Starting phenix.real_space_refine on Fri Dec 27 16:38:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq7_32087/12_2024/7vq7_32087.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq7_32087/12_2024/7vq7_32087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vq7_32087/12_2024/7vq7_32087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq7_32087/12_2024/7vq7_32087.map" model { file = "/net/cci-nas-00/data/ceres_data/7vq7_32087/12_2024/7vq7_32087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq7_32087/12_2024/7vq7_32087.cif" } resolution = 3.6 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= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Al 1 5.89 5 S 34 5.16 5 C 3942 2.51 5 N 1030 2.21 5 O 1120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6127 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3063 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 10, 'TRANS': 378} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' AL': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 5.24, per 1000 atoms: 0.86 Number of scatterers: 6127 At special positions: 0 Unit cell: (86.19, 84.162, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 Al 1 13.00 O 1120 8.00 N 1030 7.00 C 3942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.73 Conformation dependent library (CDL) restraints added in 935.9 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.743A pdb=" N ARG A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 39 removed outlier: 3.728A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.518A pdb=" N PHE A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 102 removed outlier: 3.966A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.876A pdb=" N LYS A 133 " --> pdb=" O TRP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 154 through 183 removed outlier: 3.766A pdb=" N ILE A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 214 Processing helix chain 'A' and resid 223 through 240 removed outlier: 5.001A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 267 through 293 removed outlier: 3.611A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.638A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 331 Processing helix chain 'A' and resid 335 through 356 removed outlier: 4.058A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 399 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.811A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 39 removed outlier: 3.728A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.518A pdb=" N PHE B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 102 removed outlier: 3.967A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 133 removed outlier: 3.876A pdb=" N LYS B 133 " --> pdb=" O TRP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 150 Processing helix chain 'B' and resid 154 through 183 removed outlier: 3.766A pdb=" N ILE B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 223 through 240 removed outlier: 5.000A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 267 through 293 removed outlier: 3.610A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.638A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 331 Processing helix chain 'B' and resid 335 through 356 removed outlier: 4.058A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 399 514 hydrogen bonds defined for protein. 1542 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: 1.79 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1960 1.34 - 1.46: 1387 1.46 - 1.58: 2833 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6240 Sorted by residual: bond pdb=" N HIS A 266 " pdb=" CA HIS A 266 " ideal model delta sigma weight residual 1.458 1.437 0.022 1.25e-02 6.40e+03 2.97e+00 bond pdb=" N HIS B 266 " pdb=" CA HIS B 266 " ideal model delta sigma weight residual 1.458 1.438 0.021 1.25e-02 6.40e+03 2.71e+00 bond pdb=" C TRP A 255 " pdb=" N GLU A 256 " ideal model delta sigma weight residual 1.329 1.305 0.023 1.60e-02 3.91e+03 2.11e+00 bond pdb=" C TRP B 255 " pdb=" N GLU B 256 " ideal model delta sigma weight residual 1.329 1.306 0.023 1.60e-02 3.91e+03 2.03e+00 bond pdb=" CB THR A 73 " pdb=" CG2 THR A 73 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.90e+00 ... (remaining 6235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 7745 1.30 - 2.60: 