Starting phenix.real_space_refine on Thu Jul 18 18:42:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/07_2024/8t6a_41067.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/07_2024/8t6a_41067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/07_2024/8t6a_41067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/07_2024/8t6a_41067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/07_2024/8t6a_41067.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/07_2024/8t6a_41067.cif" } resolution = 3.17 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= 0.025 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 28 5.16 5 C 1963 2.51 5 N 455 2.21 5 O 501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2947 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2903 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 23, 'TRANS': 363} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.11, per 1000 atoms: 1.06 Number of scatterers: 2947 At special positions: 0 Unit cell: (75.933, 65.549, 68.794, 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 28 16.00 O 501 8.00 N 455 7.00 C 1963 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 - 3.50 Amino acid : False - 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: 1.65 Conformation dependent library (CDL) restraints added in 520.9 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 90.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 19 through 53 removed outlier: 4.216A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix removed outlier: 3.996A pdb=" N HIS A 53 " --> pdb=" O TYR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 157 removed outlier: 4.443A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.598A pdb=" N GLY A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 151 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.649A pdb=" N ILE A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'A' and resid 226 through 246 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.467A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 310 removed outlier: 4.281A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 319 removed outlier: 3.858A pdb=" N ALA A 314 " --> pdb=" O MET A 310 " (cutoff:3.500A) Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.550A pdb=" N LEU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 414 Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 419 through 448 Proline residue: A 437 - end of helix removed outlier: 3.843A pdb=" N ALA A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.710A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 240 hydrogen bonds defined for protein. 702 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: 0.81 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 446 1.32 - 1.44: 784 1.44 - 1.56: 1743 1.56 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 3021 Sorted by residual: bond pdb=" C7 YHR A 601 " pdb=" N8 YHR A 601 " ideal model delta sigma weight residual 1.454 1.506 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C12 YHR A 601 " pdb=" C13 YHR A 601 " ideal model delta sigma weight residual 1.503 1.454 0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C13 YHR A 601 " pdb=" N8 YHR A 601 " ideal model delta sigma weight residual 1.459 1.506 -0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" C9 YHR A 601 " pdb=" N8 YHR A 601 " ideal model delta sigma weight residual 1.456 1.503 -0.047 2.00e-02 2.50e+03 5.55e+00 bond pdb=" C GLU A 312 " pdb=" N PRO A 313 " ideal model delta sigma weight residual 1.336 1.349 -0.013 9.80e-03 1.04e+04 1.74e+00 ... (remaining 3016 not shown) Histogram of bond angle deviations from ideal: 100.18 - 107.10: 121 107.10 - 114.03: 1745 114.03 - 120.96: 1564 120.96 - 127.88: 651 127.88 - 134.81: 31 Bond angle restraints: 4112 Sorted by residual: angle pdb=" C ILE A 375 " pdb=" CA ILE A 375 " pdb=" CB ILE A 375 " ideal model delta sigma weight residual 114.00 110.04 3.96 1.31e+00 5.83e-01 9.12e+00 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 116.38 -6.57 2.21e+00 2.05e-01 8.84e+00 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 112.34 117.45 -5.11 2.04e+00 2.40e-01 6.27e+00 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 110.70 113.50 -2.80 1.22e+00 6.72e-01 5.25e+00 angle pdb=" CA PRO A 236 " pdb=" C PRO A 236 " pdb=" N PRO A 237 " ideal