Starting phenix.real_space_refine on Wed Jul 1 23:02:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zz5_15035/07_2026/7zz5_15035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz5_15035/07_2026/7zz5_15035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zz5_15035/07_2026/7zz5_15035.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zz5_15035/07_2026/7zz5_15035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zz5_15035/07_2026/7zz5_15035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz5_15035/07_2026/7zz5_15035.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz5_15035/07_2026/7zz5_15035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz5_15035/07_2026/7zz5_15035.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 P 3 5.49 5 S 12 5.16 5 C 2291 2.51 5 N 636 2.21 5 O 691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3633 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3578 Classifications: {'peptide': 461} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 441} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'ACO': 1, 'BCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.01, per 1000 atoms: 0.28 Number of scatterers: 3633 At special positions: 0 Unit cell: (64.66, 73.14, 74.2, 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 12 16.00 P 3 15.00 O 691 8.00 N 636 7.00 C 2291 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: 0.28 Conformation dependent library (CDL) restraints added in 89.5 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 838 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 5 sheets defined 42.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 removed outlier: 3.516A pdb=" N VAL A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.208A pdb=" N PHE A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 62 through 74 Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.580A pdb=" N TYR A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 190 removed outlier: 3.780A pdb=" N HIS A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 266 Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.124A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.843A pdb=" N GLY A 350 " --> pdb=" O PRO A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 448 through 453 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 4.076A pdb=" N VAL A 30 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 156 Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 288 removed outlier: 6.865A pdb=" N GLU A 274 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 287 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 272 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N HIS A 207 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP A 227 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A 209 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU A 225 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER A 229 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE A 238 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN A 231 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS A 236 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A 237 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 341 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.526A pdb=" N GLY A 356 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 362 172 hydrogen bonds defined for protein. 474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.52 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 625 1.31 - 1.44: 936 1.44 - 1.57: 2118 1.57 - 1.69: 6 1.69 - 1.82: 18 Bond restraints: 3703 Sorted by residual: bond pdb=" C5A ACO A1201 " pdb=" N7A ACO A1201 " ideal model delta sigma weight residual 1.387 1.520 -0.133 1.00e-02 1.00e+04 1.78e+02 bond pdb=" C6A ACO A1201 " pdb=" N6A ACO A1201 " ideal model delta sigma weight residual 1.337 1.450 -0.113 1.00e-02 1.00e+04 1.29e+02 bond pdb=" C5P ACO A1201 " pdb=" N4P ACO A1201 " ideal model delta sigma weight residual 1.331 1.451 -0.120 1.20e-02 6.94e+03 9.98e+01 bond pdb=" C8A ACO A1201 " pdb=" N9A ACO A1201 " ideal model delta sigma weight residual 1.370 1.270 0.100 1.00e-02 1.00e+04 9.97e+01 bond pdb=" C9P ACO A1201 " pdb=" N8P ACO A1201 " ideal model delta sigma weight residual 1.333 1.453 -0.120 1.30e-02 5.92e+03 8.58e+01 ... (remaining 3698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 4951 3.46 - 6.93: 41 6.93 - 10.39: 15 10.39 - 13.85: 6 13.85 - 17.32: 3 Bond angle restraints: 5016 Sorted by residual: angle pdb=" C4A ACO A1201 " pdb=" N9A ACO A1201 " pdb=" C8A ACO A1201 " ideal model delta sigma weight residual 105.72 122.31 -16.59 1.00e+00 1.00e+00 2.75e+02 angle pdb=" P1A ACO A1201 " pdb=" O3A ACO A1201 " pdb=" P2A ACO A1201 " ideal model delta sigma weight residual 136.83 124.19 12.64 1.00e+00 1.00e+00 1.60e+02 angle pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" CD PRO A 132 " ideal model delta sigma weight residual 112.00 95.76 16.24 1.40e+00 5.10e-01 1.35e+02 angle pdb=" N3A ACO A1201 " pdb=" C4A ACO A1201 " pdb=" N9A ACO A1201 " ideal model delta sigma weight residual 127.04 137.47 -10.43 1.15e+00 7.59e-01 8.26e+01 angle pdb=" C ACO A1201 " pdb=" S1P ACO A1201 " pdb=" C2P ACO A1201 " ideal model delta sigma weight residual 101.25 110.12 -8.87 1.00e+00 1.00e+00 7.87e+01 ... (remaining 5011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 1903 17.67 - 35.33: 210 35.33 - 53.00: 59 53.00 - 70.67: 17 70.67 - 88.34: 10 Dihedral angle restraints: 2199 sinusoidal: 885 harmonic: 1314 Sorted by residual: dihedral pdb=" CA GLU A 175 " pdb=" C GLU A 175 " pdb=" N MET A 176 " pdb=" CA MET A 176 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ILE A 131 " pdb=" C ILE A 131 " pdb=" N PRO A 132 " pdb=" CA PRO A 132 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TYR A 82 " pdb=" C TYR A 82 " pdb=" N GLY A 83 " pdb=" CA GLY A 83 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 429 0.057 - 0.113: 106 0.113 - 0.170: 15 0.170 - 0.226: 1 0.226 - 0.283: 3 Chirality restraints: 554 Sorted by residual: chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3B ACO A1201 " pdb=" C2B ACO A1201 " pdb=" C4B ACO A1201 " pdb=" O3B ACO A1201 " both_signs ideal model delta sigma weight residual False -2.76 -2.49 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C2B ACO A1201 " pdb=" C1B ACO A1201 " pdb=" C3B ACO A1201 " pdb=" O2B ACO A1201 " both_signs ideal model delta sigma weight residual False -2.72 -2.47 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 551 not shown) Planarity restraints: 658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BCT A1202 " 0.084 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" O1 BCT A1202 " -0.031 2.00e-02 2.50e+03 pdb=" O2 BCT A1202 " -0.031 2.00e-02 2.50e+03 pdb=" O3 BCT A1202 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 131 " 0.083 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO A 132 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 459 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C ASP A 459 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP A 459 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 460 " 0.015 2.00e-02 2.50e+03 ... (remaining 655 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 816 2.78 - 3.31: 3348 3.31 - 3.84: 6544 3.84 - 4.37: 7545 4.37 - 4.90: 12734 Nonbonded interactions: 30987 Sorted by model distance: nonbonded pdb=" OE2 GLU A 11 " pdb=" OH TYR A 82 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 329 " pdb=" OE1 GLU A 330 " model vdw 2.332 3.040 nonbonded pdb=" OG1 THR A 296 " pdb=" OE1 GLN A 339 " model vdw 2.333 3.040 nonbonded pdb=" O LYS A 157 " pdb=" NZ LYS A 157 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLU A 46 " pdb=" OH TYR A 48 " model vdw 2.350 3.040 ... (remaining 30982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.280 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.460 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 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 : 0.008 0.173 3703 Z= 0.582 Angle : 1.042 17.316 5016 Z= 0.656 Chirality : 0.052 0.283 554 Planarity : 0.006 0.114 658 Dihedral : 17.330 88.336 1361 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.86 % Allowed : 16.49 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.36), residues: 459 helix: -0.40 (0.35), residues: 179 sheet: 0.39 (0.58), residues: 79 loop : -1.26 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 458 TYR 0.011 0.001 TYR A 82 PHE 0.028 0.002 PHE A 367 HIS 0.007 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00833 / 0.58 ( 3703) covalent geometry : angle 1.04249 / 0.66 ( 5016) hydrogen bonds : bond 0.17761 / 12.59 ( 172) hydrogen bonds : angle 7.04083 / 4.83 ( 474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.091 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 0.2961 time to fit residues: 7.5373 Evaluate side-chains 23 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.065089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053865 restraints weight = 12732.972| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.21 r_work: 0.3059 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 3703 Z= 0.134 Angle : 0.511 7.948 5016 Z= 0.273 Chirality : 0.044 0.138 554 Planarity : 0.003 0.032 658 Dihedral : 8.378 81.568 524 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.13 % Allowed : 15.69 