Starting phenix.real_space_refine on Wed Sep 17 03:33:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d68_46589/09_2025/9d68_46589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d68_46589/09_2025/9d68_46589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d68_46589/09_2025/9d68_46589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d68_46589/09_2025/9d68_46589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d68_46589/09_2025/9d68_46589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d68_46589/09_2025/9d68_46589.map" } resolution = 2.58 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= 0.006 sd= 0.177 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 S 22 5.16 5 Na 2 4.78 5 C 2115 2.51 5 N 516 2.21 5 O 587 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3242 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3227 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 12, 'TRANS': 412} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2, 'water': 6} Link IDs: {None: 7} Time building chain proxies: 0.83, per 1000 atoms: 0.26 Number of scatterers: 3242 At special positions: 0 Unit cell: (61.05, 70.95, 74.25, 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 22 16.00 Na 2 11.00 O 587 8.00 N 516 7.00 C 2115 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: 0.29 Conformation dependent library (CDL) restraints added in 123.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 84.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 19 through 42 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.715A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 117 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.564A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.614A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.656A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.504A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.822A pdb=" N ARG A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.806A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.712A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.759A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 436 through 466 removed outlier: 4.522A pdb=" N CYS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 256 hydrogen bonds defined for protein. 753 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: 0.36 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 677 1.33 - 1.45: 623 1.45 - 1.57: 1941 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 3281 Sorted by residual: bond pdb=" N ILE A 406 " pdb=" CA ILE A 406 " ideal model delta sigma weight residual 1.462 1.498 -0.036 1.17e-02 7.31e+03 9.25e+00 bond pdb=" N VAL A 417 " pdb=" CA VAL A 417 " ideal model delta sigma weight residual 1.461 1.490 -0.030 1.19e-02 7.06e+03 6.28e+00 bond pdb=" N GLN A 413 " pdb=" CA GLN A 413 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.35e-02 5.49e+03 5.91e+00 bond pdb=" N LEU A 416 " pdb=" CA LEU A 416 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.41e+00 bond pdb=" N SER A 405 " pdb=" CA SER A 405 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.51e-02 4.39e+03 3.92e+00 ... (remaining 3276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 4232 1.01 - 2.02: 148 2.02 - 3.03: 44 3.03 - 4.04: 19 4.04 - 5.05: 11 Bond angle restraints: 4454 Sorted by residual: angle pdb=" N ASN A 241 " pdb=" CA ASN A 241 " pdb=" C ASN A 241 " ideal model delta sigma weight residual 111.69 107.11 4.58 1.23e+00 6.61e-01 1.39e+01 angle pdb=" CA SER A 405 " pdb=" C SER A 405 " pdb=" O SER A 405 " ideal model delta sigma weight residual 121.84 117.62 4.22 1.16e+00 7.43e-01 1.32e+01 angle pdb=" N GLN A 413 " pdb=" CA GLN A 413 " pdb=" C GLN A 413 " ideal model delta sigma weight residual 113.23 109.35 3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" CA PRO A 412 " pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 121.67 117.82 3.85 1.22e+00 6.72e-01 9.97e+00 angle pdb=" CA ALA A 404 " pdb=" C ALA A 404 " pdb=" O ALA A 404 " ideal model delta sigma weight residual 120.70 117.42 3.28 1.08e+00 8.57e-01 9.21e+00 ... (remaining 4449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 1731 17.07 - 34.15: 166 34.15 - 51.22: 45 51.22 - 68.30: 20 68.30 - 85.37: 3 Dihedral angle restraints: 1965 sinusoidal: 746 harmonic: 1219 Sorted by residual: dihedral pdb=" CG ARG A 61 " pdb=" CD ARG A 61 " pdb=" NE ARG A 61 " pdb=" CZ ARG A 61 " ideal model delta sinusoidal sigma weight residual 90.00 134.61 -44.61 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU A 431 " pdb=" CG GLU A 431 " pdb=" CD GLU A 431 " pdb=" OE1 GLU A 431 " ideal model delta sinusoidal sigma weight residual 0.00 -85.37 85.37 1 3.00e+01 1.11e-03 9.81e+00 dihedral pdb=" CA GLU A 199 " pdb=" CB GLU A 199 " pdb=" CG GLU A 199 " pdb=" CD GLU A 199 " ideal model delta sinusoidal sigma weight residual -60.00 -119.93 59.93 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 416 0.036 - 0.072: 108 0.072 - 0.107: 32 0.107 - 0.143: 8 0.143 - 0.179: 2 Chirality restraints: 566 Sorted by residual: chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA VAL A 417 " pdb=" N