model delta sigma weight residual 117.93 120.35 -2.42 1.20e+00 6.94e-01 4.08e+00 ... (remaining 4107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 1656 11.99 - 23.97: 103 23.97 - 35.96: 38 35.96 - 47.94: 11 47.94 - 59.93: 6 Dihedral angle restraints: 1814 sinusoidal: 719 harmonic: 1095 Sorted by residual: dihedral pdb=" CA LEU A 412 " pdb=" C LEU A 412 " pdb=" N ARG A 413 " pdb=" CA ARG A 413 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA VAL A 269 " pdb=" C VAL A 269 " pdb=" N LEU A 270 " pdb=" CA LEU A 270 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB MET A 204 " pdb=" CG MET A 204 " pdb=" SD MET A 204 " pdb=" CE MET A 204 " ideal model delta sinusoidal sigma weight residual 180.00 121.62 58.38 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 294 0.028 - 0.056: 109 0.056 - 0.085: 60 0.085 - 0.113: 21 0.113 - 0.141: 5 Chirality restraints: 489 Sorted by residual: chirality pdb=" CA PHE A 348 " pdb=" N PHE A 348 " pdb=" C PHE A 348 " pdb=" CB PHE A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA PRO A 292 " pdb=" N PRO A 292 " pdb=" C PRO A 292 " pdb=" CB PRO A 292 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA TYR A 158 " pdb=" N TYR A 158 " pdb=" C TYR A 158 " pdb=" CB TYR A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 486 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C31 YHR A 601 " 0.044 2.00e-02 2.50e+03 2.11e-02 1.12e+01 pdb=" C33 YHR A 601 " -0.018 2.00e-02 2.50e+03 pdb=" C34 YHR A 601 " -0.024 2.00e-02 2.50e+03 pdb=" C35 YHR A 601 " -0.017 2.00e-02 2.50e+03 pdb=" C36 YHR A 601 " -0.011 2.00e-02 2.50e+03 pdb=" C37 YHR A 601 " -0.009 2.00e-02 2.50e+03 pdb=" C38 YHR A 601 " -0.014 2.00e-02 2.50e+03 pdb=" O39 YHR A 601 " 0.007 2.00e-02 2.50e+03 pdb=" O41 YHR A 601 " 0.026 2.00e-02 2.50e+03 pdb=" O43 YHR A 601 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 YHR A 601 " -0.018 2.00e-02 2.50e+03 1.29e-02 4.96e+00 pdb=" C11 YHR A 601 " 0.011 2.00e-02 2.50e+03 pdb=" C12 YHR A 601 " 0.004 2.00e-02 2.50e+03 pdb=" C13 YHR A 601 " -0.020 2.00e-02 2.50e+03 pdb=" C22 YHR A 601 " 0.016 2.00e-02 2.50e+03 pdb=" C23 YHR A 601 " 0.019 2.00e-02 2.50e+03 pdb=" C24 YHR A 601 " 0.009 2.00e-02 2.50e+03 pdb=" C25 YHR A 601 " -0.005 2.00e-02 2.50e+03 pdb=" C26 YHR A 601 " -0.008 2.00e-02 2.50e+03 pdb=" C27 YHR A 601 " 0.002 2.00e-02 2.50e+03 pdb=" N21 YHR A 601 " 0.007 2.00e-02 2.50e+03 pdb=" O28 YHR A 601 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 236 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.021 5.00e-02 4.00e+02 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 618 2.78 - 3.31: 2985 3.31 - 3.84: 4959 3.84 - 4.37: 5543 4.37 - 4.90: 10180 Nonbonded interactions: 24285 Sorted by model distance: nonbonded pdb=" OG SER A 200 " pdb=" OH TYR A 422 " model vdw 2.248 2.440 nonbonded pdb=" OG SER A 371 " pdb=" O PRO A 387 " model vdw 2.283 2.440 nonbonded pdb=" O LYS A 327 " pdb=" NE2 GLN A 329 " model vdw 2.367 2.520 nonbonded pdb=" O GLU A 215 " pdb=" ND2 ASN A 219 " model vdw 2.375 2.520 nonbonded pdb=" O ALA A 333 " pdb=" ND2 ASN A 388 " model vdw 2.408 2.520 ... (remaining 24280 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: 2.580 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.790 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 0.052 3021 Z= 0.253 Angle : 0.600 6.570 4112 Z= 0.308 Chirality : 0.041 0.141 489 Planarity : 0.005 0.037 500 Dihedral : 10.366 59.928 1116 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.28 % Allowed : 2.88 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.43), residues: 383 helix: 1.52 (0.30), residues: 308 sheet: None (None), residues: 0 loop : -0.80 (0.70), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.014 0.001 PHE A 238 TYR 0.014 0.001 TYR A 408 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.284 Fit side-chains REVERT: A 471 ARG cc_start: 0.7946 (ttt-90) cc_final: 0.7730 (ttt90) outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 0.1275 time to fit residues: 9.0910 Evaluate side-chains 49 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 329 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7779 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3021 Z= 0.297 Angle : 0.640 6.705 4112 Z= 0.330 Chirality : 0.044 0.150 489 Planarity : 0.005 0.036 500 Dihedral : 6.433 58.663 475 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.24 % Allowed : 7.05 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.44), residues: 383 helix: 1.72 (0.30), residues: 310 sheet: None (None), residues: 0 loop : -0.90 (0.77), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.021 0.001 PHE A 238 TYR 0.012 0.002 TYR A 49 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.232 Fit side-chains REVERT: A 411 ASP cc_start: 0.6770 (m-30) cc_final: 0.6403 (m-30) REVERT: A 471 ARG cc_start: 0.7881 (ttt-90) cc_final: 0.7459 (ttt180) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 0.1166 time to fit residues: 8.0648 Evaluate side-chains 51 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.0670 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3021 Z= 0.184 Angle : 0.571 6.564 4112 Z= 0.290 Chirality : 0.041 0.134 489 Planarity : 0.005 0.035 500 Dihedral : 6.222 57.984 475 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.21 % Allowed : 8.01 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.44), residues: 383 helix: 1.88 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -1.65 (0.75), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE A 238 TYR 0.008 0.001 TYR A 49 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.303 Fit side-chains REVERT: A 411 ASP cc_start: 0.6690 (m-30) cc_final: 0.6320 (m-30) REVERT: A 471 ARG cc_start: 0.7867 (ttt-90) cc_final: 0.7636 (ttt90) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.1194 time to fit residues: 8.1868 Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.0980 chunk 23 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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: 0.7713 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3021 Z= 0.186 Angle : 0.569 6.590 4112 Z= 0.288 Chirality : 0.041 0.133 489 Planarity : 0.005 0.035 500 Dihedral : 6.107 56.057 475 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.24 % Allowed : 10.26 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.44), residues: 383 helix: 1.99 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.57 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.000 HIS A 53 PHE 0.014 0.001 PHE A 238 TYR 0.006 0.001 TYR A 422 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.309 Fit side-chains REVERT: A 411 ASP cc_start: 0.6666 (m-30) cc_final: 0.6282 (m-30) REVERT: A 471 ARG cc_start: 0.7835 (ttt-90) cc_final: 0.7586 (ttt90) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.1246 time to fit residues: 8.1018 Evaluate side-chains 50 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3021 Z= 0.213 Angle : 0.582 6.629 4112 Z= 0.295 Chirality : 0.041 0.137 489 Planarity : 0.005 0.036 500 Dihedral : 6.052 53.461 475 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.56 % Allowed : 11.22 % Favored : 86.22 % 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: 2.14 (0.44), residues: 383 helix: 1.98 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.49 (0.79), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 53 PHE 0.016 0.001 PHE A 238 TYR 0.006 0.001 TYR A 422 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.307 Fit side-chains REVERT: A 411 ASP cc_start: 0.6678 (m-30) cc_final: 0.6296 (m-30) REVERT: A 471 ARG cc_start: 0.7824 (ttt-90) cc_final: 0.7572 (ttt90) outliers start: 8 outliers final: 7 residues processed: 50 average time/residue: 0.1133 time to fit residues: 7.2302 Evaluate side-chains 51 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 26 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3021 Z= 0.256 Angle : 0.609 6.688 4112 Z= 0.307 Chirality : 0.042 0.142 489 Planarity : 0.005 0.038 500 Dihedral : 5.991 53.533 475 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.21 % Allowed : 10.90 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.44), residues: 383 helix: 1.88 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.47 (0.79), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.018 0.002 PHE A 238 TYR 0.007 0.001 TYR A 422 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.305 Fit side-chains REVERT: A 411 ASP cc_start: 0.6715 (m-30) cc_final: 0.6331 (m-30) REVERT: A 471 ARG cc_start: 0.7842 (ttt-90) cc_final: 0.7582 (ttt90) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.1251 time to fit residues: 8.4857 Evaluate side-chains 53 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.0040 