Starting phenix.real_space_refine on Wed Jul 1 21:56:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d68_46589/07_2026/9d68_46589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d68_46589/07_2026/9d68_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9d68_46589/07_2026/9d68_46589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d68_46589/07_2026/9d68_46589.map" model { file = "/net/cci-nas-00/data/ceres_data/9d68_46589/07_2026/9d68_46589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d68_46589/07_2026/9d68_46589.cif" } 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-dev-6108/lib/python3.11/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, 6 Ad-hoc single atom residues: {' NA': 2} Classifications: {'water': 6} Link IDs: {None: 5} Chain breaks: 2 Time building chain proxies: 1.04, per 1000 atoms: 0.32 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: 0.27 Conformation dependent library (CDL) restraints added in 117.4 milliseconds 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: 0.09 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: 0.55 Time building geometry restraints manager: 0.36 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 3.210 nonbonded pdb=" O TYR A 98 " pdb="NA NA A 603 " model vdw 2.143 3.210 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.149 3.210 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 2.174 3.210 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: 2.590 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.200 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 are 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/Z covalent geometry : bond 0.00311 / 0.19 ( 3281) covalent geometry : angle 0.54907 / 0.33 ( 4454) hydrogen bonds : bond 0.21507 / 14.35 ( 256) hydrogen bonds : angle 7.20762 / 5.52 ( 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 : 0.091 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: 0.5428 time to fit residues: 31.3073 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 : 0.116 ------------------------------------------------------------------------------- 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: 0.6980 chunk 31 optimal weight: 0.0670 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3830 r_free = 0.3830 target = 0.162312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121964 restraints weight = 3160.375| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.61 r_work: 0.3172 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3281 Z= 0.142 Angle : 0.518 4.766 4454 Z= 0.279 Chirality : 0.039 0.146 566 Planarity : 0.004 0.027 544 Dihedral : 3.652 13.282 448 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.82 % Allowed : 16.38 % Favored : 80.79 % 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 are not related in a simple way. whole: 2.11 (0.39), residues: 421 helix: 1.87 (0.27), residues: 330 sheet: None (None), residues: 0 loop : -0.28 (0.60), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.006 0.001 TYR A 162 PHE 0.013 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/Z covalent geometry : bond 0.00307 / 0.14 ( 3281) covalent geometry : angle 0.51828 / 0.28 ( 4454) hydrogen bonds : bond 0.04832 / 3.20 ( 256) hydrogen bonds : angle 4.99263 / 3.87 ( 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 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.125 Fit side-chains REVERT: A 83 ASP cc_start: 0.7307 (m-30) cc_final: 0.7090 (m-30) REVERT: A 165 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7238 (pttm) REVERT: A 290 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8224 (mm) outliers start: 10 outliers final: 2 residues processed: 68 average time/residue: 0.4353 time to fit residues: 30.5532 Evaluate side-chains 59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.070 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- 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: 0.9980 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.0030 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.164865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124802 restraints weight = 3151.972| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.62 r_work: 0.3210 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3281 Z= 0.122 Angle : 0.486 4.941 4454 Z= 0.256 Chirality : 0.039 0.147 566 Planarity : 0.004 0.026 544 Dihedral : 3.456 11.283 448 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.54 % Allowed : 17.51 % 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 are not related in a simple way. whole: 2.11 (0.39), residues: 421 helix: 1.89 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.51 (0.59), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 61 TYR 0.006 0.001 TYR A 373 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/Z covalent geometry : bond 0.00258 / 0.12 ( 3281) covalent geometry : angle 0.48606 / 0.26 ( 4454) hydrogen bonds : bond 0.04300 / 2.83 ( 256) hydrogen bonds : angle 4.66861 / 3.62 ( 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 : 0.073 Fit side-chains REVERT: A 83 ASP cc_start: 0.7250 (m-30) cc_final: 0.7022 (m-30) REVERT: A 165 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7201 (pttm) REVERT: A 290 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8202 (mm) outliers start: 9 outliers final: 2 residues processed: 62 average time/residue: 0.4027 time to fit residues: 25.6961 Evaluate side-chains 58 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.161245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120597 restraints weight = 3137.616| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.62 r_work: 0.3151 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3281 Z= 0.152 Angle : 0.509 4.934 4454 Z= 0.270 Chirality : 0.040 0.150 566 Planarity : 