Starting phenix.real_space_refine on Thu Jul 18 18:25:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtb_36639/07_2024/8jtb_36639.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtb_36639/07_2024/8jtb_36639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtb_36639/07_2024/8jtb_36639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtb_36639/07_2024/8jtb_36639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtb_36639/07_2024/8jtb_36639.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtb_36639/07_2024/8jtb_36639.cif" } resolution = 2.93 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= -0.003 sd= 0.076 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 1875 2.51 5 N 432 2.21 5 O 474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A ASP 426": "OD1" <-> "OD2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "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: 2808 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2797 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.82, per 1000 atoms: 1.00 Number of scatterers: 2808 At special positions: 0 Unit cell: (57.8, 62.9, 71.4, 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 474 8.00 N 432 7.00 C 1875 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: 1.76 Conformation dependent library (CDL) restraints added in 654.8 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 676 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 19 through 49 removed outlier: 3.534A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.825A 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 132 through 157 removed outlier: 4.248A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 4.103A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.674A 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 245 removed outlier: 3.662A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (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 323 removed outlier: 3.751A 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 removed outlier: 3.517A pdb=" N GLU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.619A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.601A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.638A 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: 3.775A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (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: 3.551A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 714 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: 0.76 Time building geometry restraints manager: 1.00 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: 522 1.33 - 1.45: 662 1.45 - 1.57: 1646 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2876 Sorted by residual: bond pdb=" N SER A 179 " pdb=" CA SER A 179 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.17e-02 7.31e+03 1.34e+01 bond pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta sigma weight residual 1.463 1.500 -0.037 1.20e-02 6.94e+03 9.59e+00 bond pdb=" C SER A 179 " pdb=" O SER A 179 " ideal model delta sigma weight residual 1.234 1.270 -0.036 1.16e-02 7.43e+03 9.53e+00 bond pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.46e+00 bond pdb=" N VAL A 41 " pdb=" CA VAL A 41 " ideal model delta sigma weight residual 1.463 1.499 -0.036 1.20e-02 6.94e+03 9.03e+00 ... (remaining 2871 not shown) Histogram of bond angle deviations from ideal: 100.15 - 107.04: 117 107.04 - 113.92: 1635 113.92 - 120.81: 1408 120.81 - 127.70: 727 127.70 - 134.58: 28 Bond angle restraints: 3915 Sorted by residual: angle pdb=" CA ILE A 44 " pdb=" C ILE A 44 " pdb=" N PRO A 45 " ideal model delta sigma weight residual 120.83 123.82 -2.99 6.10e-01 2.69e+00 2.41e+01 angle pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" C SER A 179 " ideal model delta sigma weight residual 109.86 116.49 -6.63 1.55e+00 4.16e-01 1.83e+01 angle pdb=" CA VAL A 41 " pdb=" C VAL A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 120.83 123.31 -2.48 6.10e-01 2.69e+00 1.66e+01 angle pdb=" CA ILE A 44 " pdb=" C ILE A 44 " pdb=" O ILE A 44 " ideal model delta sigma weight residual 118.69 116.06 2.63 6.70e-01 2.23e+00 1.54e+01 angle pdb=" N GLN A 192 " pdb=" CA GLN A 192 " pdb=" C GLN A 192 " ideal model delta sigma weight residual 111.28 107.11 4.17 1.09e+00 8.42e-01 1.47e+01 ... (remaining 3910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 1492 17.36 - 34.73: 130 34.73 - 52.09: 46 52.09 - 69.45: 7 69.45 - 86.82: 3 Dihedral angle restraints: 1678 sinusoidal: 616 harmonic: 1062 Sorted by residual: dihedral pdb=" C ILE A 44 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual -122.00 -132.73 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C PHE A 178 " pdb=" N PHE A 178 " pdb=" CA PHE A 178 " pdb=" CB PHE A 178 " ideal model delta harmonic sigma weight residual -122.60 -132.61 10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual 123.40 132.53 -9.13 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 1675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 384 0.064 - 0.127: 66 0.127 - 0.190: 16 0.190 - 0.254: 2 0.254 - 0.317: 2 Chirality restraints: 470 Sorted by residual: chirality pdb=" CA PHE A 178 " pdb=" N PHE A 178 " pdb=" C PHE A 178 " pdb=" CB PHE A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.18 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PHE A 176 " pdb=" N PHE A 176 " pdb=" C PHE A 176 " pdb=" CB PHE A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 467 not shown) Planarity restraints: 479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 176 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.27e+00 pdb=" C PHE A 176 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE A 176 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 177 