Starting phenix.real_space_refine on Fri Dec 27 17:34:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ug6_42215/12_2024/8ug6_42215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ug6_42215/12_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/cci-nas-00/data/ceres_data/8ug6_42215/12_2024/8ug6_42215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ug6_42215/12_2024/8ug6_42215.map" model { file = "/net/cci-nas-00/data/ceres_data/8ug6_42215/12_2024/8ug6_42215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ug6_42215/12_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.20, per 1000 atoms: 0.83 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: 1.58 Conformation dependent library (CDL) restraints added in 922.2 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: 0.37 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: 1.80 Time building geometry restraints manager: 1.86 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: 1.160 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.100 Find NCS groups from input model: 0.160 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- 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 : 0.716 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: 0.1795 time to fit residues: 48.8537 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 : 0.663 ------------------------------------------------------------------------------- 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 : 0.713 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: 0.1431 time to fit residues: 35.8121 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 : 0.702 ------------------------------------------------------------------------------- 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 : 1.100 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: 0.1533 time to fit residues: 33.2261 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 : 0.742 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 321 HIS A 400 GLN B 180 ASN B 321 HIS B 400 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.6395 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= 0.213 Angle : 0.583 10.355 8698 Z= 0.291 Chirality : 0.040 0.202 1032 Planarity : 0.005 0.057 1042 Dihedral : 3.767 28.765 846 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 5.52 % Allowed : 22.99 % Favored : 71.49 % 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: 2.80 (0.29), residues: 754 helix: 2.31 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -1.31 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 155 HIS 0.003 0.001 HIS B 415 PHE 0.018 0.002 PHE B 514 TYR 0.014 0.002 TYR B 251 ARG 0.005 0.001 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 4 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 161 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.710 Fit side-chains REVERT: A 143 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.6000 (tp-100) REVERT: A 156 ILE cc_start: 0.8563 (mm) cc_final: 0.8268 (tt) REVERT: A 245 TYR cc_start: 0.5044 (t80) cc_final: 0.3275 (t80) REVERT: A 264 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7743 (tptt) REVERT: A 509 TRP cc_start: 0.7812 (t60) cc_final: 0.7485 (t60) REVERT: A 511 MET cc_start: 0.5894 (mpp) cc_final: 0.5668 (mmm) REVERT: B 143 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.5982 (tp-100) REVERT: B 156 ILE cc_start: 0.8528 (mm) cc_final: 0.8267 (tt) REVERT: B 185 MET cc_start: 0.8466 (tpp) cc_final: 0.8168 (tpp) REVERT: B 245 TYR cc_start: 0.5040 (t80) cc_final: 0.3273 (t80) REVERT: B 366 ARG cc_start: 0.2901 (OUTLIER) cc_final: 0.2480 (tpt90) outliers start: 37 outliers final: 15 residues processed: 152 average time/residue: 0.1539 time to fit residues: 31.6876 Evaluate side-chains 122 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 389 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 0.0170 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 67 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 180 ASN B 180 ASN ** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6396 Z= 0.163 Angle : 0.509 8.958 8698 Z= 0.256 Chirality : 0.038 0.183 1032 Planarity : 0.004 0.052 1042 Dihedral : 3.651 25.718 846 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.39 % Allowed : 25.82 % Favored : 71.79 % 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: 2.98 (0.29), residues: 754 helix: 2.45 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -1.34 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 76 HIS 0.002 0.000 HIS A 415 PHE 0.012 0.001 PHE A 332 TYR 0.012 0.001 TYR B 251 ARG 0.007 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 5 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 136 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.703 Fit side-chains REVERT: A 156 ILE cc_start: 0.8567 (mm) cc_final: 0.8299 (tt) REVERT: A 264 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7689 (tptt) REVERT: A 509 TRP cc_start: 0.7805 (t60) cc_final: 0.7404 (t60) REVERT: B 66 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7743 (mm) REVERT: B 156 ILE cc_start: 0.8555 (mm) cc_final: 0.8294 (tt) REVERT: B 185 MET cc_start: 0.8343 (tpp) cc_final: 0.8073 (tpp) REVERT: B 366 ARG cc_start: 0.3051 (OUTLIER) cc_final: 0.2734 (tpt170) outliers start: 16 outliers final: 11 residues processed: 135 average time/residue: 