Starting phenix.real_space_refine on Thu Jul 18 18:40:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/07_2024/8jtc_36640.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/07_2024/8jtc_36640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/07_2024/8jtc_36640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/07_2024/8jtc_36640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/07_2024/8jtc_36640.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/07_2024/8jtc_36640.cif" } resolution = 3.52 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= 0.000 sd= 0.068 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 1963 2.51 5 N 452 2.21 5 O 499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 49": "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: 2941 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2897 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.69, per 1000 atoms: 0.91 Number of scatterers: 2941 At special positions: 0 Unit cell: (56.16, 67.6, 73.84, 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 499 8.00 N 452 7.00 C 1963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 894.6 milliseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 706 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 92.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 18 through 54 removed outlier: 4.013A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.912A 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 122 through 157 removed outlier: 3.887A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.678A pdb=" N TYR A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.555A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 291 through 323 removed outlier: 4.143A 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 328 through 333 removed outlier: 4.041A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.508A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.735A 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 383 Processing helix chain 'A' and resid 384 through 414 Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 447 removed outlier: 4.556A pdb=" N TYR A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.027A pdb=" N ALA A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 469 259 hydrogen bonds defined for protein. 768 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: 0.84 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 441 1.30 - 1.43: 776 1.43 - 1.56: 1753 1.56 - 1.68: 0 1.68 - 1.81: 46 Bond restraints: 3016 Sorted by residual: bond pdb=" C12 YHR A 501 " pdb=" N21 YHR A 501 " ideal model delta sigma weight residual 1.374 1.217 0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" C31 YHR A 501 " pdb=" O30 YHR A 501 " ideal model delta sigma weight residual 1.326 1.410 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C17 YHR A 501 " pdb=" O19 YHR A 501 " ideal model delta sigma weight residual 1.325 1.408 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C22 YHR A 501 " pdb=" N21 YHR A 501 " ideal model delta sigma weight residual 1.365 1.283 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C31 YHR A 501 " pdb=" C33 YHR A 501 " ideal model delta sigma weight residual 1.486 1.549 -0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 3011 not shown) Histogram of bond angle deviations from ideal: 97.90 - 106.16: 115 106.16 - 114.41: 1792 114.41 - 122.67: 2057 122.67 - 130.92: 137 130.92 - 139.17: 12 Bond angle restraints: 4113 Sorted by residual: angle pdb=" C12 YHR A 501 " pdb=" N21 YHR A 501 " pdb=" C22 YHR A 501 " ideal model delta sigma weight residual 109.26 123.97 -14.71 3.00e+00 1.11e-01 2.40e+01 angle pdb=" N PRO A 450 " pdb=" CA PRO A 450 " pdb=" C PRO A 450 " ideal model delta sigma weight residual 113.47 108.59 4.88 1.43e+00 4.89e-01 1.16e+01 angle pdb=" CA VAL A 241 " pdb=" C VAL A 241 " pdb=" O VAL A 241 " ideal model delta sigma weight residual 121.17 117.69 3.48 1.06e+00 8.90e-01 1.08e+01 angle pdb=" CA ILE A 223 " pdb=" C ILE A 223 " pdb=" O ILE A 223 " ideal model delta sigma weight residual 121.05 117.52 3.53 1.11e+00 8.12e-01 1.01e+01 angle pdb=" N ILE A 395 " pdb=" CA ILE A 395 " pdb=" C ILE A 395 " ideal model delta sigma weight residual 110.62 107.41 3.21 1.02e+00 9.61e-01 9.93e+00 ... (remaining 4108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 1586 17.24 - 34.48: 177 34.48 - 51.72: 34 51.72 - 68.96: 3 68.96 - 86.20: 1 Dihedral angle restraints: 1801 sinusoidal: 693 harmonic: 1108 Sorted by residual: dihedral pdb=" CA GLN A 271 " pdb=" C GLN A 271 " pdb=" N PRO A 272 " pdb=" CA PRO A 272 " ideal model delta harmonic sigma weight residual 180.00 -149.93 -30.07 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA PHE A 348 " pdb=" C PHE A 348 " pdb=" N GLY A 349 " pdb=" CA GLY A 349 " ideal model delta harmonic sigma weight residual 180.00 164.02 15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA SER A 416 " pdb=" C SER A 416 " pdb=" N VAL A 417 " pdb=" CA VAL A 417 " ideal model delta harmonic sigma weight residual 180.00 164.34 15.66 0 5.00e+00 4.00e-02 9.80e+00 ... (remaining 1798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 379 0.054 - 0.107: 91 0.107 - 0.161: 16 0.161 - 0.214: 6 0.214 - 0.268: 1 Chirality restraints: 493 Sorted by residual: chirality pdb=" C13 YHR A 501 " pdb=" C12 YHR A 501 " pdb=" C14 YHR A 501 " pdb=" N8 YHR A 501 " both_signs ideal model delta sigma weight residual False -2.29 -2.56 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA TYR A 243 " pdb=" N TYR A 243 " pdb=" C TYR A 243 " pdb=" CB TYR A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CA LEU A 452 " pdb=" N LEU A 452 " pdb=" C LEU A 452 " pdb=" CB LEU A 452 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 490 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 236 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 222 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C