VAL A 417 " pdb=" C VAL A 417 " pdb=" CB VAL A 417 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA MET A 367 " pdb=" N MET A 367 " pdb=" C MET A 367 " pdb=" CB MET A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 563 not shown) Planarity restraints: 544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 367 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C MET A 367 " -0.027 2.00e-02 2.50e+03 pdb=" O MET A 367 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP A 368 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 366 " -0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C ASN A 366 " 0.023 2.00e-02 2.50e+03 pdb=" O ASN A 366 " -0.009 2.00e-02 2.50e+03 pdb=" N MET A 367 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO A 302 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.015 5.00e-02 4.00e+02 ... (remaining 541 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 45 2.67 - 3.23: 3352 3.23 - 3.78: 5199 3.78 - 4.34: 7395 4.34 - 4.90: 11912 Nonbonded interactions: 27903 Sorted by model distance: nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 603 " model vdw 2.112 2.470 nonbonded pdb=" O TYR A 98 " pdb="NA NA A 603 " model vdw 2.143 2.470 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.149 2.470 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 2.174 2.470 nonbonded pdb=" OG SER A 333 " pdb=" O CYS A 601 " model vdw 2.217 3.040 ... (remaining 27898 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: 1.740 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.750 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3281 Z= 0.187 Angle : 0.549 5.048 4454 Z= 0.326 Chirality : 0.039 0.179 566 Planarity : 0.003 0.027 544 Dihedral : 16.079 85.370 1179 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.28 % Allowed : 19.77 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.39), residues: 421 helix: 1.50 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -0.32 (0.51), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.006 0.001 TYR A 373 PHE 0.005 0.001 PHE A 218 TRP 0.008 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3281) covalent geometry : angle 0.54907 ( 4454) hydrogen bonds : bond 0.21507 ( 256) hydrogen bonds : angle 7.20762 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.076 Fit side-chains REVERT: A 165 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7427 (pttm) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.5214 time to fit residues: 30.0662 Evaluate side-chains 54 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.0030 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 347 ASN A 349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121734 restraints weight = 3169.263| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.61 r_work: 0.3161 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3281 Z= 0.137 Angle : 0.510 4.879 4454 Z= 0.273 Chirality : 0.039 0.145 566 Planarity : 0.004 0.027 544 Dihedral : 3.593 13.234 448 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.54 % Allowed : 16.38 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.39), residues: 421 helix: 1.84 (0.27), residues: 333 sheet: None (None), residues: 0 loop : -0.55 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.006 0.001 TYR A 97 PHE 0.012 0.001 PHE A 218 TRP 0.008 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3281) covalent geometry : angle 0.51039 ( 4454) hydrogen bonds : bond 0.04789 ( 256) hydrogen bonds : angle 4.95505 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.122 Fit side-chains REVERT: A 83 ASP cc_start: 0.7280 (m-30) cc_final: 0.7067 (m-30) REVERT: A 165 LYS cc_start: 0.7799 (mtmm) cc_final: 0.7217 (pttm) REVERT: A 290 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8204 (mm) outliers start: 9 outliers final: 3 residues processed: 66 average time/residue: 0.4504 time to fit residues: 30.6401 Evaluate side-chains 60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123478 restraints weight = 3148.576| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.62 r_work: 0.3187 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3281 Z= 0.124 Angle : 0.485 4.893 4454 Z= 0.254 Chirality : 0.038 0.148 566 Planarity : 0.003 0.026 544 Dihedral : 3.455 11.470 448 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.54 % Allowed : 18.08 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.39), residues: 421 helix: 1.93 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.52 (0.59), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 61 TYR 0.005 0.001 TYR A 162 PHE 0.011 0.001 PHE A 218 TRP 0.006 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3281) covalent geometry : angle 0.48519 ( 4454) hydrogen bonds : bond 0.04354 ( 256) hydrogen bonds : angle 4.66843 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.122 Fit side-chains REVERT: A 83 ASP cc_start: 0.7248 (m-30) cc_final: 0.7018 (m-30) REVERT: A 165 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7201 (pttm) outliers start: 9 outliers final: 3 residues processed: 64 average time/residue: 0.5024 time to fit residues: 33.1203 Evaluate side-chains 