Starting phenix.real_space_refine on Mon Feb 10 22:43:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xtk_33451/02_2025/7xtk_33451_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xtk_33451/02_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_33451/02_2025/7xtk_33451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xtk_33451/02_2025/7xtk_33451.map" model { file = "/net/cci-nas-00/data/ceres_data/7xtk_33451/02_2025/7xtk_33451_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xtk_33451/02_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-5592/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: 3.43, per 1000 atoms: 1.09 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: 0.81 Conformation dependent library (CDL) restraints added in 366.9 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: 0.28 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: 0.93 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.970 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- 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 : 0.358 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.7831 time to fit residues: 28.9679 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 : 0.368 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126641 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: 0.3292 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.317 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 39 average time/residue: 0.6762 time to fit residues: 27.9642 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 : 0.344 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.0270 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.153003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129140 restraints weight = 3370.456| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.85 r_work: 0.3456 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3245 Z= 0.188 Angle : 0.606 8.239 4423 Z= 0.313 Chirality : 0.038 0.170 519 Planarity : 0.006 0.058 534 Dihedral : 5.110 30.899 440 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 1.02 % Allowed : 5.88 % Favored : 93.09 % Rotamer: Outliers : 0.88 % Allowed : 7.37 % Favored : 91.74 % 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: 0.32 (0.45), residues: 391 helix: 1.43 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -4.24 (0.53), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.000 HIS A 355 PHE 0.010 0.001 PHE A 372 TYR 0.014 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 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.331 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 0.8072 time to fit residues: 32.2853 Evaluate side-chains 30 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.147712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124021 restraints weight = 3461.001| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.81 r_work: 0.3356 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3245 Z= 0.262 Angle : 0.638 6.918 4423 Z= 0.329 Chirality : 0.040 0.175 519 Planarity : 0.006 0.057 534 Dihedral : 5.193 29.948 440 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 1.02 % Allowed : 7.42 % Favored : 91.56 % Rotamer: Outliers : 1.47 % Allowed : 8.85 % Favored : 89.68 % 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: 0.32 (0.45), residues: 391 helix: 1.40 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -4.13 (0.54), residues: 90 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 0.017 0.001 PHE A 202 TYR 0.018 0.002 TYR A 139 ARG 0.004 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 37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.323 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 36 average time/residue: 0.7530 time to fit residues: 28.6306 Evaluate side-chains 30 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.148514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125186 restraints weight = 3431.123| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.79 r_work: 0.3369 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1454 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= 0.224 Angle : 0.603 6.739 4423 Z= 0.313 Chirality : 0.039 0.173 519 Planarity : 0.005 0.054 534 Dihedral : 5.127 29.612 440 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.39 % Favored : 92.84 % Rotamer: Outliers : 1.18 % Allowed : 10.62 % 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: 0.45 (0.45), residues: 391 helix: 1.46 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -4.11 (0.55), residues: 87 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 0.011 0.001 PHE A 372 TYR 0.020 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 34 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.331 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 34 average time/residue: 0.7840 time to fit residues: 28.0927 Evaluate side-chains 31 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.146521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123115 restraints weight = 3554.719| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.83 r_work: 0.3328 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3245 Z= 0.260 Angle : 0.629 7.825 4423 Z= 0.324 Chirality : 0.040 0.185 519 Planarity : 0.005 0.053 534 Dihedral : 5.172 29.504 440 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.67 % Favored : 91.56 % Rotamer: Outliers : 0.88 % Allowed : 11.80 % Favored : 87.32 % 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: 0.44 (0.44), residues: 391 helix: 1.45 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -4.04 (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 0.016 0.001 PHE A 202 TYR 0.023 0.002 TYR A 139 ARG 0.005 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 33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.267 Fit side-chains REVERT: A 58 ASN cc_start: 0.8699 (m-40) cc_final: 0.8424 (m-40) REVERT: A 67 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8098 (mt-10) outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 0.7499 time to fit residues: 25.3170 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 : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU 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: 0.7980 