (0.29), residues: 331 sheet: -0.74 (0.51), residues: 111 loop : -0.97 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 340 TRP 0.018 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 5750) covalent geometry : angle 1.04726 / 0.39 ( 7886) SS BOND : bond 0.00310 / 0.16 ( 3) SS BOND : angle 1.13735 / 0.79 ( 6) hydrogen bonds : bond 0.02477 / 1.61 ( 289) hydrogen bonds : angle 3.65400 / 2.68 ( 834) metal coordination : bond 0.00302 / 0.15 ( 4) metal coordination : angle 1.43080 / 0.88 ( 3) Misc. bond : bond 0.00009 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1594.86 seconds wall clock time: 28 minutes 6.98 seconds (1686.98 seconds total)