0.1437 time to fit residues: 26.7810 Evaluate side-chains 120 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 366 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 180 ASN B 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6396 Z= 0.184 Angle : 0.548 8.572 8698 Z= 0.269 Chirality : 0.039 0.199 1032 Planarity : 0.004 0.051 1042 Dihedral : 3.751 26.855 846 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 3.58 % Allowed : 24.63 % Favored : 71.79 % 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: 2.96 (0.29), residues: 754 helix: 2.50 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -1.64 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 76 HIS 0.002 0.000 HIS A 415 PHE 0.013 0.001 PHE B 332 TYR 0.016 0.001 TYR B 251 ARG 0.005 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 6 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 132 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.718 Fit side-chains REVERT: A 34 LEU cc_start: 0.8643 (tp) cc_final: 0.7848 (tp) REVERT: A 143 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.5959 (tp-100) REVERT: A 156 ILE cc_start: 0.8625 (mm) cc_final: 0.8329 (tt) REVERT: A 264 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7703 (tptt) REVERT: A 366 ARG cc_start: 0.3397 (OUTLIER) cc_final: 0.2911 (tpt90) REVERT: A 509 TRP cc_start: 0.7937 (t60) cc_final: 0.7507 (t60) REVERT: A 550 MET cc_start: 0.8238 (mtt) cc_final: 0.8035 (mtt) REVERT: B 34 LEU cc_start: 0.8692 (tp) cc_final: 0.7856 (tp) REVERT: B 66 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7839 (mm) REVERT: B 143 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.6063 (tp-100) REVERT: B 156 ILE cc_start: 0.8603 (mm) cc_final: 0.8300 (tt) REVERT: B 185 MET cc_start: 0.8409 (tpp) cc_final: 0.8113 (tpp) REVERT: B 366 ARG cc_start: 0.3406 (OUTLIER) cc_final: 0.2999 (tpt90) REVERT: B 509 TRP cc_start: 0.7742 (t60) cc_final: 0.7331 (t60) outliers start: 24 outliers final: 10 residues processed: 127 average time/residue: 0.1754 time to fit residues: 29.6697 Evaluate side-chains 114 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 165 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0970 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 180 ASN B 180 ASN ** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6396 Z= 0.185 Angle : 0.572 9.207 8698 Z= 0.277 Chirality : 0.040 0.262 1032 Planarity : 0.004 0.050 1042 Dihedral : 3.840 25.756 846 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.99 % Allowed : 25.22 % Favored : 71.79 % 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: 2.50 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -1.64 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 76 HIS 0.003 0.001 HIS A 415 PHE 0.012 0.001 PHE A 332 TYR 0.009 0.001 TYR B 251 ARG 0.005 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 7 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 131 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.716 Fit side-chains REVERT: A 66 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7951 (mm) REVERT: A 143 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.6114 (tp-100) REVERT: A 156 ILE cc_start: 0.8638 (mm) cc_final: 0.8298 (tt) REVERT: A 264 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7696 (tptt) REVERT: A 366 ARG cc_start: 0.3817 (OUTLIER) cc_final: 0.3226 (tpt90) REVERT: A 509 TRP cc_start: 0.8029 (t60) cc_final: 0.7634 (t60) REVERT: A 511 MET cc_start: 0.6967 (mmt) cc_final: 0.6564 (mtt) REVERT: A 550 MET cc_start: 0.8422 (mtt) cc_final: 0.8193 (mtt) REVERT: B 66 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7958 (mm) REVERT: B 143 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.6101 (tp-100) REVERT: B 156 ILE cc_start: 0.8633 (mm) cc_final: 0.8312 (tt) REVERT: B 185 MET cc_start: 0.8406 (tpp) cc_final: 0.8095 (tpp) REVERT: B 288 GLU cc_start: 0.3737 (OUTLIER) cc_final: 0.3359 (tp30) REVERT: B 366 ARG cc_start: 0.3911 (OUTLIER) cc_final: 0.3295 (tpt90) REVERT: B 509 TRP cc_start: 0.7756 (t60) cc_final: 0.7161 (t60) outliers start: 20 outliers final: 10 residues processed: 131 average time/residue: 0.1603 time to fit residues: 28.7244 Evaluate side-chains 124 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 366 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 42 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 180 ASN B 505 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.8265 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 : 0.555 8.225 8698 Z= 0.270 Chirality : 0.039 0.209 1032 Planarity : 0.004 0.050 1042 Dihedral : 3.858 26.217 846 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.69 % Allowed : 24.48 % Favored : 72.84 % 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: 3.00 (0.29), residues: 754 helix: 2.53 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -1.66 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 155 HIS 0.003 0.001 HIS B 415 PHE 0.014 0.001 PHE A 332 TYR 0.011 0.001 TYR B 251 ARG 0.004 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 8 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 131 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.709 Fit side-chains REVERT: A 66 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8043 (mm) REVERT: A 264 LYS cc_start: 0.8249 (ttmt) cc_final: 0.7709 (tptt) REVERT: A 488 HIS cc_start: 