Starting phenix.real_space_refine on Fri Aug 22 18:07:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z74_39810/08_2025/8z74_39810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z74_39810/08_2025/8z74_39810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z74_39810/08_2025/8z74_39810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z74_39810/08_2025/8z74_39810.map" model { file = "/net/cci-nas-00/data/ceres_data/8z74_39810/08_2025/8z74_39810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z74_39810/08_2025/8z74_39810.cif" } resolution = 3.01 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= 0.001 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 4372 2.51 5 N 1104 2.21 5 O 1177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6709 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 971 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 971 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "C" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2366 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain: "D" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2345 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.88, per 1000 atoms: 0.28 Number of scatterers: 6709 At special positions: 0 Unit cell: (105.04, 57.2, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1177 8.00 N 1104 7.00 C 4372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 110 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 33 " - pdb=" SG CYS B 110 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS D 102 " - pdb=" SG CYS D 181 " 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: 0.66 Conformation dependent library (CDL) restraints added in 383.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 7 sheets defined 64.8% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'C' and resid 29 through 56 removed outlier: 3.779A pdb=" N SER C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 91 removed outlier: 4.066A pdb=" N ILE C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) Proline residue: C 83 - end of helix Processing helix chain 'C' and resid 98 through 133 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'C' and resid 145 through 167 Proline residue: C 163 - end of helix Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.979A pdb=" N THR C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 211 removed outlier: 4.218A pdb=" N TRP C 195 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 233 Processing helix chain 'C' and resid 236 through 261 Processing helix chain 'C' and resid 261 through 278 removed outlier: 4.135A pdb=" N SER C 275 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 276 " --> pdb=" O MET C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 313 Proline residue: C 292 - end of helix removed outlier: 4.405A pdb=" N SER C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N CYS C 303 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Proline residue: C 306 - end of helix Processing helix chain 'C' and resid 313 through 319 Processing helix chain 'D' and resid 29 through 56 removed outlier: 3.764A pdb=" N SER D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 80 Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 98 through 133 Processing helix chain 'D' and resid 133 through 144 Processing helix chain 'D' and resid 145 through 167 Proline residue: D 163 - end of helix Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.881A pdb=" N THR D 176 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 210 removed outlier: 4.265A pdb=" N TRP D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA D 196 " --> pdb=" O SER D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 233 removed outlier: 4.088A pdb=" N HIS D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 246 removed outlier: 3.621A pdb=" N ARG D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 278 Proline residue: D 263 - end of helix removed outlier: 4.049A pdb=" N SER D 275 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU D 276 " --> pdb=" O MET D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 313 Proline residue: D 292 - end of helix removed outlier: 4.392A pdb=" N SER