Starting phenix.real_space_refine on Sat May 10 18:15:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z74_39810/05_2025/8z74_39810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z74_39810/05_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_39810/05_2025/8z74_39810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z74_39810/05_2025/8z74_39810.map" model { file = "/net/cci-nas-00/data/ceres_data/8z74_39810/05_2025/8z74_39810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z74_39810/05_2025/8z74_39810.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.71, per 1000 atoms: 0.70 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: 1.82 Conformation dependent library (CDL) restraints added in 957.8 milliseconds 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: 0.62 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: 1.83 Time building geometry restraints manager: 2.12 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 19.470 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP D 195 HIS 0.003 0.001 HIS C 231 PHE 0.025 0.001 PHE C 286 TYR 0.033 0.002 TYR D 114 ARG 0.009 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.14463 ( 440) hydrogen bonds : angle 6.65411 ( 1272) SS BOND : bond 0.00413 ( 6) SS BOND : angle 1.42272 ( 12) covalent geometry : bond 0.00333 ( 6885) covalent geometry : angle 0.62952 ( 9369) *********************** 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 : 0.657 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1789 time to fit residues: 32.9277 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 : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.172564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151158 restraints weight = 9268.663| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.11 r_work: 0.3747 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6891 Z= 0.186 Angle : 0.579 8.812 9381 Z= 0.301 Chirality : 0.041 0.148 1069 Planarity : 0.004 0.032 1139 Dihedral : 4.816 37.070 1067 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.36 % Allowed : 17.52 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP B 120 HIS 0.003 0.001 HIS C 265 PHE 0.018 0.001 PHE C 214 TYR 0.027 0.002 TYR D 114 ARG 0.005 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 440) hydrogen bonds : angle 5.48270 ( 1272) SS BOND : bond 0.00498 ( 6) SS BOND : angle 1.46514 ( 12) covalent geometry : bond 0.00405 ( 6885) covalent geometry : angle 0.57655 ( 9369) *********************** 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 : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8410 (mmm) cc_final: 0.8163 (mmt) REVERT: A 82 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.5548 (ppp) REVERT: C 204 SER cc_start: 0.8448 (m) cc_final: 0.8218 (p) REVERT: D 114 TYR cc_start: 0.8054 (m-80) cc_final: 0.7711 (m-80) outliers start: 17 outliers final: 7 residues processed: 151 average time/residue: 0.1833 time to fit residues: 37.2196 Evaluate side-chains 151 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 82 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 5 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 66 optimal weight: 30.0000 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.171580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149859 restraints weight = 9357.578| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.14 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: 0.7269 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6891 Z= 0.199 Angle : 0.579 9.057 9381 Z= 0.300 Chirality : 0.041 0.130 1069 Planarity : 0.004 0.033 1139 Dihedral : 4.849 34.907 1067 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.29), residues: 839 helix: 1.21 (0.22), residues: 484 sheet: -0.65 (0.59), residues: 94 loop : -1.30 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 120 HIS 0.003 0.001 HIS C 265 PHE 0.018 0.001 PHE C 286 TYR 0.019 0.002 TYR D 114 ARG 0.006 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 440) hydrogen bonds : angle 5.32323 ( 1272) SS BOND : bond 0.00627 ( 6) SS BOND : angle 1.63253 ( 12) covalent geometry : bond 0.00439 ( 6885) covalent geometry : angle 0.57654 ( 9369) *********************** 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 160 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8427 (mmm) cc_final: 