Starting phenix.real_space_refine on Thu Nov 14 12:09:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug6_42215/11_2024/8ug6_42215.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug6_42215/11_2024/8ug6_42215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug6_42215/11_2024/8ug6_42215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug6_42215/11_2024/8ug6_42215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug6_42215/11_2024/8ug6_42215.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug6_42215/11_2024/8ug6_42215.cif" } resolution = 3.06 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= 0.000 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 42 5.16 5 C 4156 2.51 5 N 1006 2.21 5 O 1038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6242 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3121 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 383} Chain breaks: 7 Restraints were copied for chains: B Time building chain proxies: 5.51, per 1000 atoms: 0.88 Number of scatterers: 6242 At special positions: 0 Unit cell: (87.15, 98.77, 70.55, 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 42 16.00 O 1038 8.00 N 1006 7.00 C 4156 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: 1.55 Conformation dependent library (CDL) restraints added in 891.6 milliseconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 28 through 53 removed outlier: 3.540A pdb=" N ASN A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 85 Processing helix chain 'A' and resid 101 through 128 removed outlier: 4.304A pdb=" N GLY A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 156 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 165 through 194 Processing helix chain 'A' and resid 247 through 265 Processing helix chain 'A' and resid 292 through 312 Processing helix chain 'A' and resid 322 through 353 removed outlier: 3.562A pdb=" N PHE A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 393 removed outlier: 4.506A pdb=" N GLY A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 429 removed outlier: 3.564A pdb=" N GLY A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 508 removed outlier: 3.572A pdb=" N ASP A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 530 through 563 Proline residue: A 543 - end of helix removed outlier: 3.500A pdb=" N ILE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 53 removed outlier: 3.539A pdb=" N ASN B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 85 Processing helix chain 'B' and resid 101 through 128 removed outlier: 4.304A pdb=" N GLY B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 156 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 165 through 194 Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 292 through 312 Processing helix chain 'B' and resid 322 through 353 removed outlier: 3.562A pdb=" N PHE B 353 " --> pdb=" O VAL B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 393 removed outlier: 4.505A pdb=" N GLY B 379 " --> pdb=" O GLY B 375 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 429 removed outlier: 3.564A pdb=" N GLY B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 508 removed outlier: 3.573A pdb=" N ASP B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 515 Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 530 through 563 Proline residue: B 543 - end of helix removed outlier: 3.500A pdb=" N ILE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1584 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: 1.86 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1267 1.33 - 1.45: 1564 1.45 - 1.57: 3499 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6396 Sorted by residual: bond pdb=" CA SER B 256 " pdb=" CB SER B 256 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.54e+01 bond pdb=" CA SER A 256 " pdb=" CB SER A 256 " ideal model delta sigma weight residual 1.528 1.468 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CA SER B 346 " pdb=" CB SER B 346 " ideal model delta sigma weight residual 1.528 1.479 0.049 1.56e-02 4.11e+03 9.99e+00 bond pdb=" CA SER A 346 " pdb=" CB SER A 346 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.56e-02 4.11e+03 9.85e+00 bond pdb=" N VAL A 307 " pdb=" CA VAL A 307 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.78e+00 ... (remaining 6391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 8335 1.53 - 3.06: 290 3.06 - 4.60: 57 4.60 - 6.13: 12 6.13 - 7.66: 4 Bond angle restraints: 8698 Sorted by residual: angle pdb=" N TYR B 124 " pdb=" CA TYR B 124 " pdb=" C TYR B 124 " ideal model delta sigma weight residual 111.40 106.84 4.56 1.22e+00 6.72e-01 1.40e+01 angle pdb=" N TYR A 124 " pdb=" CA TYR A 124 " pdb=" C TYR A 124 " ideal model delta sigma weight residual 111.40 106.86 4.54 1.22e+00 6.72e-01 1.39e+01 angle pdb=" C GLN A 238 " pdb=" N GLN A 239 " pdb=" CA GLN A 239 " ideal model delta sigma weight residual 120.71 114.71 6.00 1.67e+00 3.59e-01 1.29e+01 angle pdb=" C GLN B 238 " pdb=" N GLN B 239 " pdb=" CA GLN B 239 " ideal model delta sigma weight residual 120.71 114.73 5.98 1.67e+00 3.59e-01 1.28e+01 angle pdb=" CA ARG B 366 " pdb=" C ARG B 366 " pdb=" O ARG B 366 " ideal model delta sigma weight residual 122.41 118.12 4.29 1.21e+00 6.83e-01 1.26e+01 ... (remaining 8693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.55: 2886 12.55 - 25.10: 454 25.10 - 37.66: 198 37.66 - 50.21: 78 50.21 - 62.76: 22 Dihedral angle restraints: 3638 sinusoidal: 1358 harmonic: 2280 Sorted by residual: dihedral pdb=" CD ARG B 366 " pdb=" NE ARG B 366 " pdb=" CZ ARG B 366 " pdb=" NH1 ARG B 366 " ideal model delta sinusoidal sigma weight residual 0.00 -30.55 30.55 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CD ARG A 366 " pdb=" NE ARG A 366 " pdb=" CZ ARG A 366 " pdb=" NH1 ARG A 366 " ideal model delta sinusoidal sigma weight residual 0.00 -30.49 30.49 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CG ARG B 104 " pdb=" CD ARG B 104 " pdb=" NE ARG B 104 " pdb=" CZ ARG B 104 " ideal model delta sinusoidal sigma weight