GLY A 222 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY A 222 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 223 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 432 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C GLY A 432 " -0.028 2.00e-02 2.50e+03 pdb=" O GLY A 432 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 433 " 0.009 2.00e-02 2.50e+03 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 637 2.77 - 3.30: 3048 3.30 - 3.84: 5131 3.84 - 4.37: 5633 4.37 - 4.90: 10005 Nonbonded interactions: 24454 Sorted by model distance: nonbonded pdb=" OG SER A 325 " pdb=" OE1 GLN A 329 " model vdw 2.240 2.440 nonbonded pdb=" OG SER A 200 " pdb=" OH TYR A 422 " model vdw 2.398 2.440 nonbonded pdb=" OH TYR A 408 " pdb=" OG SER A 472 " model vdw 2.476 2.440 nonbonded pdb=" O MET A 402 " pdb=" N MET A 406 " model vdw 2.528 2.520 nonbonded pdb=" O MET A 397 " pdb=" OG SER A 401 " model vdw 2.534 2.440 ... (remaining 24449 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 group one per residue 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: 0.660 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.270 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.007 0.157 3016 Z= 0.456 Angle : 0.944 14.709 4113 Z= 0.488 Chirality : 0.050 0.268 493 Planarity : 0.006 0.066 500 Dihedral : 14.323 86.204 1095 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.33 % Allowed : 22.37 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: 1.13 (0.43), residues: 387 helix: 1.16 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.21 (0.77), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 451 HIS 0.002 0.001 HIS A 53 PHE 0.020 0.001 PHE A 348 TYR 0.016 0.001 TYR A 243 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.344 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.1441 time to fit residues: 10.8108 Evaluate side-chains 58 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.0470 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3016 Z= 0.202 Angle : 0.702 9.772 4113 Z= 0.331 Chirality : 0.042 0.198 493 Planarity : 0.005 0.045 500 Dihedral : 5.228 29.044 477 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.30 % Allowed : 21.05 % Favored : 76.64 % 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: 1.94 (0.43), residues: 387 helix: 1.70 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.01 (0.82), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.020 0.001 PHE A 348 TYR 0.006 0.001 TYR A 433 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.310 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 0.1502 time to fit residues: 12.6554 Evaluate side-chains 61 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3016 Z= 0.252 Angle : 0.707 9.968 4113 Z= 0.333 Chirality : 0.043 0.190 493 Planarity : 0.005 0.038 500 Dihedral : 4.735 28.914 475 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.63 % Allowed : 23.36 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.43), residues: 387 helix: 1.86 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.09 (0.80), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 353 PHE 0.018 0.001 PHE A 348 TYR 0.008 0.001 TYR A 211 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.298 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 69 average time/residue: 0.1405 time to fit residues: 11.7862 Evaluate side-chains 67 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3016 Z= 0.234 Angle : 0.693 9.909 4113 Z= 0.329 Chirality : 0.042 0.184 493 Planarity : 0.005 0.038 500 Dihedral : 4.651 26.915 475 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.28 % Allowed : 22.04 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.43), residues: 387 helix: 1.91 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.14 (0.80), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 PHE 0.017 0.001 PHE A 348 TYR 0.008 0.001 TYR A 211 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.326 Fit side-chains REVERT: A 51 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 458 ILE cc_start: 0.8525 (mt) cc_final: 0.8297 (mt) REVERT: A 462 LEU cc_start: 0.8847 (mt) cc_final: 0.8564 (mm) outliers start: 13 outliers final: 9 residues processed: 76 average time/residue: 0.1424 time to fit residues: 13.0480 Evaluate side-chains 74 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3016 Z= 0.246 Angle : 0.699 9.962 4113 Z= 0.331 Chirality : 0.042 0.176 493 Planarity : 0.005 0.038 500 Dihedral : 4.492 28.041 475 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.93 % Allowed : 22.70 % Favored : 72.37 % 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: 2.19 (0.43), residues: 387 helix: 1.96 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.41 (0.79), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 414 PHE 0.008 0.001 PHE A 176 TYR 0.007 0.001 TYR A 211 ARG 0.003 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.342 Fit side-chains REVERT: A 51 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 168 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7694 (mt) REVERT: A 458 ILE cc_start: 0.8556 (mt) cc_final: 0.8321 (mt) REVERT: A 462 LEU cc_start: 0.8908 (mt) cc_final: 0.8635 (mm) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 0.1579 time to fit residues: 13.8420 Evaluate side-chains 74 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.0010 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.0570 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3016 Z= 0.192 Angle : 0.666 9.753 4113 Z= 0.316 Chirality : 0.041 0.166 493 Planarity : 0.005 0.038 500 Dihedral : 4.430 25.677 475 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.96 % Allowed : 26.32 % Favored : 70.72 % 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: 2.25 (0.43), residues: 387 helix: 2.02 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.42 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 