589 2.60 - 3.90: 65 3.90 - 5.20: 13 5.20 - 6.50: 10 Bond angle restraints: 8422 Sorted by residual: angle pdb=" N HIS A 266 " pdb=" CA HIS A 266 " pdb=" C HIS A 266 " ideal model delta sigma weight residual 109.10 102.60 6.50 1.91e+00 2.74e-01 1.16e+01 angle pdb=" N HIS B 266 " pdb=" CA HIS B 266 " pdb=" C HIS B 266 " ideal model delta sigma weight residual 109.10 102.63 6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" CA LYS B 3 " pdb=" CB LYS B 3 " pdb=" CG LYS B 3 " ideal model delta sigma weight residual 114.10 120.24 -6.14 2.00e+00 2.50e-01 9.41e+00 angle pdb=" CA LYS A 3 " pdb=" CB LYS A 3 " pdb=" CG LYS A 3 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.38e+00 angle pdb=" C PHE B 134 " pdb=" CA PHE B 134 " pdb=" CB PHE B 134 " ideal model delta sigma weight residual 111.13 107.09 4.04 1.61e+00 3.86e-01 6.29e+00 ... (remaining 8417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 3200 16.55 - 33.10: 396 33.10 - 49.65: 112 49.65 - 66.21: 38 66.21 - 82.76: 10 Dihedral angle restraints: 3756 sinusoidal: 1494 harmonic: 2262 Sorted by residual: dihedral pdb=" CA LEU B 233 " pdb=" C LEU B 233 " pdb=" N GLU B 234 " pdb=" CA GLU B 234 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N GLU A 234 " pdb=" CA GLU A 234 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ILE B 181 " pdb=" C ILE B 181 " pdb=" N PHE B 182 " pdb=" CA PHE B 182 " ideal model delta harmonic sigma weight residual -180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 412 0.027 - 0.055: 411 0.055 - 0.082: 98 0.082 - 0.109: 40 0.109 - 0.136: 13 Chirality restraints: 974 Sorted by residual: chirality pdb=" CA PRO B 365 " pdb=" N PRO B 365 " pdb=" C PRO B 365 " pdb=" CB PRO B 365 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA PRO A 365 " pdb=" N PRO A 365 " pdb=" C PRO A 365 " pdb=" CB PRO A 365 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 298 " pdb=" N ILE B 298 " pdb=" C ILE B 298 " pdb=" CB ILE B 298 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 971 not shown) Planarity restraints: 1052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 184 " -0.023 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 185 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 184 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 185 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 365 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.017 5.00e-02 4.00e+02 ... (remaining 1049 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 68 2.64 - 3.20: 5998 3.20 - 3.77: 9393 3.77 - 4.33: 12175 4.33 - 4.90: 20108 Nonbonded interactions: 47742 Sorted by model distance: nonbonded pdb=" SD MET B 60 " pdb="AL AL A 601 " model vdw 2.070 2.380 nonbonded pdb=" O CYS A 176 " pdb=" OG SER A 180 " model vdw 2.198 3.040 nonbonded pdb=" O SER A 294 " pdb=" NE2 GLN A 297 " model vdw 2.217 3.120 nonbonded pdb=" O SER B 294 " pdb=" NE2 GLN B 297 " model vdw 2.217 3.120 nonbonded pdb=" O LYS B 228 " pdb=" ND2 ASN B 232 " model vdw 2.255 3.120 ... (remaining 47737 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' and resid 1 through 405) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.240 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.007 0.046 6240 Z= 0.480 Angle : 0.755 6.503 8422 Z= 0.452 Chirality : 0.042 0.136 974 Planarity : 0.004 0.036 1052 Dihedral : 16.807 82.757 2288 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.87 % Allowed : 7.82 % Favored : 87.32 % 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: -1.30 (0.27), residues: 766 helix: -0.48 (0.18), residues: 638 sheet: None (None), residues: 0 loop : -2.07 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 255 HIS 0.004 0.002 HIS A 259 PHE 0.017 0.002 PHE B 206 TYR 0.011 0.002 TYR B 291 ARG 0.004 0.000 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.6940 (mtt-85) cc_final: 0.6086 (ttm110) REVERT: A 230 LYS cc_start: 0.7448 (mmtt) cc_final: 0.7110 (tptp) REVERT: A 265 ARG cc_start: 0.7029 (mmt180) cc_final: 0.6633 (tpp-160) REVERT: A 304 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6693 (ttpt) REVERT: A 321 MET cc_start: 0.8308 (mtt) cc_final: 0.8093 (mtt) REVERT: A 331 MET cc_start: 0.5936 (mtm) cc_final: 0.5244 (mpp) REVERT: B 265 ARG cc_start: 0.6818 (mmt180) cc_final: 0.6558 (tpp-160) REVERT: B 321 MET cc_start: 0.8252 (mtt) cc_final: 