residual 90.00 134.89 -44.89 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 3635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 995 0.090 - 0.179: 28 0.179 - 0.269: 7 0.269 - 0.359: 0 0.359 - 0.448: 2 Chirality restraints: 1032 Sorted by residual: chirality pdb=" CB VAL B 389 " pdb=" CA VAL B 389 " pdb=" CG1 VAL B 389 " pdb=" CG2 VAL B 389 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CB VAL A 389 " pdb=" CA VAL A 389 " pdb=" CG1 VAL A 389 " pdb=" CG2 VAL A 389 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA ILE A 546 " pdb=" N ILE A 546 " pdb=" C ILE A 546 " pdb=" CB ILE A 546 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1029 not shown) Planarity restraints: 1042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 366 " 0.544 9.50e-02 1.11e+02 2.44e-01 3.64e+01 pdb=" NE ARG B 366 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG B 366 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 366 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 366 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 366 " -0.544 9.50e-02 1.11e+02 2.44e-01 3.63e+01 pdb=" NE ARG A 366 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 366 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 366 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 366 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 293 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO A 294 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " -0.032 5.00e-02 4.00e+02 ... (remaining 1039 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 964 2.75 - 3.29: 6261 3.29 - 3.83: 11054 3.83 - 4.36: 12647 4.36 - 4.90: 22100 Nonbonded interactions: 53026 Sorted by model distance: nonbonded pdb=" O PHE B 421 " pdb=" OG SER B 425 " model vdw 2.215 3.040 nonbonded pdb=" O PHE A 421 " pdb=" OG SER A 425 " model vdw 2.215 3.040 nonbonded pdb=" O ASN A 248 " pdb=" OG SER A 252 " model vdw 2.243 3.040 nonbonded pdb=" O ASN B 248 " pdb=" OG SER B 252 " model vdw 2.244 3.040 nonbonded pdb=" O VAL A 147 " pdb=" OG1 THR A 151 " model vdw 2.272 3.040 ... (remaining 53021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.210 Find NCS groups from input model: 0.140 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 6396 Z= 0.320 Angle : 0.664 7.660 8698 Z= 0.436 Chirality : 0.046 0.448 1032 Planarity : 0.012 0.244 1042 Dihedral : 16.571 62.762 2170 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 29.55 % Favored : 70.45 % 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: 1.97 (0.30), residues: 754 helix: 1.80 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -1.92 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 509 HIS 0.003 0.001 HIS A 519 PHE 0.009 0.001 PHE A 110 TYR 0.024 0.002 TYR B 560 ARG 0.004 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.675 Fit side-chains REVERT: A 245 TYR cc_start: 0.4530 (t80) cc_final: 0.2606 (t80) REVERT: B 245 TYR cc_start: 0.4502 (t80) cc_final: 0.2548 (t80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1880 time to fit residues: 51.6640 Evaluate side-chains 120 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 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 53 ASN A 139 HIS A 143 GLN A 150 GLN A 180 ASN A 333 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS B 143 GLN B 150 GLN B 180 ASN B 333 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6396 Z= 0.206 Angle : 0.571 7.065 8698 Z= 0.298 Chirality : 0.039 0.169 1032 Planarity : 0.005 0.055 1042 Dihedral : 3.724 30.562 846 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.13 % Allowed : 22.24 % Favored : 74.63 % 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: 2.62 (0.29), residues: 754 helix: 2.19 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -1.61 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.004 0.001 HIS A 165 PHE 0.009 0.002 PHE B 544 TYR 0.010 0.001 TYR B 351 ARG 0.002 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5131 (t80) cc_final: 0.2892 (t80) REVERT: B 174 MET cc_start: 0.7907 (mmt) cc_final: 0.7642 (mmt) REVERT: B 245 TYR cc_start: 0.4972 (t80) cc_final: 0.2672 (t80) outliers start: 21 outliers final: 10 residues processed: 176 average time/residue: 0.1365 time to fit residues: 34.5015 Evaluate side-chains 141 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 389 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.0040 chunk 24 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 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 150 GLN A 180 ASN A 407 HIS A 418 GLN A 519 HIS A 551 HIS B 150 GLN B 180 ASN B 400 GLN B 418 GLN B 519 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6396 Z= 0.183 Angle : 0.562 11.535 8698 Z= 0.279 Chirality : 0.038 0.175 1032 Planarity : 0.004 0.053 1042 Dihedral : 3.627 26.516 846 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.58 % Allowed : 23.28 % Favored : 73.13 % 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: 2.95 (0.29), residues: 754 helix: 2.39 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -1.08 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 184 HIS 0.002 0.001 HIS B 415 PHE 0.022 0.001 PHE B 332 TYR 0.024 0.001 TYR A 311 ARG 0.002 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.651 Fit side-chains REVERT: A 245 TYR cc_start: 0.5061 (t80) cc_final: 0.3156 (t80) REVERT: A 264 LYS cc_start: 0.7995 (ttmt) cc_final: 0.7612 (ttmt) REVERT: A 511 MET cc_start: 0.5152 (mpp) cc_final: 0.4749 (mmm) REVERT: B 174 MET cc_start: 0.8177 (mmt) cc_final: 0.7956 (mmt) REVERT: B 245 TYR cc_start: 0.4911 (t80) cc_final: 0.2998 (t80) REVERT: B 366 ARG cc_start: 0.1870 (OUTLIER) cc_final: 0.1606 (tpt170) REVERT: B 509 TRP cc_start: 0.7509 (t60) cc_final: 0.6867 (t60) REVERT: B 511 MET cc_start: 0.5203 (mpp) cc_final: 0.4806 (mmm) outliers start: 24 outliers final: 16 residues processed: 155 average time/residue: 0.1263 time to fit residues: 27.5315 Evaluate side-chains 139 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 366 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: