Starting phenix.real_space_refine on Fri Apr 5 13:34:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/04_2024/8jtc_36640_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/04_2024/8jtc_36640.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/04_2024/8jtc_36640_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/04_2024/8jtc_36640_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/04_2024/8jtc_36640_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/04_2024/8jtc_36640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/04_2024/8jtc_36640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/04_2024/8jtc_36640_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/04_2024/8jtc_36640_updated.pdb" } 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-5288/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: 2.11, per 1000 atoms: 0.72 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: 1.35 Conformation dependent library (CDL) restraints added in 559.8 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... running ksdssp... Secondary structure from input PDB file: 14 helices and 0 sheets defined 87.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 19 through 53 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 156 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 178 Processing helix chain 'A' and resid 182 through 210 Processing helix chain 'A' and resid 214 through 245 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 269 removed outlier: 4.555A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 292 through 322 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 329 through 355 removed outlier: 4.169A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Proline residue: A 336 - end of helix 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 357 through 377 Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 385 through 413 Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 446 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 449 through 468 Proline residue: A 465 - end of helix removed outlier: 4.427A pdb=" N PHE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 717 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.36 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 1.363 1.217 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C13 YHR A 501 " pdb=" N8 YHR A 501 " ideal model delta sigma weight residual 1.514 1.407 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C22 YHR A 501 " pdb=" N21 YHR A 501 " ideal model delta sigma weight residual 1.389 1.283 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C11 YHR A 501 " pdb=" C23 YHR A 501 " ideal model delta sigma weight residual 1.373 1.477 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" N ILE A 223 " pdb=" CA ILE A 223 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.19e-02 7.06e+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=" C27 YHR A 501 " pdb=" C26 YHR A 501 " pdb=" O28 YHR A 501 " ideal model delta sigma weight residual 101.89 119.99 -18.10 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C25 YHR A 501 " pdb=" C26 YHR A 501 " pdb=" O28 YHR A 501 " ideal model delta sigma weight residual 137.71 120.12 17.59 3.00e+00 1.11e-01 3.44e+01 angle pdb=" C12 YHR A 501 " pdb=" N21 YHR A 501 " pdb=" C22 YHR A 501 " ideal model delta sigma weight residual 108.09 123.97 -15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C7 YHR A 501 " pdb=" N8 YHR A 501 " pdb=" C9 YHR A 501 " ideal model delta sigma weight residual 99.45 115.07 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C11 YHR A 501 " pdb=" C10 YHR A 501 " pdb=" C9 YHR A 501 " ideal model delta sigma weight residual 118.10 103.47 14.63 3.00e+00 1.11e-01 2.38e+01 ... (remaining 4108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 1544 17.25 - 34.50: 176 34.50 - 51.75: 28 51.75 - 69.00: 3 69.00 - 86.25: 2 Dihedral angle restraints: 1753 sinusoidal: 645 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 1750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 332 0.041 - 0.082: 118 0.082 - 0.122: 28 0.122 - 0.163: 9 0.163 - 0.204: 6 Chirality restraints: 493 Sorted by residual: chirality pdb=" C16 YHR A 501 " pdb=" C15 YHR A 501 " pdb=" C17 YHR A 501 " pdb=" C3 YHR A 501 " both_signs ideal model delta sigma weight residual False 2.75 2.55 0.20 2.00e-01 2.50e+01 1.04e+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: 640 2.77 - 3.30: 3061 3.30 - 3.84: 5160 3.84 - 4.37: 5661 4.37 - 4.90: 10012 Nonbonded interactions: 24534 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 24529 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.520 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.430 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.000 ------------------------------------------------------------------------------- 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 0.146 3016 Z= 0.472 Angle : 1.064 18.102 4113 Z= 0.515 Chirality : 0.049 0.204 493 Planarity : 0.006 0.066 500 Dihedral : 14.571 86.250 1047 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 : 0.307 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.1572 time to fit residues: 11.6850 Evaluate side-chains 58 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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: 0.8980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.0470 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.0623 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= 0.237 Angle : 0.707 9.867 4113 Z= 0.332 Chirality : 0.042 0.197 493 Planarity : 0.005 0.046 500 Dihedral : 6.047 75.527 429 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.63 % Allowed : 20.72 % 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: 1.88 (0.43), residues: 387 helix: 