0.8001 (mtt) REVERT: B 331 MET cc_start: 0.6491 (mtm) cc_final: 0.5717 (mpp) outliers start: 33 outliers final: 6 residues processed: 167 average time/residue: 0.2056 time to fit residues: 43.8639 Evaluate side-chains 121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 261 GLN A 289 ASN B 193 HIS B 232 ASN B 261 GLN B 289 ASN B 293 ASN B 330 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6240 Z= 0.182 Angle : 0.485 5.241 8422 Z= 0.264 Chirality : 0.037 0.146 974 Planarity : 0.004 0.034 1052 Dihedral : 5.625 52.654 842 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.24 % Allowed : 16.67 % Favored : 80.09 % 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: 1.56 (0.30), residues: 766 helix: 1.45 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.37 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 205 PHE 0.024 0.001 PHE B 38 TYR 0.016 0.001 TYR B 40 ARG 0.004 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6215 (pptt) cc_final: 0.5397 (pptt) REVERT: A 5 ARG cc_start: 0.7016 (mtt-85) cc_final: 0.6263 (ttm110) REVERT: A 230 LYS cc_start: 0.7329 (mmtt) cc_final: 0.7111 (tptp) REVERT: A 331 MET cc_start: 0.5727 (mtm) cc_final: 0.5088 (mpp) REVERT: B 79 ASN cc_start: 0.8612 (m-40) cc_final: 0.8405 (m110) REVERT: B 331 MET cc_start: 0.6331 (mtm) cc_final: 0.5599 (mpp) REVERT: B 377 MET cc_start: 0.7133 (mmt) cc_final: 0.6885 (mtt) outliers start: 22 outliers final: 14 residues processed: 149 average time/residue: 0.2024 time to fit residues: 39.1111 Evaluate side-chains 126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 261 GLN B 261 GLN B 393 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6240 Z= 0.252 Angle : 0.498 5.319 8422 Z= 0.270 Chirality : 0.038 0.143 974 Planarity : 0.003 0.039 1052 Dihedral : 4.678 43.538 836 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.28 % Allowed : 18.58 % Favored : 77.14 % 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: 2.50 (0.31), residues: 766 helix: 2.17 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.27 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 259 PHE 0.022 0.001 PHE B 38 TYR 0.019 0.002 TYR B 40 ARG 0.003 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7270 (mtt-85) cc_final: 0.6478 (ttm110) REVERT: A 230 LYS cc_start: 0.7277 (mmtt) cc_final: 0.6902 (tptp) REVERT: A 321 MET cc_start: 0.8300 (mtt) cc_final: 0.7843 (mtt) REVERT: B 321 MET cc_start: 0.8053 (mtt) cc_final: 0.7593 (mtt) REVERT: B 331 MET cc_start: 0.6301 (mtm) cc_final: 0.5496 (mpp) REVERT: B 405 MET cc_start: 0.3551 (ttm) cc_final: 0.2187 (mpp) outliers start: 29 outliers final: 17 residues processed: 139 average time/residue: 0.1984 time to fit residues: 36.1704 Evaluate side-chains 126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 96 GLN B 393 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6240 Z= 0.186 Angle : 0.470 5.640 8422 Z= 0.253 Chirality : 0.037 0.145 974 Planarity : 0.003 0.037 1052 Dihedral : 4.229 36.376 835 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.54 % Allowed : 21.09 % Favored : 75.37 % 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: 3.03 (0.31), residues: 766 helix: 2.49 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.87 (0.62), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.003 0.001 HIS B 205 PHE 0.017 0.001 PHE B 206 TYR 0.020 0.002 TYR B 40 ARG 0.002 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7327 (mtt-85) cc_final: 0.6498 (ttm110) REVERT: A 230 LYS cc_start: 0.7009 (mmtt) cc_final: 0.6804 (tptp) REVERT: A 265 ARG cc_start: 0.6969 (tpp-160) cc_final: 0.6681 (tpp-160) REVERT: A 321 MET cc_start: 0.8123 (mtt) cc_final: 0.7577 (mtt) REVERT: A 331 MET cc_start: 0.5772 (mpp) cc_final: 0.4941 (mpp) REVERT: A 377 MET cc_start: 0.7210 (mmt) cc_final: 0.6994 (mtt) REVERT: B 244 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8141 (t) REVERT: B 321 MET cc_start: 0.7978 (mtt) cc_final: 0.7473 (mtt) REVERT: B 331 MET cc_start: 0.6173 (mtm) cc_final: 0.5397 (mpp) outliers start: 24 outliers final: 14 residues processed: 140 average time/residue: 0.1994 time to fit residues: 36.4127 Evaluate side-chains 126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 315 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 62 optimal weight: 0.0030 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 