Starting phenix.real_space_refine on Wed Mar 5 18:19:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d68_46589/03_2025/9d68_46589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d68_46589/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9d68_46589/03_2025/9d68_46589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d68_46589/03_2025/9d68_46589.map" model { file = "/net/cci-nas-00/data/ceres_data/9d68_46589/03_2025/9d68_46589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d68_46589/03_2025/9d68_46589.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.86, per 1000 atoms: 0.88 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: 0.77 Conformation dependent library (CDL) restraints added in 450.8 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: 0.33 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: 0.91 Time building geometry restraints manager: 0.92 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: 1.330 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- 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= 0.196 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (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 TRP 0.008 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.005 0.001 PHE A 218 TYR 0.006 0.001 TYR A 373 ARG 0.003 0.000 ARG A 356 *********************** 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 : 0.386 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: 1.2004 time to fit residues: 69.3304 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 : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.161263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121785 restraints weight = 3212.840| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.58 r_work: 0.3169 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1559 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= 0.176 Angle : 0.512 4.967 4454 Z= 0.274 Chirality : 0.039 0.145 566 Planarity : 0.004 0.026 544 Dihedral : 3.551 12.781 448 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.39), residues: 421 helix: 1.87 (0.27), residues: 333 sheet: None (None), residues: 0 loop : -0.56 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 19 HIS 0.000 0.000 HIS A 296 PHE 0.013 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.002 0.000 ARG A 356 *********************** 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 : 0.342 Fit side-chains REVERT: A 83 ASP cc_start: 0.7263 (m-30) cc_final: 0.7055 (m-30) REVERT: A 103 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7102 (mm) REVERT: A 165 LYS cc_start: 0.7794 (mtmm) cc_final: 0.7224 (pttm) outliers start: 9 outliers final: 3 residues processed: 66 average time/residue: 1.0550 time to fit residues: 71.9361 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 : 0.375 ------------------------------------------------------------------------------- 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 5 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.161321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120881 restraints weight = 3164.117| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.62 r_work: 0.3131 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1703 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= 0.206 Angle : 0.505 4.881 4454 Z= 0.266 Chirality : 0.040 0.155 566 Planarity : 0.004 0.026 544 Dihedral : 3.577 12.230 448 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.82 % Allowed : 16.95 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.39), residues: 421 helix: 1.81 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.53 (0.58), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.012 0.002 PHE A 218 TYR 0.006 0.001 TYR A 162 ARG 0.001 0.000 ARG A 61 *********************** 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: 10 poor density : 56 time to evaluate : 0.377 Fit side-chains REVERT: A 83 ASP cc_start: 0.7282 (m-30) cc_final: 0.7049 (m-30) REVERT: A 165 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7217 (pttm) REVERT: A 199 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6202 (pm20) outliers start: 10 outliers final: 3 residues processed: 64 average time/residue: 1.2126 time to fit residues: 79.9939 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 : 0.300 ------------------------------------------------------------------------------- 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 199 GLU 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 20 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.162863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122647 restraints weight = 3168.688| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.62 r_work: 0.3162 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3281 Z= 0.172 Angle : 0.483 4.856 4454 Z= 0.253 Chirality : 0.039 0.146 566 Planarity : 0.003 0.027 544 Dihedral : 3.513 12.000 448 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.67 % Allowed : 17.23 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.39), residues: 421 helix: 1.91 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.39 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.012 0.001 PHE A 218 TYR 0.006 0.001 TYR A 162 ARG 0.001 0.000 ARG A 93 *********************** 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: 13 poor density : 56 time to evaluate : 0.370 Fit side-chains REVERT: A 103 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7109 (mm) REVERT: A 165 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7189 (pttm) outliers start: 13 outliers final: 4 residues processed: 64 average time/residue: 1.1725 time to fit residues: 77.3857 Evaluate side-chains 60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.0030 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 = 0.162550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122249 restraints weight = 3154.294| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.63 r_work: 0.3163 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1928 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= 0.179 Angle : 0.489 4.977 4454 Z= 0.256 Chirality : 0.039 0.144 566 Planarity : 0.003 0.029 544 Dihedral : 3.512 12.165 448 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.24 % Allowed : 18.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.39), residues: 421 helix: 1.89 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.36 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.002 PHE A 218 TYR 0.006 0.001 TYR A 373 ARG 0.001 0.000 ARG A 39 *********************** 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 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.382 Fit side-chains REVERT: A 103 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7090 (mm) REVERT: A 165 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7129 (pttm) outliers start: 15 outliers final: 5 residues processed: 65 average time/residue: 1.1976 time to fit residues: 80.3690 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 : 0.370 ------------------------------------------------------------------------------- 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 145 LEU 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 37 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.162832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126341 restraints weight = 3228.671| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.47 r_work: 0.3155 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2022 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= 0.174 Angle : 0.483 4.945 4454 Z= 0.253 Chirality : 0.039 0.155 566 Planarity : 0.003 0.028 544 Dihedral : 3.502 12.148 448 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.11 % Allowed : 19.