0.5451 (m170) cc_final: 0.4956 (t70) REVERT: A 511 MET cc_start: 0.7255 (mmt) cc_final: 0.7055 (mtt) REVERT: B 66 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8030 (mm) REVERT: B 185 MET cc_start: 0.8447 (tpp) cc_final: 0.8135 (tpp) REVERT: B 264 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7704 (mmtt) REVERT: B 288 GLU cc_start: 0.3728 (OUTLIER) cc_final: 0.3322 (tp30) REVERT: B 488 HIS cc_start: 0.5604 (m170) cc_final: 0.5068 (t70) REVERT: B 509 TRP cc_start: 0.7880 (t60) cc_final: 0.7345 (t60) REVERT: B 511 MET cc_start: 0.7297 (mmm) cc_final: 0.6897 (mtt) outliers start: 18 outliers final: 11 residues processed: 129 average time/residue: 0.1473 time to fit residues: 26.8242 Evaluate side-chains 119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 374 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.8668 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= 0.189 Angle : 0.552 8.267 8698 Z= 0.271 Chirality : 0.039 0.184 1032 Planarity : 0.004 0.049 1042 Dihedral : 3.921 26.882 846 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.69 % Allowed : 24.33 % Favored : 72.99 % 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: 3.09 (0.29), residues: 754 helix: 2.60 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -1.66 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 155 HIS 0.003 0.001 HIS B 415 PHE 0.023 0.001 PHE A 353 TYR 0.023 0.002 TYR A 548 ARG 0.004 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 9 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 135 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.602 Fit side-chains REVERT: A 66 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8163 (mm) REVERT: A 264 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7747 (tptt) REVERT: A 296 LEU cc_start: 0.8237 (mt) cc_final: 0.8012 (mp) REVERT: A 488 HIS cc_start: 0.5555 (m170) cc_final: 0.4933 (t70) REVERT: A 509 TRP cc_start: 0.7812 (t60) cc_final: 0.7256 (t60) REVERT: B 264 LYS cc_start: 0.8397 (mtpt) cc_final: 0.7729 (mmtt) REVERT: B 296 LEU cc_start: 0.8291 (mt) cc_final: 0.8042 (mp) REVERT: B 488 HIS cc_start: 0.5867 (m170) cc_final: 0.5270 (t70) outliers start: 18 outliers final: 12 residues processed: 131 average time/residue: 0.1373 time to fit residues: 25.5667 Evaluate side-chains 125 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 374 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 57 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 B 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.8804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6396 Z= 0.167 Angle : 0.549 8.143 8698 Z= 0.272 Chirality : 0.038 0.180 1032 Planarity : 0.004 0.049 1042 Dihedral : 3.862 24.416 846 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.54 % Allowed : 24.03 % Favored : 73.43 % 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: 3.20 (0.29), residues: 754 helix: 2.69 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -1.77 (0.54), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 155 HIS 0.002 0.000 HIS B 415 PHE 0.023 0.001 PHE B 353 TYR 0.023 0.002 TYR A 548 ARG 0.004 0.000 ARG A 490 ********************** REFINEMENT MACRO_CYCLE 10 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 127 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.784 Fit side-chains REVERT: A 66 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8149 (mm) REVERT: A 264 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7699 (tptt) REVERT: A 288 GLU cc_start: 0.3810 (OUTLIER) cc_final: 0.3356 (tp30) REVERT: A 296 LEU cc_start: 0.8253 (mt) cc_final: 0.8026 (mp) REVERT: A 366 ARG cc_start: 0.4319 (OUTLIER) cc_final: 0.3962 (mmm160) REVERT: A 488 HIS cc_start: 0.5604 (m170) cc_final: 0.5006 (t70) REVERT: A 509 TRP cc_start: 0.7832 (t60) cc_final: 0.7308 (t60) REVERT: B 135 ILE cc_start: 0.7396 (mm) cc_final: 0.7144 (tp) REVERT: B 264 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7669 (mmtt) REVERT: B 296 LEU cc_start: 0.8274 (mt) cc_final: 0.8027 (mp) REVERT: B 488 HIS cc_start: 0.5747 (m170) cc_final: 0.5030 (t70) REVERT: B 509 TRP cc_start: 0.7856 (t60) cc_final: 0.7367 (t60) outliers start: 17 outliers final: 11 residues processed: 123 average time/residue: 0.1486 time to fit residues: 25.3695 Evaluate side-chains 123 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.0270 chunk 3 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.174524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137442 restraints weight = 9038.060| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.55 r_work: 0.3534 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.8974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6396 Z= 0.185 Angle : 0.553 8.302 8698 Z= 0.275 Chirality : 0.039 0.177 1032 Planarity : 0.004 0.050 1042 Dihedral : 3.934 25.639 846 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.54 % Allowed : 24.03 % Favored : 73.43 % 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: 3.20 (0.29), residues: 754 helix: 2.71 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -1.82 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 155 HIS 0.003 0.001 HIS B 415 PHE 0.024 0.001 PHE A 353 TYR 0.025 0.002 TYR B 548 ARG 0.004 0.000 ARG A 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.80 seconds wall clock time: 31 minutes 0.30 seconds (1860.30 seconds total)