261 GLN B 79 ASN B 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6240 Z= 0.166 Angle : 0.462 5.902 8422 Z= 0.247 Chirality : 0.036 0.157 974 Planarity : 0.003 0.036 1052 Dihedral : 3.897 26.190 834 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.24 % Allowed : 22.12 % Favored : 74.63 % 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: 3.41 (0.31), residues: 766 helix: 2.70 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.45 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 255 HIS 0.002 0.001 HIS B 205 PHE 0.012 0.001 PHE B 215 TYR 0.021 0.001 TYR B 40 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7331 (mtt-85) cc_final: 0.6267 (ttm110) REVERT: A 321 MET cc_start: 0.7958 (mtt) cc_final: 0.7396 (mtt) REVERT: A 331 MET cc_start: 0.5669 (mpp) cc_final: 0.5074 (mpp) REVERT: A 377 MET cc_start: 0.7076 (mmt) cc_final: 0.6867 (mtt) REVERT: B 244 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8145 (t) REVERT: B 321 MET cc_start: 0.7936 (mtt) cc_final: 0.7427 (mtt) REVERT: B 331 MET cc_start: 0.6226 (mtm) cc_final: 0.5352 (mpp) outliers start: 22 outliers final: 13 residues processed: 135 average time/residue: 0.1838 time to fit residues: 32.3700 Evaluate side-chains 123 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 315 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 0.0170 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6240 Z= 0.177 Angle : 0.482 8.907 8422 Z= 0.252 Chirality : 0.037 0.151 974 Planarity : 0.003 0.034 1052 Dihedral : 3.775 17.214 833 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.65 % Allowed : 23.01 % Favored : 74.34 % 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: 3.59 (0.31), residues: 766 helix: 2.81 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.26 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 255 HIS 0.003 0.001 HIS B 205 PHE 0.011 0.001 PHE B 215 TYR 0.022 0.002 TYR B 40 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7378 (mtt-85) cc_final: 0.6339 (ttm110) REVERT: A 321 MET cc_start: 0.7914 (mtt) cc_final: 0.7360 (mtt) REVERT: A 331 MET cc_start: 0.5805 (mpp) cc_final: 0.5166 (mpp) REVERT: B 159 MET cc_start: 0.7645 (tpt) cc_final: 0.7403 (tpt) REVERT: B 244 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8142 (t) REVERT: B 321 MET cc_start: 0.7867 (mtt) cc_final: 0.7370 (mtt) REVERT: B 331 MET cc_start: 0.5988 (mtm) cc_final: 0.5346 (mpp) outliers start: 18 outliers final: 12 residues processed: 126 average time/residue: 0.1975 time to fit residues: 32.7291 Evaluate side-chains 120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 315 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6240 Z= 0.197 Angle : 0.489 7.904 8422 Z= 0.260 Chirality : 0.037 0.153 974 Planarity : 0.003 0.031 1052 Dihedral : 3.771 17.568 832 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.65 % Allowed : 24.48 % Favored : 72.86 % 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: 3.63 (0.31), residues: 766 helix: 2.83 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.25 (0.65), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.002 0.001 HIS B 205 PHE 0.008 0.001 PHE B 206 TYR 0.009 0.001 TYR A 40 ARG 0.002 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7446 (mtt-85) cc_final: 0.6365 (ttm110) REVERT: A 321 MET cc_start: 0.7893 (mtt) cc_final: 0.7307 (mtt) REVERT: A 331 MET cc_start: 0.5863 (mpp) cc_final: 0.5214 (mpp) REVERT: B 244 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8103 (t) REVERT: B 321 MET cc_start: 0.7880 (mtt) cc_final: 0.7309 (mtt) REVERT: B 331 MET cc_start: 0.6031 (mtm) cc_final: 0.5243 (mpp) outliers start: 18 outliers final: 14 residues processed: 120 average time/residue: 0.1770 time to fit residues: 28.3043 Evaluate side-chains 121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 315 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.0370 chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6240 Z= 0.176 Angle : 0.498 9.898 8422 Z= 0.263 Chirality : 0.037 0.178 974 Planarity : 0.003 0.030 1052 Dihedral : 3.692 17.619 832 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.51 % Allowed : 24.34 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.72 (0.31), residues: 766 helix: 2.89 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.17 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 