60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.163578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123068 restraints weight = 3159.600| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.63 r_work: 0.3198 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3281 Z= 0.123 Angle : 0.477 4.973 4454 Z= 0.250 Chirality : 0.038 0.145 566 Planarity : 0.003 0.028 544 Dihedral : 3.464 11.871 448 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.39 % Allowed : 18.64 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.39), residues: 421 helix: 2.02 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.34 (0.58), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.006 0.001 TYR A 373 PHE 0.011 0.001 PHE A 218 TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3281) covalent geometry : angle 0.47687 ( 4454) hydrogen bonds : bond 0.04175 ( 256) hydrogen bonds : angle 4.58843 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.120 Fit side-chains REVERT: A 103 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7082 (mm) REVERT: A 165 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7097 (pttm) outliers start: 12 outliers final: 3 residues processed: 64 average time/residue: 0.5383 time to fit residues: 35.4870 Evaluate side-chains 59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.0370 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 31 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126181 restraints weight = 3175.512| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.62 r_work: 0.3222 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3281 Z= 0.109 Angle : 0.464 4.919 4454 Z= 0.241 Chirality : 0.038 0.146 566 Planarity : 0.003 0.026 544 Dihedral : 3.384 11.539 448 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.39 % Allowed : 19.21 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.39), residues: 421 helix: 2.10 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.39 (0.58), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.006 0.001 TYR A 373 PHE 0.010 0.001 PHE A 218 TRP 0.003 0.000 TRP A 19 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 3281) covalent geometry : angle 0.46420 ( 4454) hydrogen bonds : bond 0.03834 ( 256) hydrogen bonds : angle 4.47961 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.148 Fit side-chains REVERT: A 165 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7080 (pttm) REVERT: A 216 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 290 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8183 (mm) outliers start: 12 outliers final: 3 residues processed: 67 average time/residue: 0.5641 time to fit residues: 38.8455 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.0170 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.167622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127505 restraints weight = 3163.398| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.62 r_work: 0.3260 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3281 Z= 0.105 Angle : 0.459 4.801 4454 Z= 0.238 Chirality : 0.037 0.139 566 Planarity : 0.003 0.025 544 Dihedral : 3.334 11.282 448 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.54 % Allowed : 19.77 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.39), residues: 421 helix: 2.22 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.44 (0.58), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.007 0.001 TYR A 373 PHE 0.009 0.001 PHE A 218 TRP 0.003 0.000 TRP A 19 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3281) covalent geometry : angle 0.45929 ( 4454) hydrogen bonds : bond 0.03672 ( 256) hydrogen bonds : angle 4.39100 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.123 Fit side-chains REVERT: A 165 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7066 (pttm) REVERT: A 216 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8439 (mt) REVERT: A 290 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8131 (mm) outliers start: 9 outliers final: 3 residues processed: 66 average time/residue: 0.5319 time to fit residues: 36.1971 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.0170 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.164533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128018 restraints weight = 3171.524| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.47 r_work: 0.3208 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3281 Z= 0.125 Angle : 0.490 5.004 4454 Z= 0.254 Chirality : 0.038 0.145 566 Planarity : 0.003 0.025 544 Dihedral : 3.457 12.025 448 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.54 % Allowed : 20.34 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.39), residues: 421 helix: 1.89 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -0.55 (0.58), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.008 0.001 TYR A 373 PHE 0.011 0.002 PHE A 218 TRP 0.003 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3281) covalent geometry : angle 0.49000 ( 4454) hydrogen bonds : bond 0.04051 ( 256) hydrogen bonds : angle 4.51220 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.135 Fit side-chains REVERT: A 165 