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.39), residues: 459 helix: 0.59 (0.38), residues: 187 sheet: 0.72 (0.61), residues: 78 loop : -1.17 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.006 0.001 TYR A 150 PHE 0.015 0.001 PHE A 191 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 3703) covalent geometry : angle 0.51078 / 0.27 ( 5016) hydrogen bonds : bond 0.04418 / 3.06 ( 172) hydrogen bonds : angle 5.33194 / 3.78 ( 474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.137 Fit side-chains REVERT: A 155 MET cc_start: 0.7351 (tmm) cc_final: 0.6815 (tmm) REVERT: A 196 ILE cc_start: 0.4710 (OUTLIER) cc_final: 0.4286 (mp) REVERT: A 405 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.7011 (tmt170) REVERT: A 414 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8261 (t80) outliers start: 8 outliers final: 1 residues processed: 26 average time/residue: 0.3426 time to fit residues: 9.4250 Evaluate side-chains 21 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.064518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.053509 restraints weight = 12504.559| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.16 r_work: 0.3048 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3703 Z= 0.149 Angle : 0.491 7.040 5016 Z= 0.265 Chirality : 0.045 0.225 554 Planarity : 0.003 0.029 658 Dihedral : 7.603 81.455 517 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.39 % Allowed : 15.43 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.40), residues: 459 helix: 1.04 (0.39), residues: 186 sheet: 1.05 (0.64), residues: 71 loop : -0.99 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.010 0.001 TYR A 48 PHE 0.014 0.002 PHE A 146 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 3703) covalent geometry : angle 0.49120 / 0.26 ( 5016) hydrogen bonds : bond 0.03930 / 2.74 ( 172) hydrogen bonds : angle 5.07276 / 3.60 ( 474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.134 Fit side-chains REVERT: A 155 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6721 (tmm) REVERT: A 196 ILE cc_start: 0.4750 (OUTLIER) cc_final: 0.4331 (mp) REVERT: A 414 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8315 (t80) outliers start: 9 outliers final: 2 residues processed: 28 average time/residue: 0.3655 time to fit residues: 10.8115 Evaluate side-chains 22 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 224 HIS A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.064414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053507 restraints weight = 12665.290| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.19 r_work: 0.3046 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3703 Z= 0.139 Angle : 0.481 7.027 5016 Z= 0.259 Chirality : 0.044 0.156 554 Planarity : 0.003 0.027 658 Dihedral : 7.476 80.997 517 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.93 % Allowed : 15.69 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.40), residues: 459 helix: 1.17 (0.39), residues: 187 sheet: 0.87 (0.60), residues: 81 loop : -0.96 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.016 0.001 TYR A 150 PHE 0.007 0.001 PHE A 275 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 3703) covalent geometry : angle 0.48107 / 0.26 ( 5016) hydrogen bonds : bond 0.03712 / 2.59 ( 172) hydrogen bonds : angle 4.98442 / 3.53 ( 474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.200 Fit side-chains REVERT: A 57 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8944 (tp) REVERT: A 155 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6693 (tmm) REVERT: A 196 ILE cc_start: 0.5119 (OUTLIER) cc_final: 0.4726 (mp) REVERT: A 414 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8323 (t80) outliers start: 11 outliers final: 2 residues processed: 31 average time/residue: 0.5433 time to fit residues: 17.5873 Evaluate side-chains 24 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 0.0370 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 177 HIS A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.064729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053686 restraints weight = 12578.662| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.19 r_work: 0.3049 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3703 Z= 0.138 Angle : 0.500 8.199 5016 Z= 0.264 Chirality : 0.044 0.146 554 Planarity : 0.003 0.025 658 Dihedral : 7.294 79.304 517 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.66 % Allowed : 17.02 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.40), residues: 459 helix: 1.26 (0.39), residues: 186 sheet: 0.90 (0.60), residues: 81 loop : -0.97 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.012 0.001 TYR A 150 PHE 0.017 0.002 PHE A 191 HIS 0.006 