Starting phenix.real_space_refine on Tue Feb 11 00:20:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x13_21987/02_2025/6x13_21987.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x13_21987/02_2025/6x13_21987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x13_21987/02_2025/6x13_21987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x13_21987/02_2025/6x13_21987.map" model { file = "/net/cci-nas-00/data/ceres_data/6x13_21987/02_2025/6x13_21987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x13_21987/02_2025/6x13_21987.cif" } resolution = 3.66 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= 0.003 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 1 5.49 5 S 18 5.16 5 C 2067 2.51 5 N 501 2.21 5 O 549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3136 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3094 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.89, per 1000 atoms: 0.92 Number of scatterers: 3136 At special positions: 0 Unit cell: (66.5415, 78.3473, 71.9078, 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 18 16.00 P 1 15.00 O 549 8.00 N 501 7.00 C 2067 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: 0.78 Conformation dependent library (CDL) restraints added in 409.0 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 85.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 11 through 33 Processing helix chain 'A' and resid 36 through 72 removed outlier: 3.767A pdb=" N TYR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.340A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET A 59 " --> pdb=" O CYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.929A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.811A pdb=" N LEU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 107 removed outlier: 4.218A pdb=" N LYS A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 174 through 220 removed outlier: 3.850A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.771A pdb=" N TYR A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 4.362A pdb=" N GLU A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.974A pdb=" N PHE A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 295 through 309 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 334 through 349 Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 376 through 418 removed outlier: 3.754A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 771 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: 0.86 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 482 1.31 - 1.43: 788 1.43 - 1.56: 1878 1.56 - 1.68: 14 1.68 - 1.81: 34 Bond restraints: 3196 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sigma weight residual 1.331 1.410 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C39 6OU A 501 " pdb=" C40 6OU A 501 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C15 6OU A 501 " pdb=" C16 6OU A 501 " ideal model delta sigma weight residual 1.501 1.562 -0.061 2.00e-02 2.50e+03 9.21e+00 bond pdb=" C38 6OU A 501 " pdb=" C39 6OU A 501 " ideal model delta sigma weight residual 1.530 1.580 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 3191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 4263 3.09 - 6.17: 67 6.17 - 9.26: 15 9.26 - 12.35: 3 12.35 - 15.43: 1 Bond angle restraints: 4349 Sorted by residual: angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 109.38 -15.43 3.00e+00 1.11e-01 2.65e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 120.46 -10.65 2.21e+00 2.05e-01 2.32e+01 angle pdb=" N GLY A 357 " pdb=" CA GLY A 357 " pdb=" C GLY A 357 " ideal model delta sigma weight residual 113.18 121.87 -8.69 2.37e+00 1.78e-01 1.34e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 120.48 -6.58 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C THR A 275 " pdb=" N ARG A 276 " pdb=" CA ARG A 276 " ideal model delta sigma weight residual 122.08 127.30 -5.22 1.47e+00 4.63e-01 1.26e+01 ... (remaining 4344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.76: 1768 25.76 - 51.51: 101 51.51 - 77.27: 16 77.27 - 103.03: 2 103.03 - 128.78: 2 Dihedral angle restraints: 1889 sinusoidal: 707 harmonic: 1182 Sorted by residual: dihedral pdb=" CA LEU A 372 " pdb=" C LEU A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C09 6OU A 501 " pdb=" C10 6OU A 501 " pdb=" C11 6OU A 501 " pdb=" C12 6OU A 501 " ideal model delta sinusoidal sigma weight residual 179.71 -51.51 -128.78 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C20 6OU A 501 " pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " pdb=" C33 6OU A 501 " ideal model delta sinusoidal sigma weight residual -177.41 -63.97 -113.44 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 1886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 347 0.040 - 0.080: 138 0.080 - 0.119: 43 0.119 - 0.159: 7 0.159 - 0.199: 5 Chirality restraints: 540 Sorted by residual: chirality pdb=" C20 6OU A 501 " pdb=" C19 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O30 6OU A 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA LEU A 303 " pdb=" N LEU A 303 " pdb=" C LEU A 303 " pdb=" CB LEU A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA ALA A 205 " pdb=" N ALA A 205 " pdb=" C ALA A 205 " pdb=" CB ALA A 205 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 537 not shown) Planarity restraints: 533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO A 45 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 243 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C