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3021 Z= 0.224 Angle : 0.594 6.624 4112 Z= 0.300 Chirality : 0.041 0.136 489 Planarity : 0.005 0.037 500 Dihedral : 5.995 57.546 475 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.56 % Allowed : 11.86 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.44), residues: 383 helix: 1.88 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.50 (0.80), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.006 0.001 TYR A 422 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.238 Fit side-chains REVERT: A 411 ASP cc_start: 0.6698 (m-30) cc_final: 0.6325 (m-30) REVERT: A 471 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7568 (ttt90) outliers start: 8 outliers final: 8 residues processed: 50 average time/residue: 0.1106 time to fit residues: 7.0180 Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 33 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.0270 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3021 Z= 0.160 Angle : 0.559 6.537 4112 Z= 0.279 Chirality : 0.040 0.127 489 Planarity : 0.005 0.035 500 Dihedral : 5.941 65.667 475 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.24 % Allowed : 12.18 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.45), residues: 383 helix: 2.08 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -1.61 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.001 0.000 HIS A 53 PHE 0.010 0.001 PHE A 393 TYR 0.006 0.001 TYR A 211 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.298 Fit side-chains REVERT: A 411 ASP cc_start: 0.6665 (m-30) cc_final: 0.6300 (m-30) REVERT: A 471 ARG cc_start: 0.7815 (ttt-90) cc_final: 0.7552 (ttt90) outliers start: 7 outliers final: 7 residues processed: 51 average time/residue: 0.1286 time to fit residues: 8.2484 Evaluate side-chains 51 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3021 Z= 0.230 Angle : 0.593 6.643 4112 Z= 0.298 Chirality : 0.041 0.139 489 Planarity : 0.005 0.037 500 Dihedral : 5.871 68.621 474 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.24 % Allowed : 13.14 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.44), residues: 383 helix: 2.01 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -1.60 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.007 0.001 TYR A 49 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 471 ARG cc_start: 0.7813 (ttt-90) cc_final: 0.7552 (ttt90) outliers start: 7 outliers final: 7 residues processed: 49 average time/residue: 0.1200 time to fit residues: 7.4525 Evaluate side-chains 51 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3021 Z= 0.206 Angle : 0.582 6.612 4112 Z= 0.292 Chirality : 0.041 0.135 489 Planarity : 0.005 0.037 500 Dihedral : 5.901 71.540 474 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.56 % Allowed : 13.14 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.44), residues: 383 helix: 2.05 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.61 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 53 PHE 0.014 0.001 PHE A 238 TYR 0.006 0.001 TYR A 422 ARG 0.001 0.000 ARG A 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.227 Fit side-chains REVERT: A 221 MET cc_start: 0.7299 (mtm) cc_final: 0.7068 (mtt) REVERT: A 411 ASP cc_start: 0.6689 (m-30) cc_final: 0.6318 (m-30) REVERT: A 471 ARG cc_start: 0.7815 (ttt-90) cc_final: 0.7552 (ttt90) outliers start: 8 outliers final: 8 residues processed: 51 average time/residue: 0.1268 time to fit residues: 8.1487 Evaluate side-chains 53 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.180788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.165007 restraints weight = 3036.891| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 0.90 r_work: 0.3914 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3021 Z= 0.220 Angle : 0.590 6.633 4112 Z= 0.296 Chirality : 0.041 0.137 489 Planarity : 0.005 0.037 500 Dihedral : 5.948 73.370 474 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.56 % Allowed : 13.46 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.44), residues: 383 helix: 2.01 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.58 (0.80), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.006 0.001 TYR A 422 ARG 0.001 0.000 ARG A 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1168.87 seconds wall clock time: 22 minutes 56.51 seconds (1376.51 seconds total)