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 3703) covalent geometry : angle 0.49993 / 0.26 ( 5016) hydrogen bonds : bond 0.03669 / 2.55 ( 172) hydrogen bonds : angle 4.95659 / 3.51 ( 474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.089 Fit side-chains REVERT: A 57 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8933 (tp) REVERT: A 155 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6659 (tmm) REVERT: A 414 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8307 (t80) outliers start: 10 outliers final: 4 residues processed: 28 average time/residue: 0.2797 time to fit residues: 8.2397 Evaluate side-chains 25 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.064317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.053419 restraints weight = 12618.821| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.19 r_work: 0.3040 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 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 0.024 3703 Z= 0.143 Angle : 0.510 7.792 5016 Z= 0.267 Chirality : 0.044 0.151 554 Planarity : 0.003 0.024 658 Dihedral : 7.097 77.354 517 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.66 % Allowed : 16.49 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.40), residues: 459 helix: 1.30 (0.39), residues: 186 sheet: 0.92 (0.60), residues: 81 loop : -0.97 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.010 0.001 TYR A 150 PHE 0.007 0.001 PHE A 275 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 3703) covalent geometry : angle 0.50968 / 0.27 ( 5016) hydrogen bonds : bond 0.03654 / 2.54 ( 172) hydrogen bonds : angle 4.97054 / 3.50 ( 474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.091 Fit side-chains REVERT: A 57 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8956 (tp) REVERT: A 155 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6627 (tmm) REVERT: A 414 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8327 (t80) REVERT: A 458 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8004 (mtm-85) outliers start: 10 outliers final: 4 residues processed: 30 average time/residue: 0.4605 time to fit residues: 14.4640 Evaluate side-chains 28 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 458 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.0050 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.064586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.053585 restraints weight = 12761.367| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.19 r_work: 0.3045 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3703 Z= 0.141 Angle : 0.521 8.837 5016 Z= 0.273 Chirality : 0.045 0.154 554 Planarity : 0.003 0.024 658 Dihedral : 6.892 72.157 517 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.39 % Allowed : 17.55 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.40), residues: 459 helix: 1.27 (0.39), residues: 187 sheet: 0.91 (0.60), residues: 81 loop : -0.94 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.009 0.001 TYR A 150 PHE 0.007 0.001 PHE A 191 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3703) covalent geometry : angle 0.52085 / 0.27 ( 5016) hydrogen bonds : bond 0.03626 / 2.52 ( 172) hydrogen bonds : angle 4.98680 / 3.50 ( 474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.101 Fit side-chains REVERT: A 57 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8960 (tp) REVERT: A 155 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6619 (tmm) REVERT: A 414 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8306 (t80) REVERT: A 458 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8021 (mtm-85) outliers start: 9 outliers final: 3 residues processed: 28 average time/residue: 0.4622 time to fit residues: 13.5235 Evaluate side-chains 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 458 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 19 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.064751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.053732 restraints weight = 12671.937| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.19 r_work: 0.3050 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3703 Z= 0.132 Angle : 0.521 9.376 5016 Z= 0.272 Chirality : 0.044 0.155 554 Planarity : 0.003 0.022 658 Dihedral : 6.615 70.871 517 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.66 % Allowed : 17.55 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.40), residues: 459 helix: 1.29 (0.39), residues: 187 sheet: 0.89 (0.60), residues: 81 loop : -0.93 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.008 0.001 TYR A 150 PHE 0.019 0.001 PHE A 191 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 3703) covalent geometry : angle 0.52053 / 0.27 ( 5016) hydrogen