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 179 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C SER A 179 " -0.050 2.00e-02 2.50e+03 pdb=" O SER A 179 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 180 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 165 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C GLY A 165 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY A 165 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 166 " 0.013 2.00e-02 2.50e+03 ... (remaining 476 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 309 2.75 - 3.29: 2832 3.29 - 3.82: 4501 3.82 - 4.36: 5253 4.36 - 4.90: 9287 Nonbonded interactions: 22182 Sorted by model distance: nonbonded pdb=" O PRO A 236 " pdb=" OG SER A 240 " model vdw 2.211 2.440 nonbonded pdb=" O PRO A 336 " pdb=" OG SER A 340 " model vdw 2.249 2.440 nonbonded pdb=" O GLN A 142 " pdb=" ND2 ASN A 146 " model vdw 2.295 2.520 nonbonded pdb=" O ILE A 367 " pdb=" OG SER A 371 " model vdw 2.432 2.440 nonbonded pdb=" O GLN A 192 " pdb=" OG SER A 196 " model vdw 2.492 2.440 ... (remaining 22177 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: 1.340 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.300 Find NCS groups from input model: 0.020 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.006 0.048 2876 Z= 0.415 Angle : 0.936 10.379 3915 Z= 0.622 Chirality : 0.057 0.317 470 Planarity : 0.007 0.047 479 Dihedral : 15.619 86.816 1002 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.39 % Rotamer: Outliers : 1.35 % Allowed : 25.25 % Favored : 73.40 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.43), residues: 372 helix: 1.10 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -2.20 (0.63), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.017 0.002 PHE A 238 TYR 0.014 0.002 TYR A 422 ARG 0.004 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.311 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.9759 time to fit residues: 54.4165 Evaluate side-chains 45 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 371 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.0020 chunk 15 optimal weight: 0.0030 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.0050 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.2212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2876 Z= 0.171 Angle : 0.644 10.035 3915 Z= 0.319 Chirality : 0.041 0.146 470 Planarity : 0.006 0.044 479 Dihedral : 5.281 39.050 400 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.70 % Allowed : 23.57 % Favored : 72.73 % 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 (0.44), residues: 372 helix: 1.61 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -2.18 (0.69), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.012 0.001 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.286 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 62 average time/residue: 0.8949 time to fit residues: 57.3191 Evaluate side-chains 44 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8349 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2876 Z= 0.242 Angle : 0.650 10.154 3915 Z= 0.322 Chirality : 0.042 0.147 470 Planarity : 0.006 0.045 479 Dihedral : 4.794 36.479 396 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.38 % Allowed : 22.90 % Favored : 72.73 % 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: 1.81 (0.44), residues: 372 helix: 1.71 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.13 (0.69), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.022 0.002 PHE A 238 TYR 0.015 0.002 TYR A 422 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.260 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 51 average time/residue: 0.8432 time to fit residues: 44.4447 Evaluate side-chains 47 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 20 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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: 0.8316 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2876 Z= 0.196 Angle : 0.618 9.988 3915 Z= 0.304 Chirality : 0.041 0.140 470 Planarity : 0.006 0.045 479 Dihedral : 4.677 35.992 396 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.37 % Allowed : 23.57 % Favored : 73.06 % 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: 2.08 (0.45), residues: 372 helix: 1.91 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.11 (0.71), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.000 0.000 HIS A 353 PHE 0.017 0.001 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.295 Fit side-chains REVERT: A 262 ASP cc_start: 0.7610 (t0) cc_final: 0.7297 (t70) outliers start: 10 outliers final: 2 residues processed: 57 average time/residue: 0.9102 time to fit residues: 53.6439 Evaluate side-chains 50 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 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: 0.8361 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2876 Z= 0.241 Angle : 0.642 10.127 3915 Z= 0.317 Chirality : 0.042 0.136 470 Planarity : 0.006 0.046 479 Dihedral : 4.737 36.451 396 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.71 % Allowed : 20.88 % Favored : 74.41 % 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: 1.71 (0.45), residues: 372 helix: 1.65 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.66 (0.75), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.024 0.002 PHE A 238 TYR 0.017 0.002 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.294 Fit side-chains REVERT: A 275 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7604 (t) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.8647 time to fit residues: 50.9141 Evaluate side-chains 55 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 410 VAL 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: 0.2980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 