Starting phenix.real_space_refine on Thu Jul 18 18:26:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsx_36629/07_2024/8jsx_36629.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsx_36629/07_2024/8jsx_36629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsx_36629/07_2024/8jsx_36629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsx_36629/07_2024/8jsx_36629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsx_36629/07_2024/8jsx_36629.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsx_36629/07_2024/8jsx_36629.cif" } resolution = 3.16 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= -0.002 sd= 0.071 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 27 5.16 5 C 1886 2.51 5 N 436 2.21 5 O 479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2828 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2816 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.46, per 1000 atoms: 0.87 Number of scatterers: 2828 At special positions: 0 Unit cell: (57.8, 65.45, 72.25, 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 27 16.00 O 479 8.00 N 436 7.00 C 1886 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: 1.06 Conformation dependent library (CDL) restraints added in 630.4 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 92.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 48 removed outlier: 3.622A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.809A 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 Processing helix chain 'A' and resid 129 through 157 removed outlier: 4.570A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.996A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.687A 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 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.579A pdb=" N GLY A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 324 removed outlier: 3.866A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.721A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.505A pdb=" N LEU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 381 through 414 removed outlier: 4.860A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.613A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.506A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 500 1.33 - 1.45: 685 1.45 - 1.57: 1665 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2896 Sorted by residual: bond pdb=" N VAL A 234 " pdb=" CA VAL A 234 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.21e-02 6.83e+03 1.08e+01 bond pdb=" N LEU A 315 " pdb=" CA LEU A 315 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.04e-02 9.25e+03 1.08e+01 bond pdb=" N ILE A 22 " pdb=" CA ILE A 22 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N ILE A 162 " pdb=" CA ILE A 162 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" N LEU A 32 " pdb=" CA LEU A 32 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.23e-02 6.61e+03 8.46e+00 ... (remaining 2891 not shown) Histogram of bond angle deviations from ideal: 100.01 - 107.05: 116 107.05 - 114.09: 1680 114.09 - 121.13: 1546 121.13 - 128.17: 577 128.17 - 135.21: 24 Bond angle restraints: 3943 Sorted by residual: angle pdb=" CA MET A 397 " pdb=" C MET A 397 " pdb=" O MET A 397 " ideal model delta sigma weight residual 120.55 116.34 4.21 1.06e+00 8.90e-01 1.58e+01 angle pdb=" CA LEU A 32 " pdb=" C LEU A 32 " pdb=" O LEU A 32 " ideal model delta sigma weight residual 120.42 116.34 4.08 1.06e+00 8.90e-01 1.48e+01 angle pdb=" CA GLY A 235 " pdb=" C GLY A 235 " pdb=" N PRO A 236 " ideal model delta sigma weight residual 116.69 122.91 -6.22 1.71e+00 3.42e-01 1.32e+01 angle pdb=" CA GLY A 235 " pdb=" C GLY A 235 " pdb=" O GLY A 235 " ideal model delta sigma weight residual 121.52 116.42 5.10 1.43e+00 4.89e-01 1.27e+01 angle pdb=" N PHE A 389 " pdb=" CA PHE A 389 " pdb=" C PHE A 389 " ideal model delta sigma weight residual 111.07 107.29 3.78 1.07e+00 8.73e-01 1.25e+01 ... (remaining 3938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1500 17.47 - 34.94: 146 34.94 - 52.40: 41 52.40 - 69.87: 4 69.87 - 87.33: 3 Dihedral angle restraints: 1694 sinusoidal: 626 harmonic: 1068 Sorted by residual: dihedral pdb=" CB GLU A 244 " pdb=" CG GLU A 244 " pdb=" CD GLU A 244 " pdb=" OE1 GLU A 244 " ideal model delta sinusoidal sigma weight residual 0.00 85.83 -85.83 1 3.00e+01 1.11e-03 9.89e+00 dihedral pdb=" CG LYS A 290 " pdb=" CD LYS A 290 " pdb=" CE LYS A 290 " pdb=" NZ LYS A 290 " ideal model delta sinusoidal sigma weight residual 180.00 120.28 59.72 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 189 " pdb=" CB ARG A 189 " pdb=" CG ARG A 189 " pdb=" CD ARG A 189 " ideal model delta sinusoidal sigma weight residual 60.00 119.51 -59.51 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 336 0.046 - 0.093: 86 0.093 - 0.139: 37 0.139 - 0.185: 9 0.185 - 0.231: 6 Chirality restraints: 474 Sorted by residual: chirality pdb=" CA ILE A 25 " pdb=" N ILE A 25 " pdb=" C ILE A 25 " pdb=" CB ILE A 25 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LEU A 228 " pdb=" N LEU A 228 " pdb=" C LEU A 228 " pdb=" CB LEU A 228 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA VAL A 391 " pdb=" N VAL A 391 " pdb=" C VAL A 391 " pdb=" CB VAL A 391 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 471 not shown) Planarity restraints: 483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 389 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C PHE A 389 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE A 389 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 390 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 29 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ALA