Starting phenix.real_space_refine on Thu Nov 14 00:43:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/11_2024/8t6a_41067.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/11_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_41067/11_2024/8t6a_41067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/11_2024/8t6a_41067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/11_2024/8t6a_41067.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/11_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 2.98, per 1000 atoms: 1.01 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 - 3.00 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: 0.76 Conformation dependent library (CDL) restraints added in 387.2 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: 0.25 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: 0.83 Time building geometry restraints manager: 0.90 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: 0.00 - 1.31: 3965 1.31 - 2.63: 110 2.63 - 3.94: 19 3.94 - 5.26: 14 5.26 - 6.57: 4 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 3.040 nonbonded pdb=" OG SER A 371 " pdb=" O PRO A 387 " model vdw 2.283 3.040 nonbonded pdb=" O LYS A 327 " pdb=" NE2 GLN A 329 " model vdw 2.367 3.120 nonbonded pdb=" O GLU A 215 " pdb=" ND2 ASN A 219 " model vdw 2.375 3.120 nonbonded pdb=" O ALA A 333 " pdb=" ND2 ASN A 388 " model vdw 2.408 3.120 ... (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: 2.330 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: 0.020 Set scattering table: 0.030 Process input model: 12.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.342 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: 0.1489 time to fit residues: 10.7099 Evaluate side-chains 49 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 34 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7744 moved from start: 0.1106 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= 0.235 Angle : 0.615 6.665 4112 Z= 0.318 Chirality : 0.043 0.146 489 Planarity : 0.005 0.035 500 Dihedral : 6.472 70.051 475 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.60 % Allowed : 7.37 % Favored : 91.03 % 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: 1.87 (0.30), residues: 310 sheet: None (None), residues: 0 loop : -0.96 (0.76), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.017 0.001 PHE A 238 TYR 0.009 0.001 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 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.322 Fit side-chains REVERT: A 411 ASP cc_start: 0.6744 (m-30) cc_final: 0.6358 (m-30) REVERT: A 471 ARG cc_start: 0.7880 (ttt-90) cc_final: 0.7461 (ttt180) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.1274 time to fit residues: 8.6180 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 329 GLN 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: 0.6980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7778 moved from start: 0.1399 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= 0.278 Angle : 0.627 6.700 4112 Z= 0.323 Chirality : 0.043 0.144 489 Planarity : 0.005 0.038 500 Dihedral : 6.486 68.444 475 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.88 % Allowed : 8.97 % Favored : 88.14 % 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: 1.99 (0.44), residues: 383 helix: 1.83 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -0.89 (0.76), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 328 HIS 0.001 0.000 HIS A 53 PHE 0.020 0.001 PHE A 238 TYR 0.011 0.002 TYR A 49 ARG 0.001 0.000 ARG A 274 *********************** 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 to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.317 Fit side-chains REVERT: A 411 ASP cc_start: 0.6737 (m-30) cc_final: 0.6332 (m-30) REVERT: A 471 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7632 (ttt90) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 0.1285 time to fit residues: 8.7883 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7775 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3021 Z= 0.260 Angle : 0.617 6.663 4112 Z= 0.317 Chirality : 0.043 0.141 489 Planarity : 0.005 0.037 500 Dihedral : 6.439 68.137 475 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.24 % Allowed : 11.54 % 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: 2.13 (0.44), residues: 383 helix: 1.93 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -0.80 (0.77), residues: 73 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 0.018 0.002 PHE A 238 TYR 0.010 0.001 TYR A 49 ARG 0.002 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 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.349 Fit side-chains REVERT: A 329 GLN cc_start: 0.5548 (OUTLIER) cc_final: 0.4620 (mt0) REVERT: A 411 ASP cc_start: 0.6739 (m-30) cc_final: 0.6330 (m-30) REVERT: A 471 ARG cc_start: 0.7856 (ttt-90) cc_final: 0.7605 (ttt90) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.1272 time to fit residues: 8.4027 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7742 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 : 0.003 0.031 3021 Z= 0.203 Angle : 0.588 6.609 4112 Z= 0.299 Chirality : 0.041 0.136 489 Planarity : 0.005 0.036 500 Dihedral : 6.365 77.961 475 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.88 % Allowed : 11.22 % 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: 2.38 (0.44), residues: 383 helix: 2.10 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -0.71 (0.77), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.001 0.000 HIS A 53 PHE 0.013 0.001 PHE A 238 TYR 0.008 0.001 TYR A 49 ARG 0.001 0.000 ARG A 413 *********************** 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 56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.291 Fit side-chains REVERT: A 329 GLN cc_start: 0.5517 (OUTLIER) cc_final: 0.4955 (mt0) REVERT: A 355 MET cc_start: 0.7400 (ttp) cc_final: 0.7186 (ttp) REVERT: A 471 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7579 (ttt90) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 0.1270 time to fit residues: 8.7653 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.1774 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= 0.267 Angle : 0.625 6.693 4112 Z= 0.319 Chirality : 0.043 0.142 489 Planarity : 0.005 0.037 500 Dihedral : 6.393 81.558 475 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 2.24 (0.43), residues: 383 helix: 1.99 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -0.72 (0.77), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.019 0.002 PHE A 238 TYR 0.008 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 *********************** 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 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.332 Fit side-chains REVERT: A 329 GLN cc_start: 0.5538 (OUTLIER) cc_final: 0.4999 (mt0) REVERT: A 355 MET cc_start: 0.7432 (ttp) cc_final: 0.7225 (ttp) REVERT: A 411 ASP cc_start: 0.6707 (m-30) cc_final: 0.6372 (m-30) REVERT: A 471 ARG cc_start: 0.7844 (ttt-90) cc_final: 0.7580 (ttt90) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.1269 time to fit residues: 8.4182 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 24 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1819 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= 0.236 Angle : 0.609 6.630 4112 Z= 0.311 Chirality : 0.042 0.139 489 Planarity : 0.005 0.037 500 Dihedral : 6.363 82.257 475 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.24 % Allowed : 11.54 % 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: 2.28 (0.44), residues: 383 helix: 2.01 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -0.66 (0.78), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.008 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 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.336 Fit side-chains REVERT: A 355 MET cc_start: 0.7412 (ttp) cc_final: 0.7201 (ttp) REVERT: A 411 ASP cc_start: 0.6677 (m-30) cc_final: 0.6319 (m-30) REVERT: A 471 ARG cc_start: 0.7839 (ttt-90) cc_final: 0.7579 (ttt90) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.1314 time to fit residues: 8.6605 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 362 LEU 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: 0.9980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3021 Z= 0.178 Angle : 0.576 6.550 4112 Z= 0.291 Chirality : 0.041 0.133 489 Planarity : 0.005 0.036 500 Dihedral : 4.560 29.955 472 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.60 % Allowed : 11.54 % Favored : 86.86 % 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: 2.22 (0.44), residues: 383 helix: 2.01 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.36 (0.78), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.000 0.000 HIS A 414 PHE 0.011 0.001 PHE A 238 TYR 0.006 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 *********************** 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 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.420 Fit side-chains REVERT: A 411 ASP cc_start: 0.6654 (m-30) cc_final: 0.6286 (m-30) REVERT: A 445 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7684 (mttp) REVERT: A 471 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7563 (ttt90) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.1588 time to fit residues: 9.7239 Evaluate side-chains 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 362 LEU Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7754 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3021 Z= 0.227 Angle : 0.601 6.674 4112 Z= 0.304 Chirality : 0.042 0.137 489 Planarity : 0.005 0.037 500 Dihedral : 4.594 32.446 472 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.60 % Allowed : 12.18 % 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: 2.15 (0.44), residues: 383 helix: 1.96 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.33 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.007 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 *********************** 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 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.326 Fit side-chains REVERT: A 411 ASP cc_start: 0.6669 (m-30) cc_final: 0.6296 (m-30) REVERT: A 445 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7716 (mttp) REVERT: A 471 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7570 (ttt90) outliers start: 5 outliers final: 5 residues processed: 49 average time/residue: 0.1323 time to fit residues: 8.2864 Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 362 LEU Chi-restraints excluded: chain A residue 405 ILE 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: 1.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 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: 0.7771 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3021 Z= 0.244 Angle : 0.614 6.667 4112 Z= 0.311 Chirality : 0.042 0.139 489 Planarity : 0.005 0.038 500 Dihedral : 4.654 33.485 472 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.24 % Allowed : 11.86 % 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: 2.12 (0.44), residues: 383 helix: 1.94 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.32 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.008 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 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.287 Fit side-chains REVERT: A 411 ASP cc_start: 0.6707 (m-30) cc_final: 0.6358 (m-30) REVERT: A 445 LYS cc_start: 0.7924 (ttmm) cc_final: 0.7670 (mttp) REVERT: A 471 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7571 (ttt90) outliers start: 7 outliers final: 7 residues processed: 53 average time/residue: 0.1408 time to fit residues: 9.3068 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 200 SER 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 362 LEU Chi-restraints excluded: chain A residue 405 ILE 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: 1.9990 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 37 optimal weight: 0.0570 chunk 0 optimal weight: 0.9980 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.173704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153084 restraints weight = 3006.549| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.34 r_work: 0.3441 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3021 Z= 0.181 Angle : 0.578 6.598 4112 Z= 0.291 Chirality : 0.041 0.132 489 Planarity : 0.005 0.036 500 Dihedral : 4.522 30.018 472 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.92 % Allowed : 12.82 % Favored : 85.26 % 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: 2.33 (0.44), residues: 383 helix: 2.09 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.29 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.001 0.000 HIS A 53 PHE 0.012 0.001 PHE A 393 TYR 0.006 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1184.22 seconds wall clock time: 22 minutes 2.95 seconds (1322.95 seconds total)