D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS D 303 " --> pdb=" O TYR D 299 " (cutoff:3.500A) Proline residue: D 306 - end of helix Processing helix chain 'D' and resid 313 through 319 removed outlier: 3.617A pdb=" N ARG D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.848A pdb=" N VAL A 12 " --> pdb=" O SER A 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 23 removed outlier: 3.948A pdb=" N LEU A 18 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 removed outlier: 5.027A pdb=" N GLY A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG A 38 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 124 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 7 removed outlier: 5.316A pdb=" N GLY B 16 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 49 removed outlier: 4.247A pdb=" N GLY B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG B 38 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 98 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 171 Processing sheet with id=AA7, first strand: chain 'D' and resid 168 through 171 440 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2044 1.34 - 1.46: 1821 1.46 - 1.58: 2934 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 6885 Sorted by residual: bond pdb=" C VAL A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.19e-02 7.06e+03 6.24e+00 bond pdb=" CA ILE C 31 " pdb=" CB ILE C 31 " ideal model delta sigma weight residual 1.534 1.546 -0.012 6.80e-03 2.16e+04 2.90e+00 bond pdb=" CA ILE C 31 " pdb=" C ILE C 31 " ideal model delta sigma weight residual 1.520 1.532 -0.012 8.80e-03 1.29e+04 1.82e+00 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.39e+00 bond pdb=" C PRO A 99 " pdb=" O PRO A 99 " ideal model delta sigma weight residual 1.233 1.248 -0.014 1.39e-02 5.18e+03 1.06e+00 ... (remaining 6880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 9332 3.71 - 7.42: 31 7.42 - 11.12: 5 11.12 - 14.83: 0 14.83 - 18.54: 1 Bond angle restraints: 9369 Sorted by residual: angle pdb=" CA LEU D 218 " pdb=" CB LEU D 218 " pdb=" CG LEU D 218 " ideal model delta sigma weight residual 116.30 134.84 -18.54 3.50e+00 8.16e-02 2.81e+01 angle pdb=" CA LEU D 276 " pdb=" CB LEU D 276 " pdb=" CG LEU D 276 " ideal model delta sigma weight residual 116.30 126.69 -10.39 3.50e+00 8.16e-02 8.81e+00 angle pdb=" N LEU D 218 " pdb=" CA LEU D 218 " pdb=" CB LEU D 218 " ideal model delta sigma weight residual 110.28 114.87 -4.59 1.55e+00 4.16e-01 8.76e+00 angle pdb=" C PHE C 210 " pdb=" N VAL C 211 " pdb=" CA VAL C 211 " ideal model delta sigma weight residual 122.97 120.25 2.72 9.80e-01 1.04e+00 7.71e+00 angle pdb=" CB GLN B 39 " pdb=" CG GLN B 39 " pdb=" CD GLN B 39 " ideal model delta sigma weight residual 112.60 117.09 -4.49 1.70e+00 3.46e-01 6.98e+00 ... (remaining 9364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.60: 3496 13.60 - 27.19: 366 27.19 - 40.78: 171 40.78 - 54.38: 57 54.38 - 67.97: 17 Dihedral angle restraints: 4107 sinusoidal: 1646 harmonic: 2461 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 51.92 41.08 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 95 " pdb=" CB CYS A 95 " ideal model delta sinusoidal sigma weight residual 93.00 57.77 35.23 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CG ARG B 55 " pdb=" CD ARG B 55 " pdb=" NE ARG B 55 " pdb=" CZ ARG B 55 " ideal model delta sinusoidal sigma weight residual 180.00 -137.36 -42.64 2 1.50e+01 4.44e-03 9.79e+00 ... (remaining 4104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 690 0.030 - 0.061: 250 0.061 - 0.091: 78 0.091 - 0.122: 48 0.122 - 0.152: 3 Chirality restraints: 1069 Sorted by residual: chirality pdb=" CA VAL A 63 " pdb=" N VAL A 63 " pdb=" C VAL A 63 " pdb=" CB VAL A 63 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA PRO A 99 " pdb=" N PRO A 99 " pdb=" C PRO A 99 " pdb=" CB PRO A 99 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA VAL D 179 " pdb=" N VAL D 179 " pdb=" C VAL D 179 " pdb=" CB VAL D 179 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1066 not shown) Planarity restraints: 1139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 114 " -0.010 2.00e-02 2.50e+03 1.34e-02 3.60e+00 pdb=" CG TYR D 114 