26 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: 0.8340 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2876 Z= 0.208 Angle : 0.627 9.966 3915 Z= 0.306 Chirality : 0.041 0.131 470 Planarity : 0.006 0.045 479 Dihedral : 4.648 35.312 396 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.04 % Allowed : 21.55 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.45), residues: 372 helix: 1.75 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.68 (0.76), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.020 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.305 Fit side-chains REVERT: A 275 VAL cc_start: 0.7827 (OUTLIER) cc_final: 0.7587 (t) outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 0.9735 time to fit residues: 55.2768 Evaluate side-chains 53 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 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: 0.8354 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2876 Z= 0.226 Angle : 0.638 10.017 3915 Z= 0.312 Chirality : 0.042 0.128 470 Planarity : 0.006 0.045 479 Dihedral : 4.672 35.110 396 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.70 % Allowed : 22.22 % Favored : 74.07 % 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: 1.66 (0.45), residues: 372 helix: 1.66 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.98 (0.75), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.001 0.001 HIS A 414 PHE 0.020 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.298 Fit side-chains REVERT: A 275 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7596 (t) outliers start: 11 outliers final: 5 residues processed: 54 average time/residue: 0.9397 time to fit residues: 52.4272 Evaluate side-chains 52 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.0970 chunk 14 optimal weight: 0.4980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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: 0.8324 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2876 Z= 0.194 Angle : 0.628 9.833 3915 Z= 0.307 Chirality : 0.041 0.127 470 Planarity : 0.006 0.046 479 Dihedral : 4.580 33.832 396 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.70 % Allowed : 22.56 % Favored : 73.74 % 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: 1.86 (0.45), residues: 372 helix: 1.80 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.97 (0.76), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.019 0.001 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.277 Fit side-chains REVERT: A 262 ASP cc_start: 0.7850 (t0) cc_final: 0.7534 (t70) REVERT: A 275 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7583 (t) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 0.8885 time to fit residues: 47.7815 Evaluate side-chains 49 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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: 0.8342 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2876 Z= 0.216 Angle : 0.643 9.925 3915 Z= 0.314 Chirality : 0.041 0.124 470 Planarity : 0.006 0.046 479 Dihedral : 4.611 34.019 396 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.03 % Allowed : 22.22 % Favored : 74.75 % 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: 1.78 (0.45), residues: 372 helix: 1.74 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.98 (0.76), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.018 0.001 PHE A 238 TYR 0.015 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) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.314 Fit side-chains REVERT: A 275 VAL cc_start: 0.7829 (OUTLIER) cc_final: 0.7557 (t) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.9759 time to fit residues: 52.3707 Evaluate side-chains 51 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 0.0570 chunk 31 optimal weight: 0.4980 chunk 8 optimal weight: 0.0010 chunk 27 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.2102 ------------------------------------------------------------------------------- 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: 0.8262 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2876 Z= 0.163 Angle : 0.608 9.753 3915 Z= 0.293 Chirality : 0.040 0.122 470 Planarity : 0.006 0.046 479 Dihedral : 4.433 31.541 396 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.68 % Allowed : 24.92 % Favored : 73.40 % 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: 2.24 (0.46), residues: 372 helix: 2.05 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -2.84 (0.78), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 328 HIS 0.000 0.000 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.010 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.313 Fit side-chains REVERT: A 275 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7494 (t) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.9074 time to fit residues: 49.7186 Evaluate side-chains 48 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.138609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120986 restraints weight = 3370.621| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.32 r_work: 0.3188 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2876 Z= 0.239 Angle : 0.661 9.972 3915 Z= 0.323 Chirality : 0.042 0.127 470 Planarity : 0.006 0.046 479 Dihedral : 4.565 33.369 396 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.02 % Allowed : 24.92 % Favored : 73.06 % 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 (0.44), residues: 372 helix: 1.78 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -2.91 (0.79), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.022 0.002 PHE A 238 TYR 0.018 0.002 TYR A 422 ARG 0.001 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1451.44 seconds wall clock time: 29 minutes 45.85 seconds (1785.85 seconds total)