Starting phenix.real_space_refine on Mon Feb 10 23:17:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d68_46589/02_2025/9d68_46589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d68_46589/02_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_46589/02_2025/9d68_46589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d68_46589/02_2025/9d68_46589.map" model { file = "/net/cci-nas-00/data/ceres_data/9d68_46589/02_2025/9d68_46589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d68_46589/02_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-5592/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: 2.90, per 1000 atoms: 0.89 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: 0.78 Conformation dependent library (CDL) restraints added in 375.6 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: 0.31 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: 0.87 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: 1.300 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.310 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.690 ------------------------------------------------------------------------------- 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 : 0.340 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: 1.1831 time to fit residues: 68.4261 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 : 0.373 ------------------------------------------------------------------------------- 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): 0.3315 rms_B_bonded: 1.58 r_work: 0.3175 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 : 0.369 Fit side-chains REVERT: A 83 ASP cc_start: 0.7261 (m-30) cc_final: 0.7052 (m-30) REVERT: A 103 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7098 (mm) REVERT: A 165 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7219 (pttm) outliers start: 9 outliers final: 3 residues processed: 66 average time/residue: 1.0522 time to fit residues: 71.9416 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 : 0.355 ------------------------------------------------------------------------------- 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: 0.6980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 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 = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120941 restraints weight = 3164.117| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.62 r_work: 0.3132 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.362 Fit side-chains REVERT: A 83 ASP cc_start: 0.7284 (m-30) cc_final: 0.7052 (m-30) REVERT: A 165 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7220 (pttm) REVERT: A 199 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6211 (pm20) outliers start: 10 outliers final: 3 residues processed: 64 average time/residue: 1.1774 time to fit residues: 77.7010 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 : 0.389 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.162117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121893 restraints weight = 3165.507| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.62 r_work: 0.3152 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3281 Z= 0.184 Angle : 0.490 4.864 4454 Z= 0.257 Chirality : 0.039 0.148 566 Planarity : 0.004 0.028 544 Dihedral : 3.545 12.131 448 Min Nonbonded Distance : 2.134 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: 1.99 (0.39), residues: 421 helix: 1.82 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.62 (0.57), residues: 86 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 0.002 PHE A 218 TYR 0.006 0.001 TYR A 162 ARG 0.001 0.000 ARG A 61 *********************** 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 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.366 Fit side-chains REVERT: A 103 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7067 (mm) REVERT: A 165 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7195 (pttm) outliers start: 13 outliers final: 4 residues processed: 66 average time/residue: 1.1301 time to fit residues: 76.9704 Evaluate side-chains 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121909 restraints weight = 3153.525| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.63 r_work: 0.3152 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3281 Z= 0.188 Angle : 0.493 4.965 4454 Z= 0.258 Chirality : 0.039 0.146 566 Planarity : 0.004 0.030 544 Dihedral : 3.541 12.233 448 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.24 % Allowed : 17.80 % 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 (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: 1.98 (0.39), residues: 421 helix: 1.81 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.58 (0.57), residues: 86 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 0.012 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 : 0.384 Fit side-chains REVERT: A 103 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7124 (mm) outliers start: 15 outliers final: 5 residues processed: 65 average time/residue: 1.1549 time to fit residues: 77.5070 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 : 0.371 ------------------------------------------------------------------------------- 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: 2.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.161301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125641 restraints weight = 3274.361| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.45 r_work: 0.3130 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3281 Z= 0.205 Angle : 0.502 4.952 4454 Z= 0.263 Chirality : 0.039 0.160 566 Planarity : 0.004 0.029 544 Dihedral : 3.585 12.459 448 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.39 % Allowed : 19.21 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.39), residues: 421 helix: 1.78 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.58 (0.57), residues: 86 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 0.012 0.002 PHE A 218 TYR 0.007 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 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.341 Fit side-chains REVERT: A 103 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7115 (mm) REVERT: A 471 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6653 (mt-10) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 1.1386 time to fit residues: 76.2977 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 : 0.389 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 473 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 0.0470 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.164963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124936 restraints weight = 3129.073| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.61 r_work: 0.3198 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3281 Z= 0.145 Angle : 0.473 4.974 4454 Z= 0.246 Chirality : 0.038 0.148 