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR D 114 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR D 114 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR D 114 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 114 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 114 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 114 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 207 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C THR C 207 " 0.028 2.00e-02 2.50e+03 pdb=" O THR C 207 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL C 208 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 286 " 0.008 2.00e-02 2.50e+03 1.09e-02 2.08e+00 pdb=" CG PHE C 286 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 286 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 286 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 286 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 286 " -0.000 2.00e-02 2.50e+03 ... (remaining 1136 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1332 2.77 - 3.30: 6697 3.30 - 3.83: 12031 3.83 - 4.37: 13733 4.37 - 4.90: 23561 Nonbonded interactions: 57354 Sorted by model distance: nonbonded pdb=" OG SER A 54 " pdb=" OH TYR A 109 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 14 " pdb=" O SER A 129 " model vdw 2.278 3.040 nonbonded pdb=" NH1 ARG D 168 " pdb=" O CYS D 181 " model vdw 2.286 3.120 nonbonded pdb=" OE1 GLN A 125 " pdb=" OG1 THR A 127 " model vdw 2.298 3.040 nonbonded pdb=" OG SER B 14 " pdb=" O SER B 129 " model vdw 2.321 3.040 ... (remaining 57349 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 28 through 319) selection = (chain 'D' and resid 28 through 319) } 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: 1.100 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.590 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 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 : 0.003 0.059 6891 Z= 0.159 Angle : 0.631 18.538 9381 Z= 0.320 Chirality : 0.040 0.152 1069 Planarity : 0.004 0.036 1139 Dihedral : 14.940 67.974 2515 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 21.56 % Favored : 78.44 % 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 aren not related in a simple way. whole: 0.52 (0.29), residues: 839 helix: 1.39 (0.23), residues: 468 sheet: -0.06 (0.63), residues: 80 loop : -1.27 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 61 TYR 0.033 0.002 TYR D 114 PHE 0.025 0.001 PHE C 286 TRP 0.014 0.001 TRP D 195 HIS 0.003 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6885) covalent geometry : angle 0.62952 ( 9369) SS BOND : bond 0.00413 ( 6) SS BOND : angle 1.42272 ( 12) hydrogen bonds : bond 0.14463 ( 440) hydrogen bonds : angle 6.65411 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.247 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0833 time to fit residues: 15.5055 Evaluate side-chains 137 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 76 ASN B 76 ASN C 46 ASN D 46 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.172593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.151106 restraints weight = 9413.051| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.13 r_work: 0.3747 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6891 Z= 0.183 Angle : 0.577 8.763 9381 Z= 0.301 Chirality : 0.041 0.149 1069 Planarity : 0.004 0.032 1139 Dihedral : 4.799 36.927 1067 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.36 % Allowed : 17.39 % Favored : 80.25 % 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 aren not related in a simple way. whole: 0.51 (0.30), residues: 839 helix: 1.38 (0.23), residues: 477 sheet: -0.30 (0.61), residues: 94 loop : -1.28 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 61 TYR 0.027 0.002 TYR D 114 PHE 0.018 0.001 PHE C 214 TRP 0.008 0.001 TRP B 120 HIS 0.003 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6885) covalent geometry : angle 0.57531 ( 9369) SS BOND : bond 0.00523 ( 6) SS BOND : angle 1.46101 ( 12) hydrogen bonds : bond 0.05047 ( 440) hydrogen bonds : angle 5.46540 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8408 (mmm) cc_final: 0.8155 (mmt) REVERT: C 204 SER cc_start: 0.8458 (m) cc_final: 0.8232 (p) outliers start: 17 