Starting phenix.real_space_refine on Wed Mar 5 17:43:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xtk_33451/03_2025/7xtk_33451_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xtk_33451/03_2025/7xtk_33451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xtk_33451/03_2025/7xtk_33451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xtk_33451/03_2025/7xtk_33451.map" model { file = "/net/cci-nas-00/data/ceres_data/7xtk_33451/03_2025/7xtk_33451_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xtk_33451/03_2025/7xtk_33451_neut.cif" } resolution = 2.89 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= -0.001 sd= 0.062 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2105 2.51 5 N 516 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 3159 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3159 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 13, 'TRANS': 381} Chain breaks: 1 Time building chain proxies: 3.11, per 1000 atoms: 0.98 Number of scatterers: 3159 At special positions: 0 Unit cell: (72.165, 54.336, 73.014, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 528 8.00 N 516 7.00 C 2105 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: 0.75 Conformation dependent library (CDL) restraints added in 349.0 milliseconds 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 69 through 91 removed outlier: 4.200A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.672A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 112 removed outlier: 4.155A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 111 " --> pdb=" O TRP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 133 removed outlier: 3.899A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 148 through 176 removed outlier: 3.510A pdb=" N LEU A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.748A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 266 through 288 removed outlier: 3.802A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.769A pdb=" N GLU A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 324 Processing helix chain 'A' and resid 336 through 355 removed outlier: 3.542A pdb=" N LEU A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 388 removed outlier: 3.835A pdb=" N CYS A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 369 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.734A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 453 217 hydrogen bonds defined for protein. 651 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: 0.82 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 935 1.34 - 1.46: 745 1.46 - 1.58: 1549 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3245 Sorted by residual: bond pdb=" C MET A 254 " pdb=" N LEU A 255 " ideal model delta sigma weight residual 1.332 1.294 0.038 1.40e-02 5.10e+03 7.37e+00 bond pdb=" CB ARG A 205 " pdb=" CG ARG A 205 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.99e+00 bond pdb=" C VAL A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.54e+00 bond pdb=" CG LEU A 258 " pdb=" CD2 LEU A 258 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" C LEU A 251 " pdb=" O LEU A 251 " ideal model delta sigma weight residual 1.233 1.250 -0.018 1.47e-02 4.63e+03 1.45e+00 ... (remaining 3240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 4320 2.31 - 4.62: 87 4.62 - 6.92: 12 6.92 - 9.23: 2 9.23 - 11.54: 2 Bond angle restraints: 4423 Sorted by residual: angle pdb=" N ARG A 333 " pdb=" CA ARG A 333 " pdb=" C ARG A 333 " ideal model delta sigma weight residual 114.64 103.10 11.54 1.52e+00 4.33e-01 5.76e+01 angle pdb=" N ARG A 205 " pdb=" CA ARG A 205 " pdb=" C ARG A 205 " ideal model delta sigma weight residual 110.13 115.16 -5.03 1.15e+00 7.56e-01 1.91e+01 angle pdb=" N VAL A 327 " pdb=" CA VAL A 327 " pdb=" C VAL A 327 " ideal model delta sigma weight residual 106.21 110.71 -4.50 1.07e+00 8.73e-01 1.77e+01 angle pdb=" N ARG A 148 " pdb=" CA ARG A 148 " pdb=" C ARG A 148 " ideal model delta sigma weight residual 114.64 108.47 6.17 1.52e+00 4.33e-01 1.65e+01 angle pdb=" CA ARG A 333 " pdb=" C ARG A 333 " pdb=" N TRP A 334 " ideal model delta sigma weight residual 119.58 114.22 5.36 1.39e+00 5.18e-01 1.48e+01 ... (remaining 4418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 1668 16.46 - 32.91: 160 32.91 - 49.37: 29 49.37 - 65.83: 6 65.83 - 82.28: 2 Dihedral angle restraints: 1865 sinusoidal: 703 harmonic: 1162 Sorted by residual: dihedral pdb=" CA ALA A 252 " pdb=" C ALA A 252 " pdb=" N ARG A 253 " pdb=" CA ARG A 253 " ideal model delta harmonic sigma weight residual 180.00 -145.79 -34.21 0 5.00e+00 4.00e-02 4.68e+01 dihedral pdb=" CA LEU A 255 " pdb=" C LEU A 255 " pdb=" N ARG A 256 " pdb=" CA ARG A 256 " ideal model delta harmonic sigma weight residual 180.00 152.93 27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 1862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 397 0.046 - 0.092: 105 0.092 - 0.137: 16 0.137 - 0.183: 0 0.183 - 0.229: 1 Chirality restraints: 519 Sorted by residual: chirality pdb=" CA PHE A 202 " pdb=" N PHE A 202 " pdb=" C PHE A 202 " pdb=" CB PHE A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA THR A 49 " pdb=" N THR A 49 " pdb=" C THR A 49 " pdb=" CB THR A 49 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA TRP A 107 " pdb=" N TRP A 107 " pdb=" C TRP A 107 " pdb=" CB TRP A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 516 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 254 " 0.026 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C MET A 254 " -0.091 2.00e-02 2.50e+03 pdb=" O MET A 254 " 0.035 2.00e-02 2.50e+03 pdb=" N LEU A 255 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " -0.056 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A 82 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO A 70 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.038 5.00e-02 4.00e+02 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 13 2.48 - 3.08: 2206 3.08 - 3.69: 4527 3.69 - 4.29: 7039 4.29 - 4.90: 11724 Nonbonded interactions: 25509 Sorted by model distance: nonbonded pdb=" O ARG A 253 " pdb=" N