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7107 (pttm) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.5420 time to fit residues: 36.8593 Evaluate side-chains 61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.164443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127957 restraints weight = 3192.670| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.47 r_work: 0.3211 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3281 Z= 0.124 Angle : 0.487 4.952 4454 Z= 0.253 Chirality : 0.038 0.145 566 Planarity : 0.003 0.025 544 Dihedral : 3.475 12.177 448 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.69 % Allowed : 20.62 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.39), residues: 421 helix: 1.86 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -0.56 (0.57), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.007 0.001 TYR A 373 PHE 0.011 0.001 PHE A 218 TRP 0.002 0.000 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3281) covalent geometry : angle 0.48673 ( 4454) hydrogen bonds : bond 0.03986 ( 256) hydrogen bonds : angle 4.51419 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.088 Fit side-chains REVERT: A 103 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7117 (mm) REVERT: A 165 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7125 (pttm) REVERT: A 216 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8458 (mt) outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 0.5462 time to fit residues: 34.8420 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122312 restraints weight = 3156.510| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.62 r_work: 0.3166 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3281 Z= 0.139 Angle : 0.510 5.093 4454 Z= 0.264 Chirality : 0.039 0.148 566 Planarity : 0.003 0.025 544 Dihedral : 3.567 12.687 448 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.98 % Allowed : 20.34 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.39), residues: 421 helix: 1.73 (0.27), residues: 343 sheet: None (None), residues: 0 loop : -0.53 (0.57), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.008 0.001 TYR A 373 PHE 0.012 0.002 PHE A 218 TRP 0.002 0.000 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3281) covalent geometry : angle 0.50954 ( 4454) hydrogen bonds : bond 0.04225 ( 256) hydrogen bonds : angle 4.60346 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.155 Fit side-chains REVERT: A 103 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7103 (mm) REVERT: A 165 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7131 (pttm) REVERT: A 356 ARG cc_start: 0.8460 (mtt180) cc_final: 0.7404 (mtm180) REVERT: A 471 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6597 (mt-10) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.5554 time to fit residues: 37.1622 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126935 restraints weight = 3182.258| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.44 r_work: 0.3198 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3281 Z= 0.138 Angle : 0.515 4.993 4454 Z= 0.269 Chirality : 0.039 0.146 566 Planarity : 0.003 0.025 544 Dihedral : 3.564 12.619 448 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.98 % Allowed : 20.34 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.39), residues: 421 helix: 1.67 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -0.54 (0.57), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.008 0.001 TYR A 373 PHE 0.011 0.002 PHE A 218 TRP 0.001 0.000 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3281) covalent geometry : angle 0.51468 ( 4454) hydrogen bonds : bond 0.04204 ( 256) hydrogen bonds : angle 4.65458 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.131 Fit side-chains REVERT: A 103 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7111 (mm) REVERT: A 165 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7151 (pttm) REVERT: A 235 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8179 (tt) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.5398 time to fit residues: 33.3125 Evaluate side-chains 59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.162823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122231 restraints weight = 3189.060| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.62 r_work: 0.3173 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3281 Z= 0.141 Angle : 0.523 5.656 4454 Z= 0.273 Chirality : 0.039 0.147 566 Planarity : 0.003 0.025 544 Dihedral : 3.584 12.700 448 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.26 % Allowed : 19.77 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.39), residues: 421 helix: 1.64 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -0.55 (0.57), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.008 0.001 TYR A 373 PHE 0.011 0.002 PHE A 240 TRP 0.001 0.000 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3281) covalent geometry : angle 0.52333 ( 4454) hydrogen bonds : bond 0.04256 ( 256) hydrogen bonds : angle 4.68300 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.42 seconds wall clock time: 28 minutes 36.84 seconds (1716.84 seconds total)