ILE A 243 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 243 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 244 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 303 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO A 304 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.031 5.00e-02 4.00e+02 ... (remaining 530 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1023 2.85 - 3.36: 3072 3.36 - 3.88: 5111 3.88 - 4.39: 5458 4.39 - 4.90: 9825 Nonbonded interactions: 24489 Sorted by model distance: nonbonded pdb=" O LYS A 414 " pdb=" OG1 THR A 418 " model vdw 2.340 3.040 nonbonded pdb=" OD1 ASP A 390 " pdb=" NH1 ARG A 397 " model vdw 2.402 3.120 nonbonded pdb=" O GLU A 296 " pdb=" OG SER A 300 " model vdw 2.438 3.040 nonbonded pdb=" NZ LYS A 196 " pdb=" O24 6OU A 501 " model vdw 2.439 3.120 nonbonded pdb=" O SER A 171 " pdb=" NH2 ARG A 177 " model vdw 2.454 3.120 ... (remaining 24484 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 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 0.086 3196 Z= 0.439 Angle : 1.044 15.434 4349 Z= 0.516 Chirality : 0.048 0.199 540 Planarity : 0.008 0.065 533 Dihedral : 16.899 128.781 1141 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.31 % Allowed : 9.23 % Favored : 90.46 % Cbeta Deviations : 0.27 % 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: -3.73 (0.31), residues: 415 helix: -2.04 (0.20), residues: 351 sheet: None (None), residues: 0 loop : -3.62 (0.61), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 264 PHE 0.009 0.001 PHE A 210 TYR 0.017 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.264 Fit side-chains REVERT: A 35 TYR cc_start: 0.7029 (m-80) cc_final: 0.6827 (m-10) REVERT: A 59 MET cc_start: 0.9460 (tpp) cc_final: 0.9200 (mmm) REVERT: A 202 MET cc_start: 0.8192 (mmm) cc_final: 0.7863 (mmm) REVERT: A 362 MET cc_start: 0.7455 (ttm) cc_final: 0.7149 (ttm) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.1554 time to fit residues: 11.4607 Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114726 restraints weight = 4092.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116517 restraints weight = 2986.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117888 restraints weight = 2408.954| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3196 Z= 0.262 Angle : 0.653 6.886 4349 Z= 0.339 Chirality : 0.040 0.153 540 Planarity : 0.006 0.070 533 Dihedral : 11.554 96.432 481 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.23 % Allowed : 13.85 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.39), residues: 415 helix: 0.10 (0.26), residues: 350 sheet: None (None), residues: 0 loop : -3.92 (0.56), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 332 PHE 0.007 0.001 PHE A 273 TYR 0.035 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.309 Fit side-chains REVERT: A 169 MET cc_start: 0.8552 (tpp) cc_final: 0.7902 (ttm) REVERT: A 202 MET cc_start: 0.8300 (mmm) cc_final: 0.7914 (mmm) REVERT: A 362 MET cc_start: 0.7351 (ttm) cc_final: 0.6898 (ttm) outliers start: 4 outliers final: 1 residues processed: 57 average time/residue: 0.1484 time to fit residues: 10.4795 Evaluate side-chains 52 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 35 optimal weight: 0.0030 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112976 restraints weight = 4061.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.115470 restraints weight = 2683.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117191 restraints weight = 2052.142| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3196 Z= 0.202 Angle : 0.605 6.461 4349 Z= 0.313 Chirality : 0.039 0.139 540 Planarity : 0.005 0.072 533 Dihedral : 9.401 91.779 481 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.54 % Allowed : 14.77 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.42), residues: 415 helix: 0.92 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.41 (0.62), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.007 0.001 PHE A 273 TYR 0.032 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.328 Fit side-chains REVERT: A 35 TYR cc_start: 0.6927 (m-10) cc_final: 0.6671 (m-10) REVERT: A 169 MET cc_start: 0.8540 (tpp) cc_final: 0.7888 (ttm) REVERT: A 202 MET cc_start: 0.8198 (mmm) cc_final: 0.7614 (mmm) REVERT: A 276 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8133 (mtm-85) REVERT: A 362 MET cc_start: 0.7376 (ttm) cc_final: 0.6961 (ttm) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.1339 time to fit residues: 10.6911 Evaluate side-chains 55 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.097151 restraints weight = 4250.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099165 restraints weight = 2987.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100816 restraints weight = 2382.901| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3196 Z= 0.297 Angle : 0.663 7.879 4349 Z= 0.339 Chirality : 0.040 0.145 540 Planarity : 0.005 0.075 533 Dihedral : 8.538 86.204 481 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.85 % Allowed : 18.46 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.42), residues: 415 helix: 1.03 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -3.38 (0.64), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 40 PHE 0.011 0.001 PHE A 273 TYR 0.038 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.308 Fit side-chains REVERT: A 35 TYR cc_start: 0.6987 (m-10) cc_final: 0.6728 (m-10) REVERT: A 167 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7552 (m-10) REVERT: A 169 MET cc_start: 0.8577 (tpp) cc_final: 0.7976 (ttm) REVERT: A 215 TYR cc_start: 0.8146 (t80) cc_final: 0.7778 (t80) REVERT: A 298 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8332 (tt) REVERT: A 362 MET cc_start: 0.7571 (ttm) cc_final: 0.7058 (ttm) outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.1468 time to fit residues: 10.3692 Evaluate side-chains 54 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.138900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112979 restraints weight = 4209.