LEU A 255 " model vdw 1.873 3.120 nonbonded pdb=" O TYR A 139 " pdb=" NH2 ARG A 205 " model vdw 2.099 3.120 nonbonded pdb=" O PRO A 43 " pdb=" OG SER A 189 " model vdw 2.195 3.040 nonbonded pdb=" O ILE A 41 " pdb=" OG SER A 167 " model vdw 2.201 3.040 nonbonded pdb=" O LEU A 251 " pdb=" O ARG A 253 " model vdw 2.263 3.040 ... (remaining 25504 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: 4.220 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: 0.020 Set scattering table: 0.030 Process input model: 12.960 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.004 0.060 3245 Z= 0.267 Angle : 0.872 11.540 4423 Z= 0.539 Chirality : 0.041 0.229 519 Planarity : 0.008 0.087 534 Dihedral : 13.372 82.282 1119 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 1.28 % Allowed : 6.39 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.05 (0.43), residues: 391 helix: 0.43 (0.31), residues: 298 sheet: None (None), residues: 0 loop : -4.46 (0.50), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 289 PHE 0.015 0.001 PHE A 84 TYR 0.025 0.002 TYR A 139 ARG 0.007 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.7631 time to fit residues: 28.2056 Evaluate side-chains 28 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 15 optimal weight: 0.0970 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.2114 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.150787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126640 restraints weight = 3344.934| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.86 r_work: 0.3416 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3245 Z= 0.196 Angle : 0.669 8.355 4423 Z= 0.348 Chirality : 0.039 0.187 519 Planarity : 0.007 0.065 534 Dihedral : 5.294 26.696 440 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 1.02 % Allowed : 6.14 % Favored : 92.84 % Rotamer: Outliers : 0.88 % Allowed : 5.90 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.44), residues: 391 helix: 1.14 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -4.41 (0.52), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 PHE 0.008 0.001 PHE A 372 TYR 0.014 0.001 TYR A 139 ARG 0.004 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.413 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 39 average time/residue: 0.6642 time to fit residues: 27.4279 Evaluate side-chains 30 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124329 restraints weight = 3384.811| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.79 r_work: 0.3381 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3245 Z= 0.220 Angle : 0.636 8.123 4423 Z= 0.328 Chirality : 0.039 0.178 519 Planarity : 0.006 0.059 534 Dihedral : 5.206 30.949 440 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 1.02 % Allowed : 5.88 % Favored : 93.09 % Rotamer: Outliers : 0.88 % Allowed : 7.08 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.45), residues: 391 helix: 1.33 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -4.20 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.012 0.001 PHE A 372 TYR 0.015 0.001 TYR A 139 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.330 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.7921 time to fit residues: 32.4458 Evaluate side-chains 34 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.0070 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130257 restraints weight = 3458.215| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.75 r_work: 0.3435 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3245 Z= 0.182 Angle : 0.572 6.548 4423 Z= 0.299 Chirality : 0.037 0.170 519 Planarity : 0.005 0.055 534 Dihedral : 5.060 29.798 440 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.37 % Favored : 93.86 % Rotamer: Outliers : 1.77 % Allowed : 8.85 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.45), residues: 391 helix: 1.56 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -4.17 (0.53), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.009 0.001 PHE A 372 TYR 0.013 0.001 TYR A 139 ARG 0.005 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.315 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 0.7145 time to fit residues: 28.7938 Evaluate side-chains 32 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.3980 chunk 7 optimal weight: 0.0970 chunk 15 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 overall best weight: 0.2578 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.154471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131201 restraints weight = 3474.733| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.81 r_work: 0.3438 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3245 Z= 0.172 Angle : 0.551 6.534 4423 Z= 0.287 Chirality : 0.037 0.161 519 Planarity : 0.005 0.053 534 Dihedral : 4.856 28.711 440 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.88 % Favored : 93.35 % Rotamer: Outliers : 1.77 % Allowed : 9.73 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.45), residues: 391 helix: 1.59 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.98 (0.54), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.009 0.001 PHE A 372 TYR 0.011 0.001 TYR A 139 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.327 Fit side-chains REVERT: A 352 LEU cc_start: 0.8279 (tp) cc_final: 0.8040 (tp) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 0.6608 time to fit residues: 26.6574 Evaluate side-chains 31 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.0010 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126371 restraints weight = 3533.056| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.83 r_work: 0.3372 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3245 Z= 0.233 Angle : 0.605 7.874 4423 Z= 0.309 Chirality : 0.039 0.169 519 Planarity : 0.005 0.052 534 Dihedral : 4.956 29.024 440 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.16 % Favored : 92.07 % Rotamer: Outliers : 1.47 % Allowed : 10.32 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.45), residues: 391 helix: 1.55 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.98 (0.55), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.001 HIS A 355 PHE 0.014 0.001 PHE A 202 TYR 0.018 0.001 TYR A 139 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.320 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 0.7184 time to fit residues: 27.3470 Evaluate side-chains 33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 35 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 = 0.3704 r_free = 0.3704 target = 0.147374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124084 restraints weight = 3475.073| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.81 r_work: 0.3340 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3245 Z= 0.259 Angle : 0.630 9.264 4423 Z= 0.320 Chirality : 0.040 0.172 519 Planarity : 0.005 0.051 534 Dihedral : 5.018 28.822 440 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 1.02 % Allowed : 6.65 % Favored : 92.33 % Rotamer: Outliers : 1.47 % Allowed : 11.80 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.45), residues: 391 helix: 1.54 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -3.96 (0.55), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.012 0.001 PHE A 372 TYR 0.019 0.002 TYR A 139 ARG 0.006 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.333 Fit side-chains REVERT: A 58 ASN cc_start: 0.8650 (m-40) cc_final: 0.8389 (m-40) outliers start: 5 outliers final: 2 residues processed: 34 average time/residue: 0.7768 time to fit residues: 27.8698 Evaluate side-chains 31 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.0040 chunk 26 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.148064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124999 restraints weight = 3498.971| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.82 r_work: 0.3349 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3245 Z= 0.229 Angle : 0.610 9.638 4423 Z= 0.311 Chirality : 0.039 0.167 519 Planarity : 0.005 0.050 534 Dihedral : 5.001 28.381 440 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.16 % Favored : 92.07 % Rotamer: Outliers : 2.06 % Allowed : 11.21 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.45), residues: 391 helix: 1.59 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -3.91 (0.56), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.001 HIS A 355 PHE 0.013 0.001 PHE A 212 TYR 0.018 0.001 TYR A 139 ARG 0.007 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.314 Fit side-chains REVERT: A 40 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7483 (mm-40) REVERT: A 58 ASN cc_start: 0.8673 (m-40) cc_final: 0.8408 (m-40) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 0.8066 time to fit residues: 29.7244 Evaluate side-chains 32 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 138 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.145825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122569 restraints weight = 3557.217| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.83 r_work: 0.3313 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3245 Z= 0.283 Angle : 0.637 9.792 4423 Z= 0.323 Chirality : 0.040 0.172 519 Planarity : 0.005 0.050 534 Dihedral : 5.049 29.120 440 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.16 % Favored : 92.07 % Rotamer: Outliers : 1.47 % Allowed : 12.09 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.45), residues: 391 helix: 1.52 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -3.89 (0.56), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.014 0.001 PHE A 202 TYR 0.023 0.002 TYR A 139 ARG 0.008 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.332 Fit side-chains REVERT: A 58 ASN cc_start: 0.8648 (m-40) cc_final: 0.8382 (m-40) REVERT: A 148 ARG cc_start: 0.6043 (ttt180) cc_final: 0.5618 (mtm180) REVERT: A 303 ARG cc_start: 0.7920 (mtp85) cc_final: 0.7617 (mtp-110) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 1.0695 time to fit residues: 38.8548 Evaluate side-chains 32 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 138 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.146119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122990 restraints weight = 3486.868| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.81 r_work: 0.3324 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3245 Z= 0.264 Angle : 0.616 8.267 4423 Z= 0.314 Chirality : 0.040 0.168 519 Planarity : 0.005 0.051 534 Dihedral : 5.027 28.935 440 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.42 % Favored : 91.82 % Rotamer: Outliers : 1.18 % Allowed : 12.68 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.44), residues: 391 helix: 1.53 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -3.88 (0.56), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 358 PHE 0.012 0.001 PHE A 372 TYR 0.020 0.001 TYR A 139 ARG 0.008 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.356 Fit side-chains REVERT: A 40 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7435 (mm-40) REVERT: A 58 ASN cc_start: 0.8589 (m-40) cc_final: 0.8324 (m-40) outliers start: 4 outliers final: 2 residues processed: 32 average time/residue: 0.7479 time to fit residues: 25.2374 Evaluate side-chains 31 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 138 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120364 restraints weight = 3477.903| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.85 r_work: 0.3345 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3245 Z= 0.225 Angle : 0.597 10.156 4423 Z= 0.303 Chirality : 0.039 0.162 519 Planarity : 0.005 0.050 534 Dihedral : 4.928 28.466 440 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.42 % Favored : 92.07 % Rotamer: Outliers : 1.18 % Allowed : 13.27 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.45), residues: 391 helix: 1.71 (0.31), residues: 300 sheet: None (None), residues: 0 loop : -3.69 (0.56), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.001 HIS A 358 PHE 0.011 0.001 PHE A 372 TYR 0.016 0.001 TYR A 139 ARG 0.007 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.39 seconds wall clock time: 40 minutes 11.40 seconds (2411.40 seconds total)