Starting phenix.real_space_refine on Fri Dec 27 06:57:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jts_36651/12_2024/8jts_36651.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jts_36651/12_2024/8jts_36651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jts_36651/12_2024/8jts_36651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jts_36651/12_2024/8jts_36651.map" model { file = "/net/cci-nas-00/data/ceres_data/8jts_36651/12_2024/8jts_36651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jts_36651/12_2024/8jts_36651.cif" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.079 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 23 5.16 5 C 2190 2.51 5 N 534 2.21 5 O 583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3321 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 157 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.80 Number of scatterers: 3330 At special positions: 0 Unit cell: (94.1775, 58.455, 67.115, 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 23 16.00 O 583 8.00 N 534 7.00 C 2190 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 - 3.00 Amino acid : True - 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: 0.99 Conformation dependent library (CDL) restraints added in 432.5 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.670A pdb=" N CYS A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 174 through 195 Processing helix chain 'A' and resid 199 through 228 Processing helix chain 'A' and resid 232 through 258 Processing helix chain 'A' and resid 260 through 279 removed outlier: 3.668A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.896A pdb=" N TYR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 340 through 368 Processing helix chain 'A' and resid 376 through 397 removed outlier: 3.657A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 403 through 423 removed outlier: 3.865A pdb=" N MET A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 456 removed outlier: 4.146A pdb=" N ILE A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 removed outlier: 4.081A pdb=" N ASN A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.855A pdb=" N CYS A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 491 Proline residue: A 481 - end of helix removed outlier: 3.888A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 removed outlier: 3.676A pdb=" N ILE A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.986A pdb=" N LEU A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 533 1.30 - 1.43: 891 1.43 - 1.56: 1950 1.56 - 1.69: 0 1.69 - 1.82: 35 Bond restraints: 3409 Sorted by residual: bond pdb=" CA THR A 356 " pdb=" C THR A 356 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.27e-02 6.20e+03 7.52e+01 bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.447 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" N ARG A 439 " pdb=" CA ARG A 439 " ideal model delta sigma weight residual 1.459 1.363 0.095 1.24e-02 6.50e+03 5.90e+01 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.245 0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " ideal model delta sigma weight residual 1.530 1.432 0.098 1.57e-02 4.06e+03 3.91e+01 ... (remaining 3404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 4485 1.96 - 3.91: 134 3.91 - 5.87: 39 5.87 - 7.82: 12 7.82 - 9.78: 6 Bond angle restraints: 4676 Sorted by residual: angle pdb=" N THR A 356 " pdb=" CA THR A 356 " pdb=" C THR A 356 " ideal model delta sigma weight residual 111.07 102.52 8.55 1.07e+00 8.73e-01 6.38e+01 angle pdb=" C THR A 356 " pdb=" N ASP A 357 " pdb=" CA ASP A 357 " ideal model delta sigma weight residual 120.65 110.87 9.78 1.32e+00 5.74e-01 5.49e+01 angle pdb=" CA ASP A 357 " pdb=" C ASP A 357 " pdb=" N SER A 358 " ideal model delta sigma weight residual 116.92 124.94 -8.02 1.16e+00 7.43e-01 4.79e+01 angle pdb=" N GLN A 362 " pdb=" CA GLN A 362 " pdb=" C GLN A 362 " ideal model delta sigma weight residual 111.75 104.24 7.51 1.28e+00 6.10e-01 3.44e+01 angle pdb=" O ASP A 357 " pdb=" C ASP A 357 " pdb=" N SER A 358 " ideal model delta sigma weight residual 122.03 116.89 5.14 1.04e+00 9.25e-01 2.44e+01 ... (remaining 4671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1767 17.47 - 34.94: 148 34.94 - 52.41: 29 52.41 - 69.89: 7 69.89 - 87.36: 3 Dihedral angle restraints: 1954 sinusoidal: 634 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ILE A 