0.8179 (mmt) REVERT: A 82 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5659 (ppp) REVERT: C 34 ILE cc_start: 0.7409 (mt) cc_final: 0.7108 (tp) REVERT: C 204 SER cc_start: 0.8467 (m) cc_final: 0.8207 (p) REVERT: C 308 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7406 (mt) REVERT: D 277 LEU cc_start: 0.7986 (mm) cc_final: 0.7737 (mm) outliers start: 22 outliers final: 10 residues processed: 148 average time/residue: 0.1765 time to fit residues: 35.1522 Evaluate side-chains 148 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 191 VAL 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 277 LEU Chi-restraints excluded: chain C residue 308 LEU 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 83 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 41 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.172860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.150672 restraints weight = 9435.398| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.26 r_work: 0.3729 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6891 Z= 0.155 Angle : 0.560 8.112 9381 Z= 0.287 Chirality : 0.039 0.126 1069 Planarity : 0.004 0.035 1139 Dihedral : 4.613 32.522 1067 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.62 % Allowed : 17.66 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.30), residues: 839 helix: 1.31 (0.23), residues: 483 sheet: -0.77 (0.59), residues: 94 loop : -1.23 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 154 HIS 0.002 0.001 HIS A 32 PHE 0.016 0.001 PHE C 214 TYR 0.028 0.002 TYR D 114 ARG 0.006 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 440) hydrogen bonds : angle 5.16714 ( 1272) SS BOND : bond 0.00475 ( 6) SS BOND : angle 1.45640 ( 12) covalent geometry : bond 0.00336 ( 6885) covalent geometry : angle 0.55801 ( 9369) *********************** 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 170 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8411 (mmm) cc_final: 0.7897 (mmt) REVERT: A 82 MET cc_start: 0.5846 (OUTLIER) cc_final: 0.5567 (ppp) REVERT: B 92 MET cc_start: 0.4225 (tpp) cc_final: 0.3829 (tpp) REVERT: C 204 SER cc_start: 0.8344 (m) cc_final: 0.8047 (p) REVERT: D 88 TYR cc_start: 0.8523 (t80) cc_final: 0.8271 (t80) REVERT: D 133 ARG cc_start: 0.6405 (mtm180) cc_final: 0.6112 (mtm180) REVERT: D 162 MET cc_start: 0.8264 (tpp) cc_final: 0.7879 (tpp) outliers start: 26 outliers final: 17 residues processed: 158 average time/residue: 0.1644 time to fit residues: 35.1831 Evaluate side-chains 159 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 2 VAL 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 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 132 VAL 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 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 61 optimal weight: 0.0770 chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.172139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.149970 restraints weight = 9306.810| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.25 r_work: 0.3722 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6891 Z= 0.176 Angle : 0.577 11.930 9381 Z= 0.293 Chirality : 0.040 0.151 1069 Planarity : 0.004 0.037 1139 Dihedral : 4.721 32.764 1067 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.20 % Allowed : 18.50 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.30), residues: 839 helix: 1.30 (0.23), residues: 484 sheet: -0.74 (0.58), residues: 97 loop : -1.16 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 120 HIS 0.002 0.001 HIS A 32 PHE 0.018 0.001 PHE C 286 TYR 0.032 0.002 TYR D 114 ARG 0.006 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 440) hydrogen bonds : angle 5.17472 ( 1272) SS BOND : bond 0.00487 ( 6) SS BOND : angle 1.59507 ( 12) covalent geometry : bond 0.00388 ( 6885) covalent geometry : angle 0.57502 ( 9369) *********************** 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 166 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5659 (ppp) REVERT: B 92 MET cc_start: 0.4490 (tpp) cc_final: 0.4154 (tpp) REVERT: C 204 SER cc_start: 0.8399 (m) cc_final: 0.8078 (p) REVERT: C 308 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7411 (mt) REVERT: D 88 TYR cc_start: 0.8529 (t80) cc_final: 0.8254 (t80) REVERT: D 133 ARG cc_start: 0.6435 (mtm180) cc_final: 0.6144 (mtm180) REVERT: D 162 MET cc_start: 0.8266 (tpp) cc_final: 0.7882 (tpp) outliers start: 23 outliers final: 18 residues processed: 156 average time/residue: 0.1725 time to fit residues: 36.3234 Evaluate side-chains 161 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER 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 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 191 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 102 CYS Chi-restraints excluded: chain D residue 132 VAL 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 290 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.4980 chunk 60 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 47 optimal weight: 0.0770 chunk 69 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.173854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150170 restraints weight = 9221.679| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.36 r_work: 0.3738 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6891 Z= 0.139 Angle : 0.561 13.791 9381 Z= 0.281 Chirality : 0.039 0.132 1069 Planarity : 0.004 0.039 1139 Dihedral : 4.512 31.025 1067 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.17 % Allowed : 18.78 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.30), residues: 839 helix: 1.43 (0.23), residues: 483 sheet: -0.69 (0.58), residues: 97 loop : -1.19 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 279 HIS 0.002 0.000 HIS A 32 PHE 0.014 0.001 PHE C 214 TYR 0.033 0.002 TYR D 114 ARG 0.007 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 440) hydrogen bonds : angle 5.07696 ( 1272) SS BOND : bond 0.00440 ( 6) SS BOND : angle 1.42610 ( 12) covalent geometry : bond 0.00297 ( 6885) covalent geometry : angle 0.55944 ( 9369) *********************** 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 184 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5558 (ppp) REVERT: B 2 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7679 (m) REVERT: B 92 MET cc_start: 0.4655 (tpp) cc_final: 0.4328 (tpp) REVERT: C 93 TYR cc_start: 0.8436 (m-80) cc_final: 0.8018 (m-80) REVERT: C 308 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7481 (mt) REVERT: D 88 TYR cc_start: 0.8577 (t80) cc_final: 0.8349 (t80) REVERT: D 133 ARG cc_start: 0.6398 (mtm180) cc_final: 0.6123 (mtm180) REVERT: D 162 MET cc_start: 0.8212 (tpp) cc_final: 0.7840 (tpp) REVERT: D 277 LEU cc_start: 0.7954 (mm) cc_final: 0.7696 (mm) outliers start: 30 outliers final: 23 residues processed: 167 average time/residue: 0.1614 time to fit residues: 36.7961 Evaluate side-chains 174 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 2 VAL 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 66 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 187 MET 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 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 102 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 195 TRP Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 69 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.173084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151617 restraints weight = 9344.636| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.13 r_work: 0.3741 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6891 Z= 0.156 Angle : 0.586 16.465 9381 Z= 0.291 Chirality : 0.039 0.128 1069 Planarity : 0.004 0.040 1139 Dihedral : 4.606 31.686 1067 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.62 % Allowed : 20.17 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.30), residues: 839 helix: 1.41 (0.23), residues: 483 sheet: -0.66 (0.59), residues: 97 loop : -1.13 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 120 HIS 0.001 0.001 HIS A 32 PHE 0.015 0.001 PHE C 214 TYR 0.033 0.002 TYR D 114 ARG 0.007 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 440) hydrogen bonds : angle 5.08586 ( 1272) SS BOND : bond 0.00512 ( 6) SS BOND : angle 1.53503 ( 12) covalent geometry : bond 0.00339 ( 6885) covalent geometry : angle 0.58426 ( 9369) *********************** 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 : 0.624 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.8395 (mmm) cc_final: 0.8126 (mmt) REVERT: A 82 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.5581 (ppp) REVERT: B 2 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7674 (m) REVERT: