Starting phenix.real_space_refine on Fri Dec 27 17:32:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ug7_42216/12_2024/8ug7_42216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ug7_42216/12_2024/8ug7_42216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ug7_42216/12_2024/8ug7_42216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ug7_42216/12_2024/8ug7_42216.map" model { file = "/net/cci-nas-00/data/ceres_data/8ug7_42216/12_2024/8ug7_42216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ug7_42216/12_2024/8ug7_42216.cif" } resolution = 2.95 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= 0.003 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): 0.05s 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: 5.38, per 1000 atoms: 0.86 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: 1.59 Conformation dependent library (CDL) restraints added in 945.7 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: 0.52 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: 1.94 Time building geometry restraints manager: 1.83 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: 1.780 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.500 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:15.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.719 Fit side-chains REVERT: A 124 TYR cc_start: 0.7932 (t80) cc_final: 0.7683 (t80) REVERT: A 366 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7949 (mtp180) REVERT: A 563 SER cc_start: 0.7427 (t) cc_final: 0.7200 (m) REVERT: B 124 TYR cc_start: 0.7934 (t80) cc_final: 0.7691 (t80) REVERT: B 366 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7948 (mtp180) REVERT: B 563 SER cc_start: 0.7396 (t) cc_final: 0.7164 (m) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.9913 time to fit residues: 94.0075 Evaluate side-chains 80 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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: 2.9990 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 404 ASN B 53 ASN B 404 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1498 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= 0.221 Angle : 0.511 6.527 8698 Z= 0.276 Chirality : 0.038 0.126 1032 Planarity : 0.005 0.057 1042 Dihedral : 3.518 27.165 846 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.13 % Allowed : 24.33 % Favored : 72.54 % 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 (0.30), residues: 754 helix: 2.72 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -2.28 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.004 0.001 HIS B 551 PHE 0.012 0.001 PHE B 332 TYR 0.011 0.002 TYR B 58 ARG 0.002 0.000 ARG B 517 *********************** 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 117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.689 Fit side-chains REVERT: A 124 TYR cc_start: 0.8096 (t80) cc_final: 0.7749 (t80) REVERT: B 124 TYR cc_start: 0.8118 (t80) cc_final: 0.7777 (t80) outliers start: 21 outliers final: 6 residues processed: 112 average time/residue: 0.8462 time to fit residues: 101.7549 Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU 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: 3.9990 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6396 Z= 0.220 Angle : 0.496 5.601 8698 Z= 0.265 Chirality : 0.037 0.120 1032 Planarity : 0.004 0.056 1042 Dihedral : 3.533 23.431 846 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.28 % Allowed : 23.43 % Favored : 73.28 % 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: 3.43 (0.30), residues: 754 helix: 2.94 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -2.21 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 489 HIS 0.004 0.001 HIS B 415 PHE 0.014 0.001 PHE A 332 TYR 0.010 0.002 TYR B 58 ARG 0.002 0.000 ARG A 490 *********************** 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 116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.678 Fit side-chains REVERT: A 124 TYR cc_start: 0.8130 (t80) cc_final: 0.7652 (t80) REVERT: A 244 LEU cc_start: 0.8544 (mp) cc_final: 0.8258 (tt) REVERT: B 124 TYR cc_start: 0.8127 (t80) cc_final: 0.7686 (t80) REVERT: B 244 LEU cc_start: 0.8552 (mp) cc_final: 0.8262 (tt) outliers start: 22 outliers final: 4 residues processed: 114 average time/residue: 0.6886 time to fit residues: 84.7355 Evaluate side-chains 92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 389 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6396 Z= 0.301 Angle : 0.540 7.249 8698 Z= 0.283 Chirality : 0.039 0.143 1032 Planarity : 0.004 0.056 1042 Dihedral : 3.612 19.453 846 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.33 % Allowed : 23.28 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.30), residues: 754 helix: 2.79 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -2.17 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 489 HIS 0.004 0.001 HIS A 415 PHE 0.016 0.002 PHE A 332 TYR 0.014 0.002 TYR B 58 ARG 0.002 