442 " pdb=" C ILE A 442 " pdb=" N THR A 443 " pdb=" CA THR A 443 " ideal model delta harmonic sigma weight residual 180.00 151.77 28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N ASP A 357 " pdb=" CA ASP A 357 " ideal model delta harmonic sigma weight residual 180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA MET A 448 " pdb=" C MET A 448 " pdb=" N ILE A 449 " pdb=" CA ILE A 449 " ideal model delta harmonic sigma weight residual 180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 1951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 465 0.056 - 0.112: 92 0.112 - 0.168: 8 0.168 - 0.224: 2 0.224 - 0.280: 4 Chirality restraints: 571 Sorted by residual: chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ASP A 357 " pdb=" N ASP A 357 " pdb=" C ASP A 357 " pdb=" CB ASP A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA TYR A 361 " pdb=" N TYR A 361 " pdb=" C TYR A 361 " pdb=" CB TYR A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 568 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -0.070 2.00e-02 2.50e+03 4.80e-01 5.19e+03 pdb=" C03 MF8 A 601 " 0.458 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " -0.216 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " 0.227 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " 0.055 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " -1.078 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " 0.514 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " -0.349 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " 0.459 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO A 271 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 361 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C TYR A 361 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR A 361 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 362 " -0.014 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 738 2.78 - 3.31: 3476 3.31 - 3.84: 5593 3.84 - 4.37: 5722 4.37 - 4.90: 9809 Nonbonded interactions: 25338 Sorted by model distance: nonbonded pdb=" O GLY A 167 " pdb=" ND2 ASN A 463 " model vdw 2.249 3.120 nonbonded pdb=" OG SER A 424 " pdb=" OD1 ASP A 426 " model vdw 2.315 3.040 nonbonded pdb=" O GLY A 12 " pdb=" NE2 GLN A 18 " model vdw 2.327 3.120 nonbonded pdb=" OD1 ASN A 198 " pdb=" OG SER A 201 " model vdw 2.345 3.040 nonbonded pdb=" O VAL A 141 " pdb=" OG SER A 145 " model vdw 2.367 3.040 ... (remaining 25333 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 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 : 0.008 0.166 3409 Z= 0.445 Angle : 0.933 9.780 4676 Z= 0.539 Chirality : 0.049 0.280 571 Planarity : 0.021 0.480 582 Dihedral : 14.111 87.356 1104 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.31 % Allowed : 0.94 % Favored : 98.75 % 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: -0.32 (0.39), residues: 457 helix: 0.25 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.17 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 354 HIS 0.001 0.000 HIS A 260 PHE 0.021 0.002 PHE A 151 TYR 0.010 0.001 TYR A 256 ARG 0.006 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.363 Fit side-chains REVERT: A 137 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6584 (mm-30) REVERT: A 293 LYS cc_start: 0.8310 (mttm) cc_final: 0.8109 (mttm) REVERT: A 352 TYR cc_start: 0.5406 (m-80) cc_final: 0.5079 (m-80) REVERT: A 361 TYR cc_start: 0.8688 (t80) cc_final: 0.8330 (t80) REVERT: A 449 ILE cc_start: 0.8890 (tt) cc_final: 0.8569 (tt) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.1242 time to fit residues: 15.0945 Evaluate side-chains 80 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.0020 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3409 Z= 0.182 Angle : 0.596 6.904 4676 Z= 0.298 Chirality : 0.039 0.158 571 Planarity : 0.005 0.062 582 Dihedral : 4.395 19.039 479 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: 0.32 (0.39), residues: 457 helix: 0.78 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.12 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.019 0.001 PHE A 41 TYR 0.010 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.387 Fit side-chains REVERT: A 137 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6708 (mm-30) REVERT: A 352 TYR cc_start: 0.5312 (m-80) cc_final: 0.5089 (m-80) REVERT: A 449 ILE cc_start: 0.8881 (tt) cc_final: 0.8530 (tt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1133 time to fit residues: 13.9124 Evaluate side-chains 80 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 367 HIS A 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3409 Z= 0.189 Angle : 0.621 7.483 4676 Z= 0.308 Chirality : 0.040 0.161 571 Planarity : 0.005 0.062 582 Dihedral : 4.277 16.536 479 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.31 % Allowed : 5.94 % Favored : 93.75 % 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: 0.66 (0.40), residues: 457 helix: 1.05 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.08 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.000 0.000 HIS A 304 PHE 0.016 0.002 PHE A 41 TYR 0.016 0.001 TYR A 361 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.350 Fit side-chains REVERT: A 137 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6630 (mm-30) REVERT: A 449 ILE cc_start: 0.8838 (tt) cc_final: 0.8594 (tt) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1074 time to fit residues: 13.2261 Evaluate side-chains 81 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3409 Z= 0.184 Angle : 0.612 7.287 4676 Z= 0.303 Chirality : 0.040 0.178 571 Planarity : 0.005 0.062 582 Dihedral : 4.202 15.807 479 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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: 0.73 (0.40), residues: 457 helix: 1.11 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.11 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.003 0.001 HIS A 367 PHE 0.022 0.002 PHE A 151 TYR 0.011 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.360 Fit side-chains REVERT: A 137 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6513 (mm-30) REVERT: A 287 ARG cc_start: 0.8696 (ttm-80) cc_final: 0.8384 (ttm-80) REVERT: A 352 TYR cc_start: 0.5363 (m-80) cc_final: 0.5102 (m-80) REVERT: A 426 ASP cc_start: 0.8029 (p0) cc_final: 0.7493 (m-30) REVERT: A 449 ILE cc_start: 0.8823 (tt) cc_final: 0.8590 (tt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1063 time to fit residues: 13.5941 Evaluate side-chains 86 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3409 Z= 0.176 Angle : 0.609 6.760 4676 Z= 0.302 Chirality : 0.039 0.164 571 Planarity : 0.005 0.059 582 Dihedral : 4.196 15.633 479 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: 0.87 (0.40), residues: 457 helix: 1.23 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.11 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 217 HIS 0.001 0.001 HIS A 367 PHE 0.021 0.001 PHE A 41 TYR 0.010 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.350 Fit side-chains REVERT: A 137 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6436 (mm-30) REVERT: A 287 ARG cc_start: 0.8701 (ttm-80) cc_final: 0.8354 (ttm-80) REVERT: A 426 ASP cc_start: 0.8437 (p0) cc_final: 0.7936 (m-30) REVERT: A 449 ILE cc_start: 0.8862 (tt) cc_final: 0.8589 (tt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1099 time to fit residues: 13.5836 Evaluate side-chains 86 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3409 Z= 0.177 Angle : 0.627 7.127 4676 Z= 0.309 Chirality : 0.040 0.161 571 Planarity : 0.005 0.059 582 Dihedral : 4.163 14.923 479 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 0.89 (0.40), residues: 457 helix: 1.23 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.10 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 217 HIS 0.000 0.000 HIS A 367 PHE 0.021 0.001 PHE A 151 TYR 0.009 0.001 TYR A 361 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.360 Fit side-chains REVERT: A 137 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6371 (mm-30) REVERT: A 287 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8350 (ttm-80) REVERT: A 426 ASP cc_start: 0.8453 (p0) cc_final: 0.7947 (m-30) REVERT: A 449 ILE cc_start: 0.8847 (tt) cc_final: 0.8567 (tt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1135 time to fit residues: 14.0266 Evaluate side-chains 85 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.0040 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3409 Z= 0.177 Angle : 0.630 7.767 4676 Z= 0.309 Chirality : 0.040 0.257 571 Planarity : 0.005 0.059 582 Dihedral : 4.159 15.447 479 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 0.97 (0.40), residues: 457 helix: 1.30 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.08 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.019 0.001 PHE A 41 