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.39), residues: 421 helix: 1.94 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.36 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.002 PHE A 218 TYR 0.006 0.001 TYR A 373 ARG 0.002 0.000 ARG A 39 *********************** 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 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.340 Fit side-chains REVERT: A 103 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7110 (mm) REVERT: A 165 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7131 (pttm) outliers start: 11 outliers final: 5 residues processed: 63 average time/residue: 1.0989 time to fit residues: 71.4488 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 : 0.382 ------------------------------------------------------------------------------- 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 145 LEU 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 2 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.163185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122695 restraints weight = 3123.050| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.62 r_work: 0.3181 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2031 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= 0.172 Angle : 0.482 4.956 4454 Z= 0.252 Chirality : 0.039 0.151 566 Planarity : 0.003 0.027 544 Dihedral : 3.493 12.210 448 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.39), residues: 421 helix: 1.93 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.34 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 218 TYR 0.007 0.001 TYR A 373 ARG 0.001 0.000 ARG A 39 *********************** 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: 10 poor density : 56 time to evaluate : 0.355 Fit side-chains REVERT: A 103 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7101 (mm) REVERT: A 165 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7151 (pttm) outliers start: 10 outliers final: 4 residues processed: 64 average time/residue: 1.0984 time to fit residues: 72.5308 Evaluate side-chains 61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.163559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123192 restraints weight = 3122.860| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.63 r_work: 0.3173 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3281 Z= 0.175 Angle : 0.493 5.141 4454 Z= 0.256 Chirality : 0.038 0.149 566 Planarity : 0.003 0.026 544 Dihedral : 3.510 12.177 448 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.98 % Allowed : 20.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.39), residues: 421 helix: 1.92 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.36 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 218 TYR 0.008 0.001 TYR A 373 ARG 0.004 0.000 ARG A 39 *********************** 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: 7 poor density : 56 time to evaluate : 0.372 Fit side-chains REVERT: A 103 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7094 (mm) REVERT: A 165 LYS cc_start: 0.7734 (mtmm) cc_final: 0.7166 (pttm) REVERT: A 216 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8474 (mt) REVERT: A 235 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8190 (tt) REVERT: A 356 ARG cc_start: 0.8466 (mtt180) cc_final: 0.7389 (mtm180) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 1.1439 time to fit residues: 73.1934 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 235 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 21 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.163097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123292 restraints weight = 3175.873| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.60 r_work: 0.3211 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3281 Z= 0.178 Angle : 0.492 4.956 4454 Z= 0.256 Chirality : 0.039 0.149 566 Planarity : 0.003 0.026 544 Dihedral : 3.514 12.256 448 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.26 % Allowed : 20.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.39), residues: 421 helix: 1.93 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -0.48 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 218 TYR 0.009 0.001 TYR A 373 ARG 0.001 0.000 ARG A 39 *********************** 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 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.362 Fit side-chains REVERT: A 103 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7100 (mm) REVERT: A 165 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7149 (pttm) REVERT: A 216 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8460 (mt) REVERT: A 235 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8188 (tt) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 1.1368 time to fit residues: 71.5873 Evaluate side-chains 60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.163587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127855 restraints weight = 3162.408| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.44 r_work: 0.3191 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2170 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= 0.174 Angle : 0.500 6.248 4454 Z= 0.258 Chirality : 0.038 0.147 566 Planarity : 0.003 0.026 544 Dihedral : 3.501 12.329 448 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.98 % Allowed : 20.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.39), residues: 421 helix: 1.92 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -0.54 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 19 HIS 0.000 0.000 HIS A 41 PHE 0.011 0.001 PHE A 218 TYR 0.009 0.001 TYR A 373 ARG 0.003 0.000 ARG A 356 ********************** 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 : 0.339 Fit side-chains REVERT: A 103 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7129 (mm) REVERT: A 165 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7176 (pttm) REVERT: A 216 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 235 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8186 (tt) REVERT: A 419 MET cc_start: 0.7846 (ttm) cc_final: 0.7279 (mmm) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 1.0704 time to fit residues: 66.3320 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 : 0.346 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.0040 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.164585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124111 restraints weight = 3082.377| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.61 r_work: 0.3202 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2209 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= 0.165 Angle : 0.492 5.701 4454 Z= 0.254 Chirality : 0.038 0.145 566 Planarity : 0.003 0.026 544 Dihedral : 3.468 12.277 448 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.26 % Allowed : 20.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.39), residues: 421 helix: 1.93 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -0.51 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.011 0.001 PHE A 218 TYR 0.009 0.001 TYR A 373 ARG 0.003 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3158.81 seconds wall clock time: 54 minutes 45.87 seconds (3285.87 seconds total)