255 HIS 0.002 0.000 HIS B 205 PHE 0.010 0.001 PHE B 215 TYR 0.033 0.002 TYR B 291 ARG 0.001 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7466 (mtt-85) cc_final: 0.6418 (ttm110) REVERT: A 321 MET cc_start: 0.7786 (mtt) cc_final: 0.7188 (mtt) REVERT: A 331 MET cc_start: 0.5922 (mpp) cc_final: 0.5250 (mpp) REVERT: B 244 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8154 (t) REVERT: B 293 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8212 (t0) REVERT: B 321 MET cc_start: 0.7800 (mtt) cc_final: 0.7219 (mtt) REVERT: B 331 MET cc_start: 0.6110 (mtm) cc_final: 0.5201 (mpp) outliers start: 17 outliers final: 11 residues processed: 121 average time/residue: 0.1923 time to fit residues: 30.5793 Evaluate side-chains 122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6240 Z= 0.228 Angle : 0.530 9.578 8422 Z= 0.280 Chirality : 0.038 0.168 974 Planarity : 0.003 0.028 1052 Dihedral : 3.833 18.393 832 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.80 % Allowed : 24.04 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.64 (0.31), residues: 766 helix: 2.83 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.16 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.002 0.001 HIS A 193 PHE 0.014 0.001 PHE A 206 TYR 0.033 0.002 TYR B 291 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.6370 (ttm110) REVERT: A 321 MET cc_start: 0.7858 (mtt) cc_final: 0.7266 (mtt) REVERT: A 331 MET cc_start: 0.6044 (mpp) cc_final: 0.5357 (mpp) REVERT: B 244 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8204 (t) REVERT: B 321 MET cc_start: 0.7920 (mtt) cc_final: 0.7333 (mtt) REVERT: B 331 MET cc_start: 0.6067 (mtm) cc_final: 0.5297 (mpp) REVERT: B 368 MET cc_start: 0.5578 (ttt) cc_final: 0.5289 (ttt) outliers start: 19 outliers final: 15 residues processed: 121 average time/residue: 0.1897 time to fit residues: 30.2803 Evaluate side-chains 123 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.0050 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6240 Z= 0.176 Angle : 0.517 9.336 8422 Z= 0.267 Chirality : 0.036 0.175 974 Planarity : 0.003 0.028 1052 Dihedral : 3.679 17.934 832 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.36 % Allowed : 25.52 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.81 (0.31), residues: 766 helix: 2.98 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.26 (0.67), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 255 HIS 0.002 0.000 HIS B 205 PHE 0.008 0.001 PHE A 206 TYR 0.022 0.001 TYR B 40 ARG 0.002 0.000 ARG A 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7603 (mtt-85) cc_final: 0.6360 (ttm110) REVERT: A 321 MET cc_start: 0.7788 (mtt) cc_final: 0.7144 (mtt) REVERT: A 331 MET cc_start: 0.6007 (mpp) cc_final: 0.5257 (mpp) REVERT: B 106 GLU cc_start: 0.7697 (tt0) cc_final: 0.7140 (tt0) REVERT: B 244 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8140 (t) REVERT: B 293 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7865 (t0) REVERT: B 321 MET cc_start: 0.7766 (mtt) cc_final: 0.7185 (mtt) REVERT: B 331 MET cc_start: 0.6166 (mtm) cc_final: 0.5207 (mpp) REVERT: B 368 MET cc_start: 0.5360 (ttt) cc_final: 0.5061 (ttt) outliers start: 16 outliers final: 10 residues processed: 123 average time/residue: 0.1805 time to fit residues: 29.4091 Evaluate side-chains 123 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.172356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126107 restraints weight = 8164.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.129584 restraints weight = 5283.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131541 restraints weight = 4159.427| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6240 Z= 0.219 Angle : 0.537 10.181 8422 Z= 0.279 Chirality : 0.037 0.167 974 Planarity : 0.003 0.029 1052 Dihedral : 3.767 18.836 832 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.36 % Allowed : 26.11 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.83 (0.31), residues: 766 helix: 2.99 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.25 (0.66), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.003 0.001 HIS B 205 PHE 0.013 0.001 PHE B 206 TYR 0.024 0.002 TYR B 40 ARG 0.002 0.000 ARG A 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.50 seconds wall clock time: 26 minutes 44.06 seconds (1604.06 seconds total)