TYR 0.010 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.353 Fit side-chains REVERT: A 287 ARG cc_start: 0.8736 (ttm-80) cc_final: 0.8398 (ttm-80) REVERT: A 426 ASP cc_start: 0.8455 (p0) cc_final: 0.7959 (m-30) REVERT: A 449 ILE cc_start: 0.8865 (tt) cc_final: 0.8577 (tt) REVERT: A 478 ILE cc_start: 0.8888 (mt) cc_final: 0.8677 (mt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1120 time to fit residues: 13.6159 Evaluate side-chains 85 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 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 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3409 Z= 0.190 Angle : 0.645 7.765 4676 Z= 0.322 Chirality : 0.040 0.200 571 Planarity : 0.005 0.059 582 Dihedral : 4.139 15.644 479 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.41), residues: 457 helix: 1.33 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.17 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 HIS 0.000 0.000 HIS A 260 PHE 0.031 0.002 PHE A 151 TYR 0.011 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.329 Fit side-chains REVERT: A 137 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6774 (mm-30) REVERT: A 352 TYR cc_start: 0.5424 (m-80) cc_final: 0.5146 (m-80) REVERT: A 426 ASP cc_start: 0.8477 (p0) cc_final: 0.7987 (m-30) REVERT: A 449 ILE cc_start: 0.8892 (tt) cc_final: 0.8672 (tt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1109 time to fit residues: 14.3312 Evaluate side-chains 88 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 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 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3409 Z= 0.199 Angle : 0.657 7.872 4676 Z= 0.328 Chirality : 0.041 0.215 571 Planarity : 0.005 0.059 582 Dihedral : 4.253 16.568 479 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 1.06 (0.41), residues: 457 helix: 1.35 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.01 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 288 HIS 0.000 0.000 HIS A 260 PHE 0.024 0.002 PHE A 41 TYR 0.011 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.355 Fit side-chains REVERT: A 426 ASP cc_start: 0.8484 (p0) cc_final: 0.7993 (m-30) REVERT: A 449 ILE cc_start: 0.8986 (tt) cc_final: 0.8694 (tt) REVERT: A 478 ILE cc_start: 0.8889 (mt) cc_final: 0.8687 (mt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1175 time to fit residues: 14.7697 Evaluate side-chains 84 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 5.9990 chunk 42 optimal weight: 0.0030 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3409 Z= 0.184 Angle : 0.660 8.296 4676 Z= 0.326 Chirality : 0.041 0.199 571 Planarity : 0.005 0.058 582 Dihedral : 4.195 16.807 479 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.10 (0.41), residues: 457 helix: 1.42 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.10 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 288 HIS 0.000 0.000 HIS A 260 PHE 0.029 0.002 PHE A 151 TYR 0.009 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.323 Fit side-chains REVERT: A 352 TYR cc_start: 0.5383 (m-80) cc_final: 0.5073 (m-80) REVERT: A 361 TYR cc_start: 0.8156 (t80) cc_final: 0.7590 (t80) REVERT: A 426 ASP cc_start: 0.8462 (p0) cc_final: 0.7987 (m-30) REVERT: A 449 ILE cc_start: 0.8955 (tt) cc_final: 0.8631 (tt) REVERT: A 478 ILE cc_start: 0.8875 (mt) cc_final: 0.8659 (mt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1160 time to fit residues: 14.3808 Evaluate side-chains 87 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.0060 chunk 31 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.203473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.177843 restraints weight = 4888.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.182080 restraints weight = 2854.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.185175 restraints weight = 1912.948| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3409 Z= 0.194 Angle : 0.657 7.801 4676 Z= 0.328 Chirality : 0.041 0.212 571 Planarity : 0.005 0.058 582 Dihedral : 4.230 16.697 479 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.16 (0.41), residues: 457 helix: 1.51 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.08 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.020 0.002 PHE A 41 TYR 0.010 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1045.98 seconds wall clock time: 20 minutes 6.45 seconds (1206.45 seconds total)