0.004 0.030 544 Dihedral : 3.639 12.526 448 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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 are not related in a simple way. whole: 1.92 (0.39), residues: 421 helix: 1.76 (0.27), residues: 336 sheet: None (None), residues: 0 loop : -0.63 (0.58), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.007 0.001 TYR A 373 PHE 0.012 0.002 PHE A 218 TRP 0.004 0.001 TRP A 19 HIS 0.001 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 3281) covalent geometry : angle 0.50853 / 0.27 ( 4454) hydrogen bonds : bond 0.04624 / 3.02 ( 256) hydrogen bonds : angle 4.74769 / 3.66 ( 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 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.075 Fit side-chains REVERT: A 199 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6197 (pm20) REVERT: A 467 LYS cc_start: 0.7269 (ttpt) cc_final: 0.6827 (ttmt) outliers start: 12 outliers final: 5 residues processed: 66 average time/residue: 0.4006 time to fit residues: 27.2744 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 : 0.078 ------------------------------------------------------------------------------- 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 145 LEU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 244 SER 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: 0.0870 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.0060 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.166100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130126 restraints weight = 3158.023| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.46 r_work: 0.3249 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2215 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= 0.111 Angle : 0.469 4.904 4454 Z= 0.246 Chirality : 0.038 0.138 566 Planarity : 0.003 0.027 544 Dihedral : 3.475 12.569 448 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.82 % Allowed : 20.06 % 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 are not related in a simple way. whole: 2.27 (0.39), residues: 421 helix: 2.01 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.40 (0.57), residues: 89 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 0.001 PHE A 218 TRP 0.004 0.001 TRP A 19 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 3281) covalent geometry : angle 0.46904 / 0.25 ( 4454) hydrogen bonds : bond 0.03902 / 2.56 ( 256) hydrogen bonds : angle 4.48241 / 3.48 ( 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 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.115 Fit side-chains REVERT: A 83 ASP cc_start: 0.7268 (m-30) cc_final: 0.7022 (m-30) REVERT: A 165 LYS cc_start: 0.7734 (mtmm) cc_final: 0.7156 (pttm) REVERT: A 216 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8418 (mt) REVERT: A 290 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8174 (mm) outliers start: 10 outliers final: 2 residues processed: 64 average time/residue: 0.4346 time to fit residues: 28.6220 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 : 0.068 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 6 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127530 restraints weight = 3214.992| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.45 r_work: 0.3213 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3281 Z= 0.134 Angle : 0.492 4.941 4454 Z= 0.258 Chirality : 0.039 0.155 566 Planarity : 0.003 0.029 544 Dihedral : 3.546 12.577 448 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.39 % Allowed : 19.77 % Favored : 76.84 % 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 are not related in a simple way. whole: 2.13 (0.39), residues: 421 helix: 1.92 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.45 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.009 0.001 TYR A 373 PHE 0.011 0.002 PHE A 218 TRP 0.003 0.000 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 3281) covalent geometry : angle 0.49188 / 0.26 ( 4454) hydrogen bonds : bond 0.04234 / 2.75 ( 256) hydrogen bonds : angle 4.58007 / 3.54 ( 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 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.082 Fit side-chains REVERT: A 165 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7202 (pttm) REVERT: A 467 LYS cc_start: 0.7267 (ttpt) cc_final: 0.6814 (ttmt) outliers start: 12 outliers final: 4 residues processed: 65 average time/residue: 0.4037 time to fit residues: 27.0482 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 : 0.069 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128938 restraints weight = 3202.283| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.47 r_work: 0.3214 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3281 Z= 0.118 Angle : 0.478 4.916 4454 Z= 0.250 Chirality : 0.038 0.147 566 Planarity : 0.003 0.027 544 Dihedral : 3.492 12.859 448 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.54 % Allowed : 20.62 % Favored : 76.84 % 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 are not related in a simple way. whole: 2.18 (0.39), residues: 421 helix: 1.96 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.49 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.009 0.001 TYR A 373 PHE 0.011 0.001 PHE A 218 TRP 0.003 0.001 TRP A 276 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 3281) covalent geometry : angle 0.47847 / 0.25 ( 4454) hydrogen bonds : bond 0.03985 / 2.60 ( 256) hydrogen bonds : angle 4.49530 / 3.48 ( 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 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.122 Fit side-chains REVERT: A 165 LYS cc_start: 0.7715 (mtmm) cc_final: 0.7094 (pttm) REVERT: A 216 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8451 (mt) REVERT: A 235 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8186 (tt) outliers