A 29 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA A 29 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 391 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C VAL A 391 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL A 391 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 392 " -0.012 2.00e-02 2.50e+03 ... (remaining 480 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1143 2.93 - 3.42: 3031 3.42 - 3.92: 4500 3.92 - 4.41: 4879 4.41 - 4.90: 8640 Nonbonded interactions: 22193 Sorted by model distance: nonbonded pdb=" O MET A 397 " pdb=" OG SER A 401 " model vdw 2.440 2.440 nonbonded pdb=" N ASN A 128 " pdb=" OD1 ASN A 128 " model vdw 2.450 2.520 nonbonded pdb=" O ALA A 29 " pdb=" OD1 ASP A 33 " model vdw 2.489 3.040 nonbonded pdb=" OH TYR A 433 " pdb=" OAD E5E A 501 " model vdw 2.490 2.440 nonbonded pdb=" O LEU A 186 " pdb=" OG SER A 190 " model vdw 2.554 2.440 ... (remaining 22188 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.005 0.050 2896 Z= 0.347 Angle : 0.843 10.206 3943 Z= 0.571 Chirality : 0.056 0.231 474 Planarity : 0.006 0.039 483 Dihedral : 15.280 87.334 1014 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.00 % Allowed : 20.67 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.46), residues: 374 helix: 2.28 (0.31), residues: 312 sheet: None (None), residues: 0 loop : -2.87 (0.68), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.019 0.002 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.004 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.318 Fit side-chains REVERT: A 306 MET cc_start: 0.8481 (ttt) cc_final: 0.7867 (ttt) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.1595 time to fit residues: 8.1433 Evaluate side-chains 40 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 166 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 0.0170 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2896 Z= 0.266 Angle : 0.657 10.245 3943 Z= 0.320 Chirality : 0.043 0.148 474 Planarity : 0.006 0.042 483 Dihedral : 4.997 37.725 406 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.67 % Allowed : 20.00 % Favored : 78.33 % 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: 2.20 (0.45), residues: 374 helix: 2.16 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.45 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.003 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.018 0.001 TYR A 422 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.320 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.1494 time to fit residues: 8.2586 Evaluate side-chains 41 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.0050 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.3210 ------------------------------------------------------------------------------- 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: 0.8415 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2896 Z= 0.170 Angle : 0.599 10.308 3943 Z= 0.288 Chirality : 0.040 0.143 474 Planarity : 0.006 0.047 483 Dihedral : 4.155 14.641 402 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.00 % Allowed : 20.67 % Favored : 77.33 % 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: 2.49 (0.45), residues: 374 helix: 2.35 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -2.24 (0.72), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.348 Fit side-chains REVERT: A 334 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7495 (m-80) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.1388 time to fit residues: 8.1463 Evaluate side-chains 41 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 0 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8452 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2896 Z= 0.203 Angle : 0.614 10.301 3943 Z= 0.295 Chirality : 0.041 0.161 474 Planarity : 0.006 0.046 483 Dihedral : 4.110 14.657 402 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.00 % Allowed : 20.67 % Favored : 76.33 % 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: 2.51 (0.45), residues: 374 helix: 2.33 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.22 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.287 Fit side-chains REVERT: A 334 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7481 (m-80) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.1450 time to fit residues: 8.7142 Evaluate side-chains 46 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 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: 0.8471 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2896 Z= 0.217 Angle : 0.625 10.317 3943 Z= 0.300 Chirality : 0.042 0.154 474 Planarity : 0.006 0.046 483 Dihedral : 4.160 15.241 402 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.00 % Allowed : 21.67 % Favored : 75.33 % 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: 2.39 (0.45), residues: 374 helix: 2.19 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.26 (0.73), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.328 Fit side-chains REVERT: A 329 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.5881 (mt0) REVERT: A 334 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7495 (m-80) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.1533 time to fit residues: 8.5096 Evaluate side-chains 44 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.0020 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.0040 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.3800 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2896 Z= 0.178 Angle : 0.604 10.313 3943 Z= 0.289 Chirality : 0.041 0.151 474 Planarity : 0.006 0.045 483 Dihedral : 4.127 14.753 402 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.00 % Allowed : 21.33 % Favored : 75.67 % 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: 2.55 (0.45), residues: 374 helix: 2.30 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.13 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.262 Fit side-chains REVERT: A 329 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.5882 (mt0) REVERT: A 334 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7461 (m-80) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.1459 time to fit residues: 8.3742 Evaluate side-chains 46 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8473 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2896 Z= 0.224 Angle : 0.648 10.328 3943 Z= 0.304 Chirality : 0.042 0.149 474 Planarity : 0.006 0.044 483 Dihedral : 4.143 15.316 402 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.67 % Allowed : 21.67 % Favored : 75.67 % 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: 2.36 (0.45), residues: 374 helix: 2.18 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.33 (0.72), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.295 Fit side-chains REVERT: A 329 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.5876 (mt0) REVERT: A 334 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7531 (m-80) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.1492 time to fit residues: 8.0466 Evaluate side-chains 45 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.0020 chunk 3 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3046 ------------------------------------------------------------------------------- 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: 0.8417 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2896 Z= 0.170 Angle : 0.618 10.293 3943 Z= 0.288 Chirality : 0.041 0.149 474 Planarity : 0.006 0.041 483 Dihedral : 4.094 14.276 402 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.33 % Allowed : 22.33 % Favored : 75.33 % 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: 2.60 (0.46), residues: 374 helix: 2.37 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.30 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.013 0.001 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.256 Fit side-chains REVERT: A 306 MET cc_start: 0.8437 (tpp) cc_final: 0.8170 (ttt) REVERT: A 329 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.5822 (mt0) REVERT: A 334 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7496 (m-80) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.1508 time to fit residues: 8.0389 Evaluate side-chains 44 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8484 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2896 Z= 0.240 Angle : 0.656 10.348 3943 Z= 0.309 Chirality : 0.042 0.147 474 Planarity : 0.006 0.041 483 Dihedral : 4.154 15.312 402 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.67 % Allowed : 22.00 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.45), residues: 374 helix: 2.12 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.49 (0.73), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.017 0.001 PHE A 238 TYR 0.018 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.245 Fit side-chains REVERT: A 329 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.5839 (mt0) REVERT: A 334 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7523 (m-80) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.1458 time to fit residues: 7.8300 Evaluate side-chains 46 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.0670 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.0010 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.4324 ------------------------------------------------------------------------------- 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: 0.8443 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2896 Z= 0.188 Angle : 0.631 10.310 3943 Z= 0.297 Chirality : 0.041 0.149 474 Planarity : 0.006 0.041 483 Dihedral : 4.136 14.814 402 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.67 % Allowed : 21.67 % Favored : 75.67 % 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: 2.37 (0.45), residues: 374 helix: 2.20 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.45 (0.72), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.014 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.311 Fit side-chains REVERT: A 329 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.5809 (mt0) REVERT: A 334 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7488 (m-80) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 0.1446 time to fit residues: 8.0356 Evaluate side-chains 46 residues out of total 304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 0 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.144587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127415 restraints weight = 3332.727| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.41 r_work: 0.2957 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2896 Z= 0.187 Angle : 0.637 10.315 3943 Z= 0.299 Chirality : 0.041 0.147 474 Planarity : 0.006 0.041 483 Dihedral : 4.095 14.405 402 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.33 % Allowed : 22.33 % Favored : 75.33 % 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: 2.36 (0.45), residues: 374 helix: 2.20 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.49 (0.72), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 328 HIS 0.001 0.001 HIS A 414 PHE 0.014 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.001 0.000 ARG A 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 946.58 seconds wall clock time: 20 minutes 25.60 seconds (1225.60 seconds total)