outliers final: 7 residues processed: 151 average time/residue: 0.0866 time to fit residues: 17.6434 Evaluate side-chains 149 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 304 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.171415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.149754 restraints weight = 9318.071| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.13 r_work: 0.3730 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6891 Z= 0.207 Angle : 0.584 9.224 9381 Z= 0.302 Chirality : 0.041 0.131 1069 Planarity : 0.004 0.033 1139 Dihedral : 4.880 35.147 1067 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.06 % Allowed : 17.39 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.29), residues: 839 helix: 1.20 (0.22), residues: 484 sheet: -0.65 (0.59), residues: 94 loop : -1.29 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 61 TYR 0.031 0.002 TYR D 114 PHE 0.018 0.001 PHE C 214 TRP 0.008 0.001 TRP B 120 HIS 0.004 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 6885) covalent geometry : angle 0.58127 ( 9369) SS BOND : bond 0.00490 ( 6) SS BOND : angle 1.65806 ( 12) hydrogen bonds : bond 0.04969 ( 440) hydrogen bonds : angle 5.34030 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8438 (mmm) cc_final: 0.8200 (mmt) REVERT: C 34 ILE cc_start: 0.7392 (mt) cc_final: 0.7106 (tp) REVERT: C 204 SER cc_start: 0.8462 (m) cc_final: 0.8199 (p) REVERT: C 308 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7417 (mt) REVERT: D 277 LEU cc_start: 0.7986 (mm) cc_final: 0.7743 (mm) outliers start: 22 outliers final: 10 residues processed: 148 average time/residue: 0.0836 time to fit residues: 16.6664 Evaluate side-chains 146 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 195 TRP Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 244 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 56 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 83 optimal weight: 0.0570 chunk 82 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.173122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150965 restraints weight = 9443.270| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.26 r_work: 0.3732 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6891 Z= 0.150 Angle : 0.554 7.977 9381 Z= 0.284 Chirality : 0.039 0.125 1069 Planarity : 0.004 0.035 1139 Dihedral : 4.590 32.591 1067 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.34 % Allowed : 17.39 % Favored : 79.28 % 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 aren not related in a simple way. whole: 0.42 (0.30), residues: 839 helix: 1.33 (0.23), residues: 483 sheet: -0.78 (0.58), residues: 94 loop : -1.24 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 61 TYR 0.031 0.002 TYR D 114 PHE 0.015 0.001 PHE C 214 TRP 0.007 0.001 TRP D 279 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6885) covalent geometry : angle 0.55203 ( 9369) SS BOND : bond 0.00460 ( 6) SS BOND : angle 1.45109 ( 12) hydrogen bonds : bond 0.04640 ( 440) hydrogen bonds : angle 5.16720 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8401 (mmm) cc_final: 0.7880 (mmt) REVERT: C 204 SER cc_start: 0.8351 (m) cc_final: 0.8055 (p) REVERT: D 88 TYR cc_start: 0.8532 (t80) cc_final: 0.8284 (t80) REVERT: D 133 ARG cc_start: 0.6409 (mtm180) cc_final: 0.6116 (mtm180) REVERT: D 162 MET cc_start: 0.8260 (tpp) cc_final: 0.7908 (tpp) outliers start: 24 outliers final: 15 residues processed: 156 average time/residue: 0.0814 time to fit residues: 17.2893 Evaluate side-chains 156 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 195 TRP Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 304 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 57 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.173603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151562 restraints weight = 9483.503| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.26 r_work: 0.3735 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6891 Z= 0.141 Angle : 0.555 11.835 9381 Z= 0.280 Chirality : 0.039 0.148 1069 Planarity : 0.004 0.036 1139 Dihedral : 4.563 32.476 1067 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.48 % Allowed : 18.36 % Favored : 78.16 % 