bonds : bond 0.03572 / 2.48 ( 172) hydrogen bonds : angle 4.96400 / 3.49 ( 474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.145 Fit side-chains REVERT: A 57 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8948 (tp) REVERT: A 155 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6720 (tmm) REVERT: A 176 MET cc_start: 0.6417 (mmt) cc_final: 0.6141 (mpm) REVERT: A 414 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8268 (t80) REVERT: A 458 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7991 (mtm-85) outliers start: 10 outliers final: 5 residues processed: 29 average time/residue: 0.4538 time to fit residues: 13.8036 Evaluate side-chains 28 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 458 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.064564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.053576 restraints weight = 12466.375| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.16 r_work: 0.3046 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3703 Z= 0.139 Angle : 0.523 9.518 5016 Z= 0.273 Chirality : 0.045 0.157 554 Planarity : 0.003 0.022 658 Dihedral : 6.334 64.438 517 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.39 % Allowed : 17.29 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.40), residues: 459 helix: 1.28 (0.39), residues: 187 sheet: 0.87 (0.60), residues: 81 loop : -0.90 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.008 0.001 TYR A 150 PHE 0.007 0.001 PHE A 42 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 3703) covalent geometry : angle 0.52278 / 0.27 ( 5016) hydrogen bonds : bond 0.03647 / 2.53 ( 172) hydrogen bonds : angle 4.97093 / 3.50 ( 474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.149 Fit side-chains REVERT: A 57 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8935 (tp) REVERT: A 155 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6715 (tmm) REVERT: A 414 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8271 (t80) outliers start: 9 outliers final: 5 residues processed: 28 average time/residue: 0.3208 time to fit residues: 9.4909 Evaluate side-chains 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.064327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.053311 restraints weight = 12729.206| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.18 r_work: 0.3039 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3703 Z= 0.158 Angle : 0.555 9.733 5016 Z= 0.291 Chirality : 0.045 0.162 554 Planarity : 0.003 0.026 658 Dihedral : 6.301 63.411 517 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.86 % Allowed : 18.62 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.40), residues: 459 helix: 1.27 (0.39), residues: 187 sheet: 0.84 (0.60), residues: 81 loop : -0.89 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.008 0.001 TYR A 150 PHE 0.021 0.002 PHE A 191 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 3703) covalent geometry : angle 0.55502 / 0.29 ( 5016) hydrogen bonds : bond 0.03750 / 2.61 ( 172) hydrogen bonds : angle 5.10637 / 3.58 ( 474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.174 Fit side-chains REVERT: A 57 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8952 (tp) REVERT: A 155 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6628 (tmm) REVERT: A 176 MET cc_start: 0.6594 (mmt) cc_final: 0.6351 (mpm) REVERT: A 414 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8313 (t80) outliers start: 7 outliers final: 4 residues processed: 27 average time/residue: 0.3076 time to fit residues: 8.8474 Evaluate side-chains 25 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 13 optimal weight: 0.0000 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.065147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054125 restraints weight = 12465.728| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.18 r_work: 0.3065 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3703 Z= 0.118 Angle : 0.539 9.749 5016 Z= 0.282 Chirality : 0.045 0.157 554 Planarity : 0.003 0.023 658 Dihedral : 6.002 60.424 517 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.13 % Allowed : 18.62 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.40), residues: 459 helix: 1.32 (0.39), residues: 187 sheet: 0.83 (0.60), residues: 82 loop : -0.92 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.008 0.001 TYR A 150 PHE 0.006 0.001 PHE A 275 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 3703) covalent geometry : angle 0.53886 / 0.28 ( 5016) hydrogen bonds : bond 0.03482 / 2.42 ( 172) hydrogen bonds : angle 4.99203 / 3.52 ( 474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.25 seconds wall clock time: 24 minutes 3.47 seconds (1443.47 seconds total)