Starting phenix.real_space_refine on Mon Sep 23 13:36:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/09_2024/7xtk_33451_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/09_2024/7xtk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/09_2024/7xtk_33451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/09_2024/7xtk_33451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/09_2024/7xtk_33451_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/09_2024/7xtk_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-5461/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: 3.01, per 1000 atoms: 0.95 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 393.8 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: 0.36 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: 0.84 Time building geometry restraints manager: 0.96 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: 1.540 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.330 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: 0.010 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.500 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.347 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.7767 time to fit residues: 28.6922 Evaluate side-chains 28 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.319 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 39 average time/residue: 0.6574 time to fit residues: 27.1870 Evaluate side-chains 30 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0060 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3245 Z= 0.202 Angle : 0.621 8.109 4423 Z= 0.321 Chirality : 0.038 0.175 519 Planarity : 0.006 0.060 534 Dihedral : 5.166 30.794 440 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.56 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: 0.25 (0.45), residues: 391 helix: 1.33 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -4.20 (0.54), 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 0.011 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 fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.350 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 0.8228 time to fit residues: 32.8497 Evaluate side-chains 33 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 0.6980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3245 Z= 0.292 Angle : 0.665 6.920 4423 Z= 0.343 Chirality : 0.041 0.179 519 Planarity : 0.006 0.058 534 Dihedral : 5.306 30.431 440 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 1.02 % Allowed : 7.93 % Favored : 91.05 % Rotamer: Outliers : 1.47 % Allowed : 8.26 % Favored : 90.27 % 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: 0.19 (0.44), residues: 391 helix: 1.31 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -4.23 (0.54), residues: 89 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 0.021 0.001 PHE A 202 TYR 0.023 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 38 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.443 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 37 average time/residue: 0.6512 time to fit residues: 25.6628 Evaluate side-chains 31 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.0270 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1504 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= 0.251 Angle : 0.619 6.631 4423 Z= 0.321 Chirality : 0.039 0.180 519 Planarity : 0.005 0.055 534 Dihedral : 5.224 30.055 440 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.39 % Favored : 92.84 % Rotamer: Outliers : 1.47 % Allowed : 10.03 % Favored : 88.50 % 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: 0.36 (0.44), residues: 391 helix: 1.39 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -4.12 (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 358 PHE 0.012 0.001 PHE A 372 TYR 0.021 0.002 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 fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.356 Fit side-chains REVERT: A 58 ASN cc_start: 0.8811 (m-40) cc_final: 0.8519 (m-40) outliers start: 5 outliers final: 1 residues processed: 38 average time/residue: 0.9699 time to fit residues: 38.4245 Evaluate side-chains 32 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.0060 chunk 4 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3245 Z= 0.196 Angle : 0.587 7.877 4423 Z= 0.302 Chirality : 0.038 0.177 519 Planarity : 0.005 0.053 534 Dihedral : 5.070 28.656 440 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.65 % Favored : 92.58 % 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: 0.60 (0.45), residues: 391 helix: 1.55 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.98 (0.56), residues: 87 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 0.015 0.001 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 35 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.359 Fit side-chains REVERT: A 67 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7718 (mt-10) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 0.9057 time to fit residues: 31.3388 Evaluate side-chains 33 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 88 ASP 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 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.0270 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3245 Z= 0.232 Angle : 0.608 9.150 4423 Z= 0.311 Chirality : 0.039 0.185 519 Planarity : 0.005 0.052 534 Dihedral : 5.023 28.507 440 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.91 % Favored : 92.33 % Rotamer: Outliers : 1.77 % Allowed : 12.09 % 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: 0.63 (0.45), residues: 391 helix: 1.56 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.94 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.012 0.001 PHE A 372 TYR 0.018 0.001 TYR A 139 ARG 0.007 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 fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.350 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 34 average time/residue: 0.8245 time to fit residues: 29.6105 Evaluate side-chains 31 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1770 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= 0.262 Angle : 0.621 9.691 4423 Z= 0.316 Chirality : 0.040 0.180 519 Planarity : 0.005 0.051 534 Dihedral : 5.082 28.989 440 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.67 % Favored : 91.56 % 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 (0.45), residues: 391 helix: 1.49 (0.31), residues: 306 sheet: None (None), residues: 0 loop : -3.89 (0.58), residues: 85 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 0.020 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 35 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.352 Fit side-chains REVERT: A 40 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7334 (mm-40) REVERT: A 58 ASN cc_start: 0.8763 (m-40) cc_final: 0.8486 (m-40) outliers start: 4 outliers final: 1 residues processed: 34 average time/residue: 0.7743 time to fit residues: 27.7923 Evaluate side-chains 32 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3245 Z= 0.266 Angle : 0.623 9.777 4423 Z= 0.318 Chirality : 0.040 0.176 519 Planarity : 0.005 0.051 534 Dihedral : 5.032 28.865 440 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.91 % Favored : 92.33 % 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: 0.60 (0.45), residues: 391 helix: 1.47 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -3.85 (0.58), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 358 PHE 0.012 0.001 PHE A 372 TYR 0.021 0.002 TYR A 139 ARG 0.007 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 37 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.356 Fit side-chains REVERT: A 40 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7311 (mm-40) REVERT: A 58 ASN cc_start: 0.8750 (m-40) cc_final: 0.8472 (m-40) REVERT: A 148 ARG cc_start: 0.5981 (ttt180) cc_final: 0.5633 (mtm180) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.9647 time to fit residues: 36.2374 Evaluate side-chains 36 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1850 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= 0.263 Angle : 0.614 8.083 4423 Z= 0.314 Chirality : 0.040 0.173 519 Planarity : 0.005 0.051 534 Dihedral : 5.054 28.827 440 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.93 % Favored : 91.30 % 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: 0.69 (0.45), residues: 391 helix: 1.55 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.68 (0.58), 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 358 PHE 0.012 0.001 PHE A 372 TYR 0.021 0.002 TYR A 139 ARG 0.007 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 39 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.347 Fit side-chains REVERT: A 40 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7357 (mm-40) REVERT: A 58 ASN cc_start: 0.8744 (m-40) cc_final: 0.8467 (m-40) REVERT: A 148 ARG cc_start: 0.5964 (ttt180) cc_final: 0.5641 (mtm180) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.9720 time to fit residues: 38.4351 Evaluate side-chains 36 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 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 = 0.3686 r_free = 0.3686 target = 0.145566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122237 restraints weight = 3538.182| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.84 r_work: 0.3306 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1901 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= 0.258 Angle : 0.620 10.067 4423 Z= 0.314 Chirality : 0.040 0.172 519 Planarity : 0.005 0.050 534 Dihedral : 5.030 28.665 440 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.93 % Favored : 91.56 % Rotamer: Outliers : 1.18 % Allowed : 13.57 % Favored : 85.25 % 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: 0.71 (0.44), residues: 391 helix: 1.55 (0.30), residues: 304 sheet: None (None), residues: 0 loop : -3.64 (0.58), 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 358 PHE 0.012 0.001 PHE A 372 TYR 0.020 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: 1372.36 seconds wall clock time: 24 minutes 47.54 seconds (1487.54 seconds total)