1.70 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.23 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.001 0.000 HIS A 53 PHE 0.020 0.001 PHE A 348 TYR 0.007 0.001 TYR A 211 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 75 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.258 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.1434 time to fit residues: 12.5946 Evaluate side-chains 64 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 300 SER Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.0793 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= 0.242 Angle : 0.695 9.908 4113 Z= 0.327 Chirality : 0.042 0.189 493 Planarity : 0.005 0.039 500 Dihedral : 5.861 72.826 429 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.96 % Allowed : 23.68 % Favored : 73.36 % 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: 1.91 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.35 (0.77), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.018 0.001 PHE A 348 TYR 0.008 0.001 TYR A 211 ARG 0.005 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 75 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.338 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.1493 time to fit residues: 13.0441 Evaluate side-chains 67 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 270 LEU Chi-restraints excluded: chain A residue 300 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3016 Z= 0.239 Angle : 0.685 9.843 4113 Z= 0.324 Chirality : 0.042 0.181 493 Planarity : 0.005 0.039 500 Dihedral : 5.531 69.558 427 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.61 % Allowed : 23.36 % Favored : 72.04 % 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: 1.94 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.30 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 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 84 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.291 Fit side-chains REVERT: A 51 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8308 (tt) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.1416 time to fit residues: 13.7601 Evaluate side-chains 73 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 270 LEU 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: 0.7980 chunk 15 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.0020 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 overall best weight: 0.3746 ------------------------------------------------------------------------------- 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: 0.7810 moved from start: 0.1226 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= 0.200 Angle : 0.678 9.713 4113 Z= 0.321 Chirality : 0.041 0.169 493 Planarity : 0.005 0.038 500 Dihedral : 5.377 65.139 427 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.63 % Allowed : 26.64 % 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: 2.16 (0.44), residues: 387 helix: 1.91 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.29 (0.79), 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 414 PHE 0.008 0.001 PHE A 238 TYR 0.007 0.001 TYR A 211 ARG 0.005 0.001 ARG A 357 *********************** 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 74 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.245 Fit side-chains REVERT: A 23 LEU cc_start: 0.9128 (tp) cc_final: 0.8887 (tp) REVERT: A 458 ILE cc_start: 0.8555 (mt) cc_final: 0.8225 (mp) REVERT: A 462 LEU cc_start: 0.8857 (mt) cc_final: 0.8577 (mm) outliers start: 8 outliers final: 7 residues processed: 71 average time/residue: 0.1518 time to fit residues: 12.9988 Evaluate side-chains 69 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 212 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 312 GLU 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: 0.5980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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: 0.1268 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= 0.216 Angle : 0.675 9.771 4113 Z= 0.319 Chirality : 0.041 0.170 493 Planarity : 0.005 0.039 500 Dihedral : 5.311 63.765 427 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.95 % Allowed : 26.32 % 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: 2.19 (0.44), residues: 387 helix: 1.92 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.24 (0.79), 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 0.009 0.001 PHE A 348 TYR 0.007 0.001 TYR A 211 ARG 0.005 0.001 ARG A 357 *********************** 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 77 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.366 Fit side-chains REVERT: A 23 LEU cc_start: 0.9113 (tp) cc_final: 0.8871 (tp) REVERT: A 168 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7647 (mt) REVERT: A 458 ILE cc_start: 0.8579 (mt) cc_final: 0.8238 (mp) REVERT: A 462 LEU cc_start: 0.8866 (mt) cc_final: 0.8575 (mm) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.1499 time to fit residues: 13.3692 Evaluate side-chains 70 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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 270 LEU Chi-restraints excluded: chain A residue 312 GLU 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: 0.9980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.0570 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.1390 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= 0.222 Angle : 0.677 9.825 4113 Z= 0.320 Chirality : 0.041 0.169 493 Planarity : 0.005 0.039 500 Dihedral : 5.296 63.497 427 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 2.16 (0.44), residues: 387 helix: 1.92 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.31 (0.79), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.000 0.000 HIS A 414 PHE 0.008 0.001 PHE A 238 TYR 0.007 0.001 