B 92 MET cc_start: 0.4611 (tpp) cc_final: 0.4296 (tpp) REVERT: C 93 TYR cc_start: 0.8428 (m-80) cc_final: 0.8023 (m-80) REVERT: C 308 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7465 (mt) REVERT: D 88 TYR cc_start: 0.8589 (t80) cc_final: 0.8354 (t80) REVERT: D 90 TYR cc_start: 0.8159 (t80) cc_final: 0.7940 (t80) REVERT: D 107 TYR cc_start: 0.8447 (t80) cc_final: 0.7897 (t80) REVERT: D 133 ARG cc_start: 0.6270 (mtm180) cc_final: 0.6027 (mtm180) REVERT: D 162 MET cc_start: 0.8225 (tpp) cc_final: 0.7768 (tpp) outliers start: 26 outliers final: 19 residues processed: 165 average time/residue: 0.1532 time to fit residues: 34.5231 Evaluate side-chains 170 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 2 VAL 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 191 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 262 MET Chi-restraints excluded: chain D residue 290 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.0570 chunk 82 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.172759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148931 restraints weight = 9240.738| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.36 r_work: 0.3724 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6891 Z= 0.170 Angle : 0.616 19.209 9381 Z= 0.305 Chirality : 0.040 0.139 1069 Planarity : 0.004 0.041 1139 Dihedral : 4.616 30.988 1067 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.62 % Allowed : 21.14 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.30), residues: 839 helix: 1.40 (0.23), residues: 483 sheet: -0.73 (0.58), residues: 97 loop : -1.15 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 120 HIS 0.002 0.001 HIS D 265 PHE 0.017 0.001 PHE C 214 TYR 0.035 0.002 TYR D 114 ARG 0.008 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 440) hydrogen bonds : angle 5.11007 ( 1272) SS BOND : bond 0.00523 ( 6) SS BOND : angle 1.61921 ( 12) covalent geometry : bond 0.00376 ( 6885) covalent geometry : angle 0.61358 ( 9369) *********************** 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 172 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.5612 (ppp) REVERT: B 92 MET cc_start: 0.4780 (tpp) cc_final: 0.4496 (tpp) REVERT: C 197 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7630 (m-90) REVERT: D 90 TYR cc_start: 0.8169 (t80) cc_final: 0.7961 (t80) REVERT: D 107 TYR cc_start: 0.8478 (t80) cc_final: 0.7913 (t80) REVERT: D 133 ARG cc_start: 0.6282 (mtm180) cc_final: 0.6034 (mtm180) REVERT: D 162 MET cc_start: 0.8245 (tpp) cc_final: 0.7796 (tpp) REVERT: D 277 LEU cc_start: 0.7939 (mm) cc_final: 0.7719 (mm) outliers start: 26 outliers final: 20 residues processed: 158 average time/residue: 0.1701 time to fit residues: 36.2150 Evaluate side-chains 167 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 197 TRP 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 D residue 48 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 68 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.172998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149298 restraints weight = 9263.519| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.35 r_work: 0.3724 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6891 Z= 0.161 Angle : 0.617 20.136 9381 Z= 0.305 Chirality : 0.040 0.141 1069 Planarity : 0.004 0.041 1139 Dihedral : 4.584 30.402 1067 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.20 % Allowed : 21.14 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.30), residues: 839 helix: 1.42 (0.23), residues: 483 sheet: -0.82 (0.57), residues: 97 loop : -1.15 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 120 HIS 0.002 0.001 HIS C 231 PHE 0.016 0.001 PHE C 214 TYR 0.033 0.002 TYR D 114 ARG 0.009 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 440) hydrogen bonds : angle 5.09279 ( 1272) SS BOND : bond 0.00581 ( 6) SS BOND : angle 1.60432 ( 12) covalent geometry : bond 0.00352 ( 6885) covalent geometry : angle 0.61503 ( 9369) *********************** 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 170 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5543 (ppp) REVERT: B 92 MET cc_start: 0.4722 (tpp) cc_final: 0.4476 (tpp) REVERT: C 93 TYR cc_start: 0.8406 (m-80) cc_final: 0.7996 (m-80) REVERT: C 197 TRP cc_start: 0.8173 (OUTLIER) cc_final: 0.7573 (m-90) REVERT: D 88 TYR cc_start: 