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 aren not related in a simple way. whole: 0.54 (0.30), residues: 839 helix: 1.42 (0.23), residues: 483 sheet: -0.68 (0.58), residues: 97 loop : -1.21 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 61 TYR 0.031 0.002 TYR D 114 PHE 0.014 0.001 PHE C 214 TRP 0.007 0.001 TRP D 279 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6885) covalent geometry : angle 0.55284 ( 9369) SS BOND : bond 0.00415 ( 6) SS BOND : angle 1.44512 ( 12) hydrogen bonds : bond 0.04545 ( 440) hydrogen bonds : angle 5.08560 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 TYR cc_start: 0.8348 (m-80) cc_final: 0.7926 (m-80) REVERT: C 204 SER cc_start: 0.8276 (m) cc_final: 0.7961 (p) REVERT: C 308 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7235 (mt) REVERT: D 88 TYR cc_start: 0.8482 (t80) cc_final: 0.8239 (t80) REVERT: D 133 ARG cc_start: 0.6239 (mtm180) cc_final: 0.5978 (mtm180) REVERT: D 162 MET cc_start: 0.8014 (tpp) cc_final: 0.7634 (tpp) outliers start: 25 outliers final: 17 residues processed: 155 average time/residue: 0.0808 time to fit residues: 17.0075 Evaluate side-chains 158 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 195 TRP Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 304 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.171871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147940 restraints weight = 9277.466| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.37 r_work: 0.3710 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6891 Z= 0.209 Angle : 0.612 14.267 9381 Z= 0.307 Chirality : 0.041 0.139 1069 Planarity : 0.004 0.039 1139 Dihedral : 4.829 32.538 1067 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.20 % Allowed : 19.33 % Favored : 77.47 % 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 aren not related in a simple way. whole: 0.38 (0.30), residues: 839 helix: 1.29 (0.23), residues: 484 sheet: -0.88 (0.58), residues: 94 loop : -1.20 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 61 TYR 0.033 0.002 TYR D 114 PHE 0.020 0.001 PHE C 286 TRP 0.011 0.001 TRP A 120 HIS 0.002 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 6885) covalent geometry : angle 0.60881 ( 9369) SS BOND : bond 0.00612 ( 6) SS BOND : angle 1.78376 ( 12) hydrogen bonds : bond 0.04801 ( 440) hydrogen bonds : angle 5.20603 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: B 92 MET cc_start: 0.4289 (OUTLIER) cc_final: 0.3859 (tpp) REVERT: C 308 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7524 (mt) REVERT: D 90 TYR cc_start: 0.8162 (t80) cc_final: 0.7942 (t80) REVERT: D 133 ARG cc_start: 0.6443 (mtm180) cc_final: 0.6170 (mtm180) REVERT: D 162 MET cc_start: 0.8324 (tpp) cc_final: 0.7930 (tpp) outliers start: 23 outliers final: 16 residues processed: 161 average time/residue: 0.0767 time to fit residues: 17.0276 Evaluate side-chains 158 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 195 TRP Chi-restraints excluded: chain D residue 262 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS B 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.173018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151568 restraints weight = 9356.132| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.13 r_work: 0.3743 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6891 Z= 0.150 Angle : 0.586 16.882 9381 Z= 0.291 Chirality : 0.039 0.127 1069 Planarity : 0.004 0.040 1139 Dihedral : 4.558 30.623 1067 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.62 % Allowed : 20.45 % Favored : 75.94 % 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 aren not related in a simple way. whole: 0.49 (0.30), residues: 839 helix: 1.42 (0.23), residues: 483 sheet: -0.86 (0.58), residues: 94 loop : -1.23 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 61 TYR 0.031 0.002 TYR D 114 PHE 0.016 0.001 PHE C 214 TRP 0.007 0.001 TRP A 120 HIS 0.001 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6885) covalent geometry : angle 0.58413 ( 9369) SS BOND : bond 0.00404 ( 6) SS BOND : angle 1.49266 ( 12) hydrogen bonds : bond 0.04562 ( 440) hydrogen bonds : angle 5.11632 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8403 (mmm) cc_final: 0.8139 (mmt) REVERT: B 92 MET cc_start: 0.4150 (OUTLIER) cc_final: 0.3713 (tpp) REVERT: C 249 ILE cc_start: 0.7539 (tp) cc_final: 0.7158 (tt) REVERT: C 308 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7466 (mt) REVERT: D 88 TYR cc_start: 0.8585 (t80) cc_final: 0.8347 (t80) REVERT: D 90 TYR cc_start: 0.8148 (t80) cc_final: 0.7927 (t80) REVERT: D 107 TYR cc_start: 0.8446 (t80) cc_final: 0.7890 (t80) REVERT: D 133 ARG cc_start: 0.6396 (mtm180) cc_final: 0.6125 (mtm180) REVERT: D 162 MET cc_start: 0.8192 (tpp) cc_final: 0.7748 (tpp) REVERT: D 277 LEU cc_start: 0.7953 (mm) cc_final: 0.7725 (mm) outliers start: 26 outliers final: 18 residues processed: 165 average time/residue: 0.0802 time to fit residues: 18.0001 Evaluate side-chains 169 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 195 TRP Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 262 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 0.0970 chunk 60 optimal weight: 0.0000 chunk 67 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 63 optimal weight: 0.2980 chunk 82 optimal weight: 0.1980 overall best weight: 0.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS B 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.176240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.154726 restraints weight = 9572.927| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.16 r_work: 0.3781 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6891 Z= 0.114 Angle : 0.568 18.254 9381 Z= 0.279 Chirality : 0.037 0.125 1069 Planarity : 0.004 0.040 1139 Dihedral : 4.305 29.057 1067 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.36 % Allowed : 21.84 % Favored : 75.80 % 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 aren not related in a simple way. whole: 0.73 (0.30), residues: 839 helix: 1.63 (0.23), residues: 483 sheet: -0.52 (0.61), residues: 87 loop : -1.27 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 61 TYR 0.029 0.001 TYR D 114 PHE 0.010 0.001 PHE A 37 TRP 0.010 0.001 TRP D 279 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 6885) covalent geometry : angle 0.56738 ( 9369) SS BOND : bond 0.00407 ( 6) SS BOND : angle 1.11062 ( 12) hydrogen bonds : bond 0.04258 ( 440) hydrogen bonds : angle 4.91007 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.8257 (mmm) cc_final: 0.8039 (mmt) REVERT: A 82 MET cc_start: 0.5671 (OUTLIER) cc_final: 0.5413 (ppp) REVERT: A 109 TYR cc_start: 0.7721 (m-80) cc_final: 0.7208 (m-80) REVERT: B 92 MET cc_start: 0.3988 (OUTLIER) cc_final: 0.3506 (tpp) REVERT: C 93 TYR cc_start: 0.8322 (m-80) cc_final: 0.7782 (m-80) REVERT: C 114 TYR cc_start: 0.7859 (m-80) cc_final: 0.7615 (m-80) REVERT: C 162 MET cc_start: 0.8025 (tpp) cc_final: 0.7804 (tpp) REVERT: C 197 TRP cc_start: 0.8092 (OUTLIER) cc_final: 0.7465 (m-90) REVERT: C 198 GLU cc_start: 0.7573 (tt0) cc_final: 0.7326 (tt0) REVERT: C 249 ILE cc_start: 0.7423 (tp) cc_final: 0.7081 (tt) REVERT: D 82 LEU cc_start: 0.8017 (mt) cc_final: 0.7799 (mt) REVERT: D 88 TYR cc_start: 0.8502 (t80) cc_final: 0.8219 (t80) REVERT: D 107 TYR cc_start: 0.8443 (t80) cc_final: 0.7967 (t80) REVERT: D 133 ARG cc_start: 0.6251 (mtm180) cc_final: 0.6013 (mtm180) REVERT: D 162 MET cc_start: 0.8122 (tpp) cc_final: 0.7724 (tpp) REVERT: D 198 GLU cc_start: 0.7584 (tt0) cc_final: 0.7371 (tt0) outliers start: 17 outliers final: 9 residues processed: 159 average time/residue: 0.0765 time to fit residues: 16.7489 Evaluate side-chains 158 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 262 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS B 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.172610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148570 restraints weight = 9324.678| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.39 r_work: 0.3717 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6891 Z= 0.216 Angle : 0.655 19.988 9381 Z= 0.325 Chirality : 0.042 0.145 1069 Planarity : 0.004 0.042 1139 Dihedral : 4.809 33.033 1067 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.23 % Allowed : 22.95 % Favored : 74.83 % 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 aren not related in a simple way. whole: 0.50 (0.30), residues: 839 helix: 1.41 (0.23), residues: 