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115769 restraints weight = 2708.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117325 restraints weight = 2052.600| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3196 Z= 0.214 Angle : 0.608 6.831 4349 Z= 0.313 Chirality : 0.039 0.137 540 Planarity : 0.005 0.078 533 Dihedral : 7.793 78.472 481 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.69 % Allowed : 18.15 % Favored : 78.15 % 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: 1.07 (0.42), residues: 415 helix: 1.38 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.12 (0.67), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.009 0.001 PHE A 261 TYR 0.037 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.320 Fit side-chains REVERT: A 103 MET cc_start: 0.8609 (tpp) cc_final: 0.8256 (mmm) REVERT: A 167 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7556 (m-10) REVERT: A 169 MET cc_start: 0.8545 (tpp) cc_final: 0.7962 (ttm) REVERT: A 236 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: A 276 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.7927 (mtm-85) REVERT: A 298 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8162 (tt) REVERT: A 323 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 362 MET cc_start: 0.7537 (ttm) cc_final: 0.6988 (ttm) outliers start: 12 outliers final: 5 residues processed: 64 average time/residue: 0.1348 time to fit residues: 10.7651 Evaluate side-chains 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 5 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.147512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122391 restraints weight = 4286.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125341 restraints weight = 2713.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127171 restraints weight = 2022.804| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3196 Z= 0.187 Angle : 0.595 6.418 4349 Z= 0.307 Chirality : 0.039 0.143 540 Planarity : 0.005 0.080 533 Dihedral : 7.336 72.092 481 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.69 % Allowed : 19.38 % Favored : 76.92 % 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: 1.49 (0.43), residues: 415 helix: 1.67 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.99 (0.70), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.008 0.001 PHE A 273 TYR 0.035 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.284 Fit side-chains REVERT: A 167 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7471 (m-10) REVERT: A 169 MET cc_start: 0.8462 (tpp) cc_final: 0.7937 (ttm) REVERT: A 215 TYR cc_start: 0.8056 (t80) cc_final: 0.7742 (t80) REVERT: A 219 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 276 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.7996 (mtm-85) REVERT: A 298 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8177 (tt) REVERT: A 362 MET cc_start: 0.7512 (ttm) cc_final: 0.6936 (ttm) outliers start: 12 outliers final: 3 residues processed: 67 average time/residue: 0.1401 time to fit residues: 11.7123 Evaluate side-chains 56 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.099168 restraints weight = 4222.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101279 restraints weight = 2986.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.102572 restraints weight = 2388.337| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3196 Z= 0.242 Angle : 0.674 14.074 4349 Z= 0.332 Chirality : 0.040 0.228 540 Planarity : 0.005 0.081 533 Dihedral : 7.428 74.419 481 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.77 % Allowed : 20.62 % Favored : 76.62 % 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: 1.43 (0.42), residues: 415 helix: 1.59 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.78 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.010 0.001 PHE A 273 TYR 0.033 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.371 Fit side-chains REVERT: A 167 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7551 (m-10) REVERT: A 169 MET cc_start: 0.8550 (tpp) cc_final: 0.7949 (ttm) REVERT: A 215 TYR cc_start: 0.8060 (t80) cc_final: 0.7741 (t80) REVERT: A 276 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.7982 (mtm-85) REVERT: A 298 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8243 (tt) REVERT: A 323 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7433 (t80) REVERT: A 362 MET cc_start: 0.7584 (ttm) cc_final: 0.6982 (ttm) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.1402 time to fit residues: 10.7025 Evaluate side-chains 60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.124443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.098936 restraints weight = 4227.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.101002 restraints weight = 3015.