0.8543 (t80) cc_final: 0.8289 (t80) REVERT: D 90 TYR cc_start: 0.8157 (t80) cc_final: 0.7900 (t80) REVERT: D 107 TYR cc_start: 0.8455 (t80) cc_final: 0.7872 (t80) REVERT: D 133 ARG cc_start: 0.6295 (mtm180) cc_final: 0.6029 (mtm180) REVERT: D 162 MET cc_start: 0.8225 (tpp) cc_final: 0.7737 (tpp) REVERT: D 277 LEU cc_start: 0.7918 (mm) cc_final: 0.7684 (mm) outliers start: 23 outliers final: 17 residues processed: 157 average time/residue: 0.1737 time to fit residues: 36.8289 Evaluate side-chains 167 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 2 VAL 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 197 TRP 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 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 Chi-restraints excluded: chain D residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 0.0060 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 47 optimal weight: 8.9990 chunk 82 optimal weight: 0.0980 overall best weight: 0.2212 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.175161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153540 restraints weight = 9561.658| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.18 r_work: 0.3764 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1768 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= 0.122 Angle : 0.601 19.977 9381 Z= 0.295 Chirality : 0.038 0.138 1069 Planarity : 0.004 0.040 1139 Dihedral : 4.382 28.975 1067 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.36 % Allowed : 22.25 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.30), residues: 839 helix: 1.53 (0.23), residues: 483 sheet: -0.82 (0.58), residues: 91 loop : -1.20 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.002 0.001 HIS C 231 PHE 0.012 0.001 PHE C 214 TYR 0.031 0.001 TYR D 114 ARG 0.010 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 440) hydrogen bonds : angle 4.96292 ( 1272) SS BOND : bond 0.00249 ( 6) SS BOND : angle 1.23888 ( 12) covalent geometry : bond 0.00255 ( 6885) covalent geometry : angle 0.60014 ( 9369) ********************** 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 162 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5426 (ppp) REVERT: B 92 MET cc_start: 0.4705 (tpp) cc_final: 0.4460 (tpp) REVERT: C 93 TYR cc_start: 0.8383 (m-80) cc_final: 0.7944 (m-80) REVERT: C 114 TYR cc_start: 0.7841 (m-80) cc_final: 0.7590 (m-80) REVERT: C 197 TRP cc_start: 0.8127 (OUTLIER) cc_final: 0.7521 (m-90) REVERT: D 88 TYR cc_start: 0.8515 (t80) cc_final: 0.8290 (t80) REVERT: D 107 TYR cc_start: 0.8441 (t80) cc_final: 0.7944 (t80) REVERT: D 133 ARG cc_start: 0.6234 (mtm180) cc_final: 0.5993 (mtm180) REVERT: D 162 MET cc_start: 0.8138 (tpp) cc_final: 0.7710 (tpp) REVERT: D 277 LEU cc_start: 0.7866 (mm) cc_final: 0.7626 (mm) outliers start: 17 outliers final: 13 residues processed: 152 average time/residue: 0.1817 time to fit residues: 36.9625 Evaluate side-chains 161 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain C residue 48 LEU 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 244 ARG Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 8 optimal weight: 0.0370 chunk 31 optimal weight: 0.3980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.173940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.150081 restraints weight = 9359.638| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.38 r_work: 0.3735 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6891 Z= 0.153 Angle : 0.619 20.293 9381 Z= 0.305 Chirality : 0.040 0.146 1069 Planarity : 0.004 0.042 1139 Dihedral : 4.573 30.854 1067 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.78 % Allowed : 22.11 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.30), residues: 839 helix: 1.47 (0.23), residues: 483 sheet: -1.14 (0.54), residues: 107 loop : -1.12 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 120 HIS 0.002 0.001 HIS C 231 PHE 0.016 0.001 PHE C 214 TYR 0.032 0.002 TYR D 114 ARG 0.009 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 440) hydrogen bonds : angle 5.01593 ( 1272) SS BOND : bond 0.00471 ( 6) SS BOND : angle 1.51164 ( 12) covalent geometry : bond 0.00338 ( 6885) covalent geometry : angle 0.61669 ( 9369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4021.44 seconds wall clock time: 70 minutes 10.10 seconds (4210.10 seconds total)