484 sheet: -0.76 (0.58), residues: 97 loop : -1.25 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 61 TYR 0.035 0.002 TYR D 114 PHE 0.019 0.001 PHE C 214 TRP 0.010 0.001 TRP D 195 HIS 0.010 0.002 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 6885) covalent geometry : angle 0.65185 ( 9369) SS BOND : bond 0.00581 ( 6) SS BOND : angle 1.93442 ( 12) hydrogen bonds : bond 0.04647 ( 440) hydrogen bonds : angle 5.09280 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5517 (OUTLIER) cc_final: 0.5283 (ppp) REVERT: B 92 MET cc_start: 0.3948 (tpp) cc_final: 0.3543 (tpp) REVERT: D 88 TYR cc_start: 0.8491 (t80) cc_final: 0.8253 (t80) REVERT: D 133 ARG cc_start: 0.6071 (mtm180) cc_final: 0.5842 (mtm180) REVERT: D 162 MET cc_start: 0.7958 (tpp) cc_final: 0.7545 (tpp) REVERT: D 277 LEU cc_start: 0.7846 (mm) cc_final: 0.7635 (mm) outliers start: 16 outliers final: 12 residues processed: 154 average time/residue: 0.0809 time to fit residues: 16.8909 Evaluate side-chains 162 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 195 TRP Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 262 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 65 optimal weight: 0.2980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.174370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152770 restraints weight = 9413.293| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.17 r_work: 0.3753 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6891 Z= 0.135 Angle : 0.616 19.797 9381 Z= 0.302 Chirality : 0.039 0.128 1069 Planarity : 0.004 0.041 1139 Dihedral : 4.451 29.717 1067 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.67 % Allowed : 23.92 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.30), residues: 839 helix: 1.51 (0.23), residues: 483 sheet: -0.76 (0.59), residues: 97 loop : -1.24 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 61 TYR 0.032 0.002 TYR D 114 PHE 0.014 0.001 PHE C 214 TRP 0.008 0.001 TRP D 279 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6885) covalent geometry : angle 0.61499 ( 9369) SS BOND : bond 0.00375 ( 6) SS BOND : angle 1.34010 ( 12) hydrogen bonds : bond 0.04390 ( 440) hydrogen bonds : angle 5.00235 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5792 (OUTLIER) cc_final: 0.5528 (ppp) REVERT: B 92 MET cc_start: 0.4092 (tpp) cc_final: 0.3640 (tpp) REVERT: C 114 TYR cc_start: 0.7857 (m-80) cc_final: 0.7585 (m-80) REVERT: C 197 TRP cc_start: 0.8161 (OUTLIER) cc_final: 0.7544 (m-90) REVERT: D 88 TYR cc_start: 0.8528 (t80) cc_final: 0.8282 (t80) REVERT: D 107 TYR cc_start: 0.8429 (t80) cc_final: 0.7903 (t80) REVERT: D 133 ARG cc_start: 0.6223 (mtm180) cc_final: 0.5980 (mtm180) REVERT: D 162 MET cc_start: 0.8149 (tpp) cc_final: 0.7714 (tpp) REVERT: D 277 LEU cc_start: 0.7888 (mm) cc_final: 0.7671 (mm) outliers start: 12 outliers final: 10 residues processed: 156 average time/residue: 0.0821 time to fit residues: 17.2819 Evaluate side-chains 160 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 262 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 39 GLN B 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.172862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149021 restraints weight = 9289.815| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.37 r_work: 0.3721 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6891 Z= 0.188 Angle : 0.650 20.344 9381 Z= 0.321 Chirality : 0.041 0.140 1069 Planarity : 0.004 0.043 1139 Dihedral : 4.705 31.136 1067 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.09 % Allowed : 23.37 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.30), residues: 839 helix: 1.41 (0.23), residues: 483 sheet: -0.82 (0.59), residues: 97 loop : -1.27 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 61 TYR 0.034 0.002 TYR D 114 PHE 0.019 0.001 PHE C 214 TRP 0.008 0.001 TRP A 120 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6885) covalent geometry : angle 0.64798 ( 9369) SS BOND : bond 0.00564 ( 6) SS BOND : angle 1.70207 ( 12) hydrogen bonds : bond 0.04590 ( 440) hydrogen bonds : angle 5.10694 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2024.23 seconds wall clock time: 35 minutes 27.46 seconds (2127.46 seconds total)