PHE 0.008 0.001 PHE A 348 TYR 0.006 0.001 TYR A 211 ARG 0.003 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.308 Fit side-chains REVERT: A 51 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 458 ILE cc_start: 0.8544 (mt) cc_final: 0.8304 (mt) REVERT: A 462 LEU cc_start: 0.8864 (mt) cc_final: 0.8609 (mm) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.1575 time to fit residues: 13.8677 Evaluate side-chains 73 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3016 Z= 0.220 Angle : 0.691 9.910 4113 Z= 0.325 Chirality : 0.041 0.168 493 Planarity : 0.005 0.039 500 Dihedral : 4.429 27.184 475 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.28 % Allowed : 25.66 % Favored : 70.07 % 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: 2.29 (0.43), residues: 387 helix: 2.02 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.32 (0.81), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 PHE 0.014 0.001 PHE A 27 TYR 0.007 0.001 TYR A 211 ARG 0.004 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.352 Fit side-chains REVERT: A 51 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8245 (tt) REVERT: A 168 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7700 (mt) REVERT: A 458 ILE cc_start: 0.8533 (mt) cc_final: 0.8286 (mt) REVERT: A 462 LEU cc_start: 0.8875 (mt) cc_final: 0.8610 (mm) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.1534 time to fit residues: 13.5230 Evaluate side-chains 77 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3016 Z= 0.243 Angle : 0.700 9.906 4113 Z= 0.330 Chirality : 0.042 0.175 493 Planarity : 0.005 0.039 500 Dihedral : 4.402 26.297 475 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.61 % Allowed : 25.33 % Favored : 70.07 % 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: 2.25 (0.43), residues: 387 helix: 1.94 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.06 (0.82), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 PHE 0.014 0.001 PHE A 27 TYR 0.007 0.001 TYR A 211 ARG 0.003 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.324 Fit side-chains REVERT: A 51 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 156 ILE cc_start: 0.8629 (tt) cc_final: 0.8351 (tp) REVERT: A 168 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7717 (mt) REVERT: A 176 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7381 (t80) REVERT: A 458 ILE cc_start: 0.8537 (mt) cc_final: 0.8258 (mt) REVERT: A 462 LEU cc_start: 0.8882 (mt) cc_final: 0.8619 (mm) outliers start: 14 outliers final: 8 residues processed: 74 average time/residue: 0.1599 time to fit residues: 14.0714 Evaluate side-chains 76 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3016 Z= 0.241 Angle : 0.700 9.979 4113 Z= 0.330 Chirality : 0.042 0.171 493 Planarity : 0.005 0.039 500 Dihedral : 4.427 27.475 475 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.61 % Allowed : 25.66 % Favored : 69.74 % 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: 2.20 (0.44), residues: 387 helix: 1.97 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.30 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 414 PHE 0.014 0.001 PHE A 27 TYR 0.007 0.001 TYR A 211 ARG 0.004 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.342 Fit side-chains REVERT: A 156 ILE cc_start: 0.8599 (tt) cc_final: 0.8314 (tp) REVERT: A 168 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7720 (mt) REVERT: A 176 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7385 (t80) REVERT: A 458 ILE cc_start: 0.8537 (mt) cc_final: 0.8254 (mt) REVERT: A 462 LEU cc_start: 0.8882 (mt) cc_final: 0.8618 (mm) outliers start: 14 outliers final: 11 residues processed: 76 average time/residue: 0.1615 time to fit residues: 14.7465 Evaluate side-chains 78 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3016 Z= 0.207 Angle : 0.690 9.819 4113 Z= 0.324 Chirality : 0.041 0.171 493 Planarity : 0.005 0.039 500 Dihedral : 4.417 25.628 475 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.61 % Allowed : 25.00 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.44), residues: 387 helix: 2.04 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -1.34 (0.82), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 328 HIS 0.001 0.000 HIS A 53 PHE 0.025 0.001 PHE A 348 TYR 0.007 0.001 TYR A 211 ARG 0.004 0.001 ARG A 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.318 Fit side-chains REVERT: A 156 ILE cc_start: 0.8598 (tt) cc_final: 0.8325 (tp) REVERT: A 168 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7699 (mt) REVERT: A 176 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7375 (t80) REVERT: A 326 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7366 (mtm-85) REVERT: A 458 ILE cc_start: 0.8533 (mt) cc_final: 0.8322 (mt) REVERT: A 462 LEU cc_start: 0.8875 (mt) cc_final: 0.8612 (mm) outliers start: 14 outliers final: 11 residues processed: 76 average time/residue: 0.1427 time to fit residues: 13.0416 Evaluate side-chains 77 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124548 restraints weight = 4324.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127827 restraints weight = 2161.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130010 restraints weight = 1322.290| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3016 Z= 0.245 Angle : 0.707 9.971 4113 Z= 0.335 Chirality : 0.042 0.170 493 Planarity : 0.005 0.039 500 Dihedral : 4.420 27.239 475 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.62 % Allowed : 26.64 % Favored : 69.74 % 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: 2.22 (0.44), residues: 387 helix: 1.98 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.29 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.000 HIS A 53 PHE 0.024 0.001 PHE A 348 TYR 0.008 0.001 TYR A 211 ARG 0.004 0.000 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1028.49 seconds wall clock time: 21 minutes 27.47 seconds (1287.47 seconds total)