start: 9 outliers final: 4 residues processed: 63 average time/residue: 0.4136 time to fit residues: 26.9473 Evaluate side-chains 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 235 ILE 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: 0.5980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126546 restraints weight = 3191.007| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.47 r_work: 0.3193 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 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 : 0.003 0.033 3281 Z= 0.139 Angle : 0.510 5.014 4454 Z= 0.268 Chirality : 0.039 0.150 566 Planarity : 0.003 0.028 544 Dihedral : 3.564 12.437 448 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.26 % Allowed : 21.19 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.39), residues: 421 helix: 1.88 (0.27), residues: 331 sheet: None (None), residues: 0 loop : -0.63 (0.56), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.009 0.001 TYR A 373 PHE 0.011 0.002 PHE A 218 TRP 0.002 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 3281) covalent geometry : angle 0.51028 / 0.27 ( 4454) hydrogen bonds : bond 0.04256 / 2.77 ( 256) hydrogen bonds : angle 4.63061 / 3.56 ( 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 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.121 Fit side-chains REVERT: A 467 LYS cc_start: 0.7273 (ttpt) cc_final: 0.6812 (ttmt) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.4986 time to fit residues: 32.9109 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 : 0.119 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.163317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127066 restraints weight = 3152.378| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.45 r_work: 0.3185 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3281 Z= 0.138 Angle : 0.516 5.223 4454 Z= 0.273 Chirality : 0.039 0.149 566 Planarity : 0.003 0.027 544 Dihedral : 3.577 12.414 448 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.26 % Allowed : 21.47 % Favored : 76.27 % 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 are not related in a simple way. whole: 1.97 (0.39), residues: 421 helix: 1.82 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -0.59 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.009 0.001 TYR A 373 PHE 0.011 0.002 PHE A 218 TRP 0.002 0.000 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 3281) covalent geometry : angle 0.51588 / 0.27 ( 4454) hydrogen bonds : bond 0.04210 / 2.75 ( 256) hydrogen bonds : angle 4.68222 / 3.60 ( 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 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.119 Fit side-chains REVERT: A 165 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7175 (pttm) REVERT: A 216 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 235 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 356 ARG cc_start: 0.8482 (mtt180) cc_final: 0.7413 (mtm180) REVERT: A 467 LYS cc_start: 0.7242 (ttpt) cc_final: 0.6758 (ttmt) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.5225 time to fit residues: 34.4735 Evaluate side-chains 61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.073 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.0570 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124033 restraints weight = 3127.188| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.60 r_work: 0.3208 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3281 Z= 0.132 Angle : 0.519 4.893 4454 Z= 0.271 Chirality : 0.039 0.147 566 Planarity : 0.003 0.027 544 Dihedral : 3.555 12.319 448 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.98 % Allowed : 21.75 % Favored : 76.27 % 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 are not related in a simple way. whole: 2.00 (0.39), residues: 421 helix: 1.84 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -0.58 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.009 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 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 3281) covalent geometry : angle 0.51867 / 0.27 ( 4454) hydrogen bonds : bond 0.04122 / 2.69 ( 256) hydrogen bonds : angle 4.64773 / 3.57 ( 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 : 0.119 Fit side-chains REVERT: A 165 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7092 (pttm) REVERT: A 235 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8191 (tt) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 0.5060 time to fit residues: 31.8145 Evaluate side-chains 58 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 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 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: 0.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 22 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127103 restraints weight = 3190.972| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.48 r_work: 0.3198 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3281 Z= 0.142 Angle : 0.529 5.620 4454 Z= 0.277 Chirality : 0.040 0.149 566 Planarity : 0.003 0.027 544 Dihedral : 3.603 12.562 448 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.41 % Allowed : 21.47 % 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 are not related in a simple way. whole: 1.93 (0.39), residues: 421 helix: 1.79 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -0.60 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.009 0.001 TYR A 373 PHE 0.011 0.002 PHE A 218 TRP 0.002 0.000 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 3281) covalent geometry : angle 0.52899 / 0.28 ( 4454) hydrogen bonds : bond 0.04257 / 2.77 ( 256) hydrogen bonds : angle 4.70038 / 3.61 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1411.89 seconds wall clock time: 24 minutes 50.61 seconds (1490.61 seconds total)