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.102423 restraints weight = 2401.560| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3196 Z= 0.257 Angle : 0.668 10.638 4349 Z= 0.334 Chirality : 0.040 0.160 540 Planarity : 0.005 0.082 533 Dihedral : 7.474 74.008 481 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.46 % Allowed : 21.85 % Favored : 75.69 % 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: 1.47 (0.42), residues: 415 helix: 1.61 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.71 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.011 0.001 PHE A 273 TYR 0.032 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.300 Fit side-chains REVERT: A 167 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7592 (m-10) REVERT: A 169 MET cc_start: 0.8562 (tpp) cc_final: 0.7959 (ttm) REVERT: A 215 TYR cc_start: 0.8107 (t80) cc_final: 0.7770 (t80) REVERT: A 276 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.7905 (mtm-85) REVERT: A 298 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8255 (tt) REVERT: A 323 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7476 (t80) REVERT: A 362 MET cc_start: 0.7581 (ttm) cc_final: 0.7006 (ttm) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 0.1447 time to fit residues: 10.2583 Evaluate side-chains 58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.126844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.101063 restraints weight = 4209.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.103191 restraints weight = 2923.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.104836 restraints weight = 2298.730| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3196 Z= 0.227 Angle : 0.653 10.983 4349 Z= 0.326 Chirality : 0.040 0.163 540 Planarity : 0.005 0.082 533 Dihedral : 7.314 70.306 481 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.77 % Allowed : 21.23 % Favored : 76.00 % 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: 1.63 (0.42), residues: 415 helix: 1.72 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.70 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.011 0.001 PHE A 273 TYR 0.032 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.364 Fit side-chains REVERT: A 167 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7545 (m-10) REVERT: A 169 MET cc_start: 0.8545 (tpp) cc_final: 0.7978 (ttm) REVERT: A 215 TYR cc_start: 0.8055 (t80) cc_final: 0.7742 (t80) REVERT: A 276 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.7877 (mtm-85) REVERT: A 298 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 323 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7492 (t80) REVERT: A 362 MET cc_start: 0.7571 (ttm) cc_final: 0.6966 (ttm) outliers start: 9 outliers final: 5 residues processed: 62 average time/residue: 0.1444 time to fit residues: 11.2144 Evaluate side-chains 62 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.0070 chunk 25 optimal weight: 0.0170 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.105118 restraints weight = 4148.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.107210 restraints weight = 2858.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108802 restraints weight = 2254.969| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3196 Z= 0.185 Angle : 0.639 10.456 4349 Z= 0.319 Chirality : 0.039 0.180 540 Planarity : 0.005 0.078 533 Dihedral : 7.042 62.383 481 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.46 % Allowed : 21.85 % Favored : 75.69 % 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: 1.89 (0.43), residues: 415 helix: 1.90 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.61 (0.72), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 264 PHE 0.010 0.001 PHE A 273 TYR 0.042 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.334 Fit side-chains REVERT: A 56 MET cc_start: 0.8994 (tmm) cc_final: 0.8734 (tmm) REVERT: A 59 MET cc_start: 0.9299 (tpp) cc_final: 0.9013 (mmm) REVERT: A 167 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: A 169 MET cc_start: 0.8435 (tpp) cc_final: 0.7940 (ttm) REVERT: A 215 TYR cc_start: 0.7934 (t80) cc_final: 0.7715 (t80) REVERT: A 219 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7899 (mm-30) REVERT: A 276 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.7987 (mtm-85) REVERT: A 323 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7423 (t80) REVERT: A 362 MET cc_start: 0.7503 (ttm) cc_final: 0.6850 (ttm) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 0.1355 time to fit residues: 11.1004 Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 323 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.126631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.101471 restraints weight = 4199.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.103312 restraints weight = 2982.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.104804 restraints weight = 2397.314| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3196 Z= 0.237 Angle : 0.661 10.499 4349 Z= 0.330 Chirality : 0.040 0.169 540 Planarity : 0.005 0.076 533 Dihedral : 7.044 63.012 481 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.85 % Allowed : 22.15 % Favored : 76.00 % 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: 1.80 (0.42), residues: 415 helix: 1.82 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.49 (0.73), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.009 0.001 PHE A 273 TYR 0.038 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1256.03 seconds wall clock time: 23 minutes 10.28 seconds (1390.28 seconds total)