Starting phenix.real_space_refine on Thu Jul 18 19:42:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayb_43984/07_2024/9ayb_43984_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayb_43984/07_2024/9ayb_43984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayb_43984/07_2024/9ayb_43984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayb_43984/07_2024/9ayb_43984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayb_43984/07_2024/9ayb_43984_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayb_43984/07_2024/9ayb_43984_neut.cif" } resolution = 3.19 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 16 5.16 5 C 2236 2.51 5 N 523 2.21 5 O 572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 416": "OD1" <-> "OD2" 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: 3347 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3347 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 18, 'TRANS': 409} Chain breaks: 1 Time building chain proxies: 2.62, per 1000 atoms: 0.78 Number of scatterers: 3347 At special positions: 0 Unit cell: (61.254, 81.18, 66.42, 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 16 16.00 O 572 8.00 N 523 7.00 C 2236 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: 1.26 Conformation dependent library (CDL) restraints added in 590.1 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 37 through 68 removed outlier: 3.993A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 120 removed outlier: 4.833A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 134 through 152 removed outlier: 4.596A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 224 removed outlier: 4.321A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.863A pdb=" N GLY A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 248 removed outlier: 4.077A pdb=" N PHE A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 248 " --> pdb=" O TRP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 288 through 319 removed outlier: 3.670A pdb=" N TRP A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.684A pdb=" N ASN A 327 " --> pdb=" O ASN A 323 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 328 through 355 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 359 through 382 Proline residue: A 375 - end of helix removed outlier: 3.594A pdb=" N PHE A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 403 removed outlier: 3.553A pdb=" N ALA A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.616A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 435 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 Processing helix chain 'A' and resid 483 through 487 245 hydrogen bonds defined for protein. 717 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: 0.86 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 986 1.34 - 1.46: 793 1.46 - 1.57: 1645 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3449 Sorted by residual: bond pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 bond pdb=" C PRO A 191 " pdb=" O PRO A 191 " ideal model delta sigma weight residual 1.246 1.239 0.006 8.50e-03 1.38e+04 5.28e-01 bond pdb=" C TRP A 339 " pdb=" O TRP A 339 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.15e-02 7.56e+03 5.13e-01 bond pdb=" CA ILE A 435 " pdb=" C ILE A 435 " ideal model delta sigma weight residual 1.520 1.526 -0.006 8.80e-03 1.29e+04 4.73e-01 bond pdb=" N THR A 448 " pdb=" CA THR A 448 " ideal model delta sigma weight residual 1.464 1.457 0.007 1.05e-02 9.07e+03 4.40e-01 ... (remaining 3444 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.19: 104 107.19 - 113.90: 1919 113.90 - 120.61: 1551 120.61 - 127.32: 1081 127.32 - 134.03: 52 Bond angle restraints: 4707 Sorted by residual: angle pdb=" C THR A 434 " pdb=" N ILE A 435 " pdb=" CA ILE A 435 " ideal model delta sigma weight residual 120.24 122.57 -2.33 6.30e-01 2.52e+00 1.37e+01 angle pdb=" C ILE A 435 " pdb=" CA ILE A 435 " pdb=" CB ILE A 435 " ideal model delta sigma weight residual 114.35 111.13 3.22 1.06e+00 8.90e-01 9.25e+00 angle pdb=" N VAL A 283 " pdb=" CA VAL A 283 " pdb=" C VAL A 283 " ideal model delta sigma weight residual 112.35 109.91 2.44 1.20e+00 6.94e-01 4.15e+00 angle pdb=" C VAL A 283 " pdb=" CA VAL A 283 " pdb=" CB VAL A 283 " ideal model delta sigma weight residual 114.00 111.59 2.41 1.31e+00 5.83e-01 3.39e+00 angle pdb=" N SER A 408 " pdb=" CA SER A 408 " pdb=" C SER A 408 " ideal model delta sigma weight residual 113.72 111.56 2.16 1.30e+00 5.92e-01 2.75e+00 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 1730 14.88 - 29.76: 159 29.76 - 44.64: 49 44.64 - 59.52: 5 59.52 - 74.39: 1 Dihedral angle restraints: 1944 sinusoidal: 718 harmonic: 1226 Sorted by residual: dihedral pdb=" CA TRP A 246 " pdb=" C TRP A 246 " pdb=" N LEU A 247 " pdb=" CA LEU A 247 " ideal model delta harmonic sigma weight residual -180.00 -164.00 -16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N LYS A 278 " pdb=" CA LYS A 278 " pdb=" CB LYS A 278 " pdb=" CG LYS A 278 " ideal model delta sinusoidal sigma weight residual -180.00 -121.39 -58.61 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA PHE A 305 " pdb=" C PHE A 305 " pdb=" N TYR A 306 " pdb=" CA TYR A 306 " ideal model delta harmonic sigma weight residual 180.00 164.72 15.28 0 5.00e+00 4.00e-02 9.34e+00 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 316 0.027 - 0.054: 128 0.054 - 0.082: 66 0.082 - 0.109: 22 0.109 - 0.136: 3 Chirality restraints: 535 Sorted by residual: chirality pdb=" CA VAL A 280 " pdb=" N VAL A 280 " pdb=" C VAL A 280 " pdb=" CB VAL A 280 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA PHE A 305 " pdb=" N PHE A 305 " pdb=" C PHE A 305 " pdb=" CB PHE A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 532 not shown) Planarity restraints: 571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 163 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 307 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C THR A 307 " 0.025 2.00e-02 2.50e+03 pdb=" O THR A 307 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 308 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO A 375 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.018 5.00e-02 4.00e+02 ... (remaining 568 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1064 2.83 - 3.35: 3452 3.35 - 3.87: 5641 3.87 - 4.38: 6447 4.38 - 4.90: 11290 Nonbonded interactions: 27894 Sorted by model distance: nonbonded pdb=" O MET A 372 " pdb=" ND2 ASN A 467 " model vdw 2.313 2.520 nonbonded pdb=" O ASN A 357 " pdb=" OD1 ASN A 357 " model vdw 2.317 3.040 nonbonded pdb=" O CYS A 406 " pdb=" OG SER A 411 " model vdw 2.358 2.440 nonbonded pdb=" O THR A 448 " pdb=" OG1 THR A 448 " model vdw 2.388 2.440 nonbonded pdb=" NZ LYS A 136 " pdb=" O VAL A 248 " model vdw 2.439 2.520 ... (remaining 27889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.750 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.003 0.031 3449 Z= 0.175 Angle : 0.518 4.214 4707 Z= 0.314 Chirality : 0.038 0.136 535 Planarity : 0.005 0.037 571 Dihedral : 12.732 74.394 1164 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.57 % Allowed : 7.93 % Favored : 91.50 % 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: 1.23 (0.41), residues: 424 helix: 1.15 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -0.04 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 292 HIS 0.003 0.001 HIS A 255 PHE 0.014 0.001 PHE A 232 TYR 0.009 0.001 TYR A 306 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.299 Fit side-chains REVERT: A 137 MET cc_start: 0.7869 (mmt) cc_final: 0.7605 (mmt) REVERT: A 175 GLU cc_start: 0.7972 (tt0) cc_final: 0.7638 (tt0) REVERT: A 182 MET cc_start: 0.7843 (tpp) cc_final: 0.7459 (tpt) REVERT: A 273 GLN cc_start: 0.8055 (mt0) cc_final: 0.7837 (mt0) outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.1558 time to fit residues: 7.2297 Evaluate side-chains 35 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3449 Z= 0.196 Angle : 0.528 4.935 4707 Z= 0.278 Chirality : 0.041 0.200 535 Planarity : 0.005 0.040 571 Dihedral : 5.327 49.489 459 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.12 % Allowed : 7.93 % Favored : 88.95 % 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: 1.64 (0.41), residues: 424 helix: 1.50 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -0.20 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.001 0.000 HIS A 298 PHE 0.017 0.002 PHE A 232 TYR 0.008 0.001 TYR A 119 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.333 Fit side-chains REVERT: A 175 GLU cc_start: 0.8055 (tt0) cc_final: 0.7813 (tt0) REVERT: A 182 MET cc_start: 0.7687 (tpp) cc_final: 0.7152 (tpt) REVERT: A 273 GLN cc_start: 0.8137 (mt0) cc_final: 0.7920 (mt0) outliers start: 11 outliers final: 6 residues processed: 38 average time/residue: 0.1647 time to fit residues: 7.8394 Evaluate side-chains 34 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 316 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3449 Z= 0.186 Angle : 0.495 4.954 4707 Z= 0.261 Chirality : 0.040 0.124 535 Planarity : 0.005 0.041 571 Dihedral : 5.310 51.870 459 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.55 % Allowed : 8.50 % Favored : 88.95 % 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: 1.60 (0.41), residues: 424 helix: 1.54 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.74 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 189 HIS 0.001 0.000 HIS A 183 PHE 0.017 0.001 PHE A 51 TYR 0.008 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.429 Fit side-chains REVERT: A 175 GLU cc_start: 0.8068 (tt0) cc_final: 0.7859 (tt0) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.1638 time to fit residues: 7.6224 Evaluate side-chains 32 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 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: 0.7441 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3449 Z= 0.194 Angle : 0.489 5.015 4707 Z= 0.256 Chirality : 0.040 0.123 535 Planarity : 0.005 0.040 571 Dihedral : 5.298 54.037 459 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.55 % Allowed : 9.35 % Favored : 88.10 % 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: 1.67 (0.41), residues: 424 helix: 1.63 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.88 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.001 0.001 HIS A 183 PHE 0.018 0.001 PHE A 51 TYR 0.008 0.001 TYR A 306 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.349 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 35 average time/residue: 0.1581 time to fit residues: 7.1387 Evaluate side-chains 34 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7439 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3449 Z= 0.187 Angle : 0.485 5.295 4707 Z= 0.251 Chirality : 0.039 0.118 535 Planarity : 0.005 0.040 571 Dihedral : 5.438 59.415 459 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.55 % Allowed : 11.05 % Favored : 86.40 % 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: 1.75 (0.41), residues: 424 helix: 1.71 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.93 (0.56), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.001 0.000 HIS A 298 PHE 0.018 0.001 PHE A 51 TYR 0.009 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.293 