TYR A 211 ARG 0.005 0.001 ARG A 357 *********************** 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 81 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.328 Fit side-chains REVERT: A 168 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7651 (mt) REVERT: A 458 ILE cc_start: 0.8575 (mt) cc_final: 0.8282 (mp) REVERT: A 462 LEU cc_start: 0.8899 (mt) cc_final: 0.8626 (mm) outliers start: 13 outliers final: 12 residues processed: 77 average time/residue: 0.1544 time to fit residues: 14.3996 Evaluate side-chains 73 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 212 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 270 LEU 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: 0.9980 chunk 29 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.1379 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= 0.236 Angle : 0.688 9.844 4113 Z= 0.326 Chirality : 0.041 0.172 493 Planarity : 0.005 0.039 500 Dihedral : 5.323 63.892 427 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.61 % Allowed : 26.97 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.44), residues: 387 helix: 1.88 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.28 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.000 0.000 HIS A 414 PHE 0.009 0.001 PHE A 348 TYR 0.007 0.001 TYR A 211 ARG 0.005 0.001 ARG A 357 *********************** 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 78 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.318 Fit side-chains REVERT: A 51 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 168 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7652 (mt) REVERT: A 458 ILE cc_start: 0.8580 (mt) cc_final: 0.8263 (mp) REVERT: A 462 LEU cc_start: 0.8906 (mt) cc_final: 0.8627 (mm) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.1551 time to fit residues: 13.8105 Evaluate side-chains 76 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 270 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1447 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= 0.258 Angle : 0.700 9.910 4113 Z= 0.333 Chirality : 0.042 0.174 493 Planarity : 0.005 0.039 500 Dihedral : 5.403 65.198 427 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.61 % Allowed : 26.64 % Favored : 68.75 % 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: 2.06 (0.44), residues: 387 helix: 1.85 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.31 (0.77), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.008 0.001 PHE A 393 TYR 0.008 0.001 TYR A 211 ARG 0.005 0.001 ARG A 357 *********************** 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 78 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.327 Fit side-chains REVERT: A 51 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8349 (tt) REVERT: A 168 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7665 (mt) REVERT: A 211 TYR cc_start: 0.7210 (m-80) cc_final: 0.6418 (m-80) REVERT: A 402 MET cc_start: 0.8207 (mmt) cc_final: 0.7900 (mmm) REVERT: A 462 LEU cc_start: 0.8911 (mt) cc_final: 0.8640 (mm) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.1599 time to fit residues: 14.2176 Evaluate side-chains 76 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 270 LEU 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: 0.7980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3016 Z= 0.268 Angle : 0.712 9.916 4113 Z= 0.339 Chirality : 0.042 0.177 493 Planarity : 0.005 0.040 500 Dihedral : 5.464 65.940 427 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.93 % Allowed : 26.64 % Favored : 68.42 % 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: 2.03 (0.44), residues: 387 helix: 1.83 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.32 (0.77), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.001 0.000 HIS A 53 PHE 0.026 0.001 PHE A 348 TYR 0.008 0.001 TYR A 211 ARG 0.007 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 80 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.323 Fit side-chains REVERT: A 51 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8301 (tt) REVERT: A 168 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7675 (mt) REVERT: A 211 TYR cc_start: 0.7225 (m-80) cc_final: 0.6431 (m-80) REVERT: A 326 ARG cc_start: 0.8561 (ttm-80) cc_final: 0.8052 (mtm180) REVERT: A 402 MET cc_start: 0.8217 (mmt) cc_final: 0.7915 (mmm) outliers start: 15 outliers final: 12 residues processed: 77 average time/residue: 0.1516 time to fit residues: 14.0193 Evaluate side-chains 77 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 232 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 270 LEU 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: 0.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 0.0010 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.137396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124378 restraints weight = 4363.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127598 restraints weight = 2181.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129777 restraints weight = 1334.348| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1484 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= 0.242 Angle : 0.705 9.836 4113 Z= 0.333 Chirality : 0.042 0.173 493 Planarity : 0.005 0.040 500 Dihedral : 5.417 64.319 427 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.61 % Allowed : 26.64 % Favored : 68.75 % 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: 1.99 (0.44), residues: 387 helix: 1.82 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.41 (0.77), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.000 HIS A 53 PHE 0.024 0.001 PHE A 348 TYR 0.008 0.001 TYR A 49 ARG 0.006 0.001 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1080.03 seconds wall clock time: 20 minutes 2.57 seconds (1202.57 seconds total)