566 Planarity : 0.003 0.027 544 Dihedral : 3.445 11.802 448 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.45 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: 2.14 (0.39), residues: 421 helix: 1.92 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.54 (0.57), residues: 86 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 0.006 0.001 TYR A 373 ARG 0.002 0.000 ARG A 356 *********************** 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 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.359 Fit side-chains REVERT: A 103 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7074 (mm) REVERT: A 165 LYS cc_start: 0.7734 (mtmm) cc_final: 0.7095 (pttm) REVERT: A 216 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8465 (mt) REVERT: A 235 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8182 (tt) REVERT: A 290 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8141 (mm) outliers start: 11 outliers final: 3 residues processed: 66 average time/residue: 1.0397 time to fit residues: 70.9838 Evaluate side-chains 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 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 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 39 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7738 ------------------------------------------------------------------------------- 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 = 0.162693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121905 restraints weight = 3115.875| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.62 r_work: 0.3158 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2043 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= 0.192 Angle : 0.495 4.964 4454 Z= 0.259 Chirality : 0.039 0.152 566 Planarity : 0.004 0.028 544 Dihedral : 3.543 12.391 448 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.54 % Allowed : 20.06 % 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: 2.04 (0.39), residues: 421 helix: 1.85 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.57 (0.57), residues: 86 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 0.012 0.002 PHE A 218 TYR 0.013 0.002 TYR A 285 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 65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.379 Fit side-chains REVERT: A 103 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7126 (mm) REVERT: A 165 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7114 (pttm) REVERT: A 467 LYS cc_start: 0.7225 (ttpt) cc_final: 0.6746 (ttmt) outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 1.1616 time to fit residues: 75.4466 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 : 0.355 ------------------------------------------------------------------------------- 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 120 VAL 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: 3.9990 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 17 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 = 0.3837 r_free = 0.3837 target = 0.163108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123212 restraints weight = 3181.794| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.60 r_work: 0.3187 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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= 0.178 Angle : 0.494 5.789 4454 Z= 0.257 Chirality : 0.039 0.149 566 Planarity : 0.003 0.027 544 Dihedral : 3.534 12.520 448 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.98 % Allowed : 21.19 % 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 (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: 2.04 (0.39), residues: 421 helix: 1.87 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.67 (0.56), residues: 86 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 0.013 0.001 TYR A 285 ARG 0.002 0.000 ARG A 356 *********************** 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 61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.408 Fit side-chains REVERT: A 103 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7104 (mm) REVERT: A 165 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7108 (pttm) REVERT: A 235 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8177 (tt) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 1.1270 time to fit residues: 69.8718 Evaluate side-chains 60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 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 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: 0.9980 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.162745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122136 restraints weight = 3108.831| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.62 r_work: 0.3173 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3281 Z= 0.197 Angle : 0.507 5.173 4454 Z= 0.264 Chirality : 0.039 0.151 566 Planarity : 0.004 0.027 544 Dihedral : 3.570 12.644 448 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 1.95 (0.39), residues: 421 helix: 1.80 (0.27), residues: 336 sheet: None (None), residues: 0 loop : -0.72 (0.56), residues: 85 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 0.002 PHE A 218 TYR 0.014 0.002 TYR A 285 ARG 0.002 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: 8 poor density : 53 time to evaluate : 0.397 Fit side-chains REVERT: A 103 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7067 (mm) REVERT: A 165 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7125 (pttm) REVERT: A 235 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8181 (tt) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 1.1793 time to fit residues: 71.7545 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 : 0.324 ------------------------------------------------------------------------------- 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 120 VAL 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: 0.7980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 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 = 0.3842 r_free = 0.3842 target = 0.163666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123179 restraints weight = 3075.921| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.59 r_work: 0.3167 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3281 Z= 0.180 Angle : 0.499 4.950 4454 Z= 0.260 Chirality : 0.039 0.148 566 Planarity : 0.003 0.026 544 Dihedral : 3.528 12.508 448 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.69 % Allowed : 20.62 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.99 (0.39), residues: 421 helix: 1.85 (0.27), residues: 336 sheet: None (None), residues: 0 loop : -0.77 (0.56), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.000 0.000 HIS A 41 PHE 0.011 0.001 PHE A 218 TYR 0.013 0.001 TYR A 285 ARG 0.002 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3135.44 seconds wall clock time: 56 minutes 3.82 seconds (3363.82 seconds total)