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.0770 chunk 35 optimal weight: 0.9980 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.148718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125440 restraints weight = 3460.296| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.81 r_work: 0.3358 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 0.050 3245 Z= 0.210 Angle : 0.594 9.286 4423 Z= 0.305 Chirality : 0.038 0.178 519 Planarity : 0.005 0.051 534 Dihedral : 5.053 28.924 440 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.65 % Favored : 92.58 % 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: 1.54 (0.31), residues: 306 sheet: None (None), residues: 0 loop : -3.90 (0.57), residues: 85 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 0.010 0.001 PHE A 372 TYR 0.016 0.001 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 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.378 Fit side-chains REVERT: A 67 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8096 (mt-10) outliers start: 7 outliers final: 1 residues processed: 35 average time/residue: 0.7863 time to fit residues: 28.9964 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 : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU 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: 2.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.145384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121723 restraints weight = 3481.732| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.85 r_work: 0.3356 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3245 Z= 0.239 Angle : 0.603 9.426 4423 Z= 0.307 Chirality : 0.039 0.180 519 Planarity : 0.005 0.051 534 Dihedral : 5.026 28.377 440 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.67 % Favored : 91.56 % Rotamer: Outliers : 1.47 % Allowed : 12.39 % 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 (0.45), residues: 391 helix: 1.50 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.88 (0.57), 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 0.012 0.001 PHE A 372 TYR 0.019 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: 5 poor density : 31 time to evaluate : 0.355 Fit side-chains REVERT: A 40 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7514 (mm-40) REVERT: A 58 ASN cc_start: 0.8700 (m-40) cc_final: 0.8420 (m-40) outliers start: 5 outliers final: 1 residues processed: 35 average time/residue: 0.8616 time to fit residues: 31.7397 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 40 GLN 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: 0.6980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.144778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120992 restraints weight = 3534.323| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.88 r_work: 0.3339 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3245 Z= 0.242 Angle : 0.608 9.883 4423 Z= 0.310 Chirality : 0.039 0.177 519 Planarity : 0.005 0.051 534 Dihedral : 4.966 28.198 440 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.91 % Favored : 92.33 % Rotamer: Outliers : 1.18 % Allowed : 12.39 % 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: 0.64 (0.45), residues: 391 helix: 1.53 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.84 (0.57), 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 0.013 0.001 PHE A 212 TYR 0.020 0.001 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 34 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.332 Fit side-chains REVERT: A 40 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7421 (mm-40) REVERT: A 58 ASN cc_start: 0.8661 (m-40) cc_final: 0.8373 (m-40) outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 0.7680 time to fit residues: 26.7063 Evaluate side-chains 33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 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: 0.6980 chunk 2 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.138691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114585 restraints weight = 3516.617| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.88 r_work: 0.3318 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1778 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= 0.263 Angle : 0.612 8.124 4423 Z= 0.313 Chirality : 0.040 0.174 519 Planarity : 0.005 0.051 534 Dihedral : 5.030 28.669 440 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.67 % Favored : 91.56 % Rotamer: Outliers : 1.18 % Allowed : 12.39 % 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: 0.63 (0.45), residues: 391 helix: 1.52 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.85 (0.57), residues: 86 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 0.023 0.002 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 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.312 Fit side-chains REVERT: A 40 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7407 (mm-40) REVERT: A 58 ASN cc_start: 0.8625 (m-40) cc_final: 0.8337 (m-40) REVERT: A 148 ARG cc_start: 0.5960 (ttt180) cc_final: 0.5538 (mtm180) REVERT: A 303 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7691 (mtp-110) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 1.0758 time to fit residues: 41.3111 Evaluate side-chains 36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.0870 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.142521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118732 restraints weight = 3499.998| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.86 r_work: 0.3348 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3245 Z= 0.214 Angle : 0.590 10.292 4423 Z= 0.300 Chirality : 0.039 0.167 519 Planarity : 0.005 0.050 534 Dihedral : 4.931 28.066 440 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.65 % Favored : 92.84 % Rotamer: Outliers : 1.18 % Allowed : 12.98 % Favored : 85.84 % 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: 0.75 (0.45), residues: 391 helix: 1.61 (0.30), residues: 305 sheet: None (None), residues: 0 loop : -3.80 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 PHE 0.010 0.001 PHE A 212 TYR 0.015 0.001 TYR A 139 ARG 0.008 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.06 seconds wall clock time: 39 minutes 29.95 seconds (2369.95 seconds total)