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 35 average time/residue: 0.1557 time to fit residues: 6.9259 Evaluate side-chains 32 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.0060 chunk 21 optimal weight: 0.0070 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4614 ------------------------------------------------------------------------------- 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: 0.7409 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3449 Z= 0.149 Angle : 0.464 5.510 4707 Z= 0.240 Chirality : 0.038 0.118 535 Planarity : 0.005 0.040 571 Dihedral : 5.107 53.760 459 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.27 % Allowed : 11.61 % Favored : 86.12 % 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: 1.88 (0.41), residues: 424 helix: 1.79 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.88 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 339 HIS 0.001 0.000 HIS A 183 PHE 0.017 0.001 PHE A 51 TYR 0.009 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.347 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 33 average time/residue: 0.1682 time to fit residues: 7.0678 Evaluate side-chains 31 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 481 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7429 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3449 Z= 0.185 Angle : 0.492 5.761 4707 Z= 0.251 Chirality : 0.039 0.118 535 Planarity : 0.005 0.040 571 Dihedral : 4.584 53.852 458 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.55 % Allowed : 12.75 % Favored : 84.70 % 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: 1.90 (0.41), residues: 424 helix: 1.82 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.90 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.001 0.001 HIS A 298 PHE 0.018 0.001 PHE A 51 TYR 0.008 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 0.335 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 32 average time/residue: 0.1682 time to fit residues: 6.8128 Evaluate side-chains 32 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.0060 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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: 0.7403 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3449 Z= 0.153 Angle : 0.478 5.724 4707 Z= 0.244 Chirality : 0.038 0.117 535 Planarity : 0.005 0.040 571 Dihedral : 4.528 52.313 458 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.98 % Allowed : 12.46 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.41), residues: 424 helix: 1.88 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.76 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 339 HIS 0.001 0.000 HIS A 298 PHE 0.017 0.001 PHE A 51 TYR 0.009 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.344 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 32 average time/residue: 0.1644 time to fit residues: 6.7345 Evaluate side-chains 32 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 481 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7438 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3449 Z= 0.215 Angle : 0.513 6.172 4707 Z= 0.260 Chirality : 0.040 0.118 535 Planarity : 0.005 0.040 571 Dihedral : 4.559 51.304 458 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.98 % Allowed : 12.46 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.41), residues: 424 helix: 1.79 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -0.91 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.002 0.001 HIS A 298 PHE 0.019 0.001 PHE A 51 TYR 0.008 0.001 TYR A 119 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.320 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.1598 time to fit residues: 6.5286 Evaluate side-chains 31 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 13 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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: 0.7401 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3449 Z= 0.161 Angle : 0.486 6.076 4707 Z= 0.246 Chirality : 0.038 0.115 535 Planarity : 0.005 0.041 571 Dihedral : 4.544 51.519 458 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.42 % Allowed : 12.75 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.41), residues: 424 helix: 1.86 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.73 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.001 0.000 HIS A 298 PHE 0.016 0.001 PHE A 51 TYR 0.008 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.330 Fit side-chains REVERT: A 175 GLU cc_start: 0.7841 (tt0) cc_final: 0.7530 (tt0) outliers start: 5 outliers final: 5 residues processed: 29 average time/residue: 0.1648 time to fit residues: 6.1424 Evaluate side-chains 30 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.140642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099785 restraints weight = 3615.194| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.38 r_work: 0.3041 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3449 Z= 0.168 Angle : 0.498 6.857 4707 Z= 0.249 Chirality : 0.039 0.117 535 Planarity : 0.005 0.041 571 Dihedral : 4.526 52.752 458 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.70 % Allowed : 12.75 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.41), residues: 424 helix: 1.85 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.73 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.001 0.000 HIS A 298 PHE 0.017 0.001 PHE A 51 TYR 0.008 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1055.02 seconds wall clock time: 20 minutes 21.36 seconds (1221.36 seconds total)