0.000 ARG B 490 *********************** 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 112 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.623 Fit side-chains REVERT: A 124 TYR cc_start: 0.8182 (t80) cc_final: 0.7794 (t80) REVERT: A 128 PHE cc_start: 0.7859 (p90) cc_final: 0.7063 (p90) REVERT: A 244 LEU cc_start: 0.8602 (mp) cc_final: 0.8092 (tt) REVERT: B 124 TYR cc_start: 0.8176 (t80) cc_final: 0.7762 (t80) REVERT: B 244 LEU cc_start: 0.8602 (mp) cc_final: 0.8125 (tt) outliers start: 29 outliers final: 13 residues processed: 109 average time/residue: 0.6854 time to fit residues: 81.3720 Evaluate side-chains 95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 372 LEU 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: 1.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 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 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6396 Z= 0.167 Angle : 0.483 8.807 8698 Z= 0.250 Chirality : 0.036 0.116 1032 Planarity : 0.004 0.053 1042 Dihedral : 3.438 18.442 846 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.28 % Allowed : 25.07 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.31), residues: 754 helix: 3.01 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -2.05 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 76 HIS 0.003 0.001 HIS B 551 PHE 0.012 0.001 PHE B 332 TYR 0.010 0.001 TYR B 548 ARG 0.002 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 109 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.686 Fit side-chains REVERT: A 124 TYR cc_start: 0.8118 (t80) cc_final: 0.7746 (t80) REVERT: B 124 TYR cc_start: 0.8124 (t80) cc_final: 0.7792 (t80) outliers start: 22 outliers final: 11 residues processed: 106 average time/residue: 0.6734 time to fit residues: 77.7151 Evaluate side-chains 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 404 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6396 Z= 0.160 Angle : 0.484 8.109 8698 Z= 0.248 Chirality : 0.036 0.116 1032 Planarity : 0.004 0.052 1042 Dihedral : 3.383 18.047 846 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.43 % Allowed : 24.33 % Favored : 72.24 % 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: 3.68 (0.30), residues: 754 helix: 3.11 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -2.06 (0.54), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.003 0.001 HIS B 551 PHE 0.012 0.001 PHE B 332 TYR 0.010 0.001 TYR A 548 ARG 0.001 0.000 ARG B 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 110 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.723 Fit side-chains REVERT: A 124 TYR cc_start: 0.8094 (t80) cc_final: 0.7773 (t80) REVERT: B 124 TYR cc_start: 0.8083 (t80) cc_final: 0.7752 (t80) outliers start: 23 outliers final: 12 residues processed: 108 average time/residue: 0.8533 time to fit residues: 98.8610 Evaluate side-chains 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6396 Z= 0.168 Angle : 0.481 7.484 8698 Z= 0.248 Chirality : 0.036 0.116 1032 Planarity : 0.004 0.052 1042 Dihedral : 3.363 17.916 846 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 3.71 (0.30), residues: 754 helix: 3.13 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -2.06 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.003 0.001 HIS B 551 PHE 0.012 0.001 PHE B 332 TYR 0.009 0.001 TYR A 548 ARG 0.001 0.000 ARG B 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 111 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.759 Fit side-chains REVERT: A 124 TYR cc_start: 0.8084 (t80) cc_final: 0.7751 (t80) REVERT: A 128 PHE cc_start: 0.7808 (p90) cc_final: 0.7068 (p90) REVERT: B 124 TYR cc_start: 0.8091 (t80) cc_final: 0.7530 (t80) REVERT: B 128 PHE cc_start: 0.7840 (p90) cc_final: 0.7083 (p90) REVERT: B 242 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6104 (m-10) outliers start: 20 outliers final: 11 residues processed: 110 average time/residue: 0.7791 time to fit residues: 92.6864 Evaluate side-chains 102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 404 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6396 Z= 0.166 Angle : 0.485 7.171 8698 Z= 0.250 Chirality : 0.036 0.116 1032 Planarity : 0.004 0.051 1042 Dihedral : 3.355 17.972 846 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.69 % Allowed : 25.97 % Favored : 71.34 % 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: 3.71 (0.30), residues: 754 helix: 3.12 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -2.00 (0.54), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.003 0.001 HIS B 551 PHE 0.011 0.001 PHE B 332 TYR 0.009 0.001 TYR A 548 ARG 0.001 0.000 ARG B 517 *********************** 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 108 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.708 Fit side-chains REVERT: A 124 TYR cc_start: 0.8022 (t80) cc_final: 0.7756 (t80) REVERT: A 128 PHE cc_start: 0.7806 (p90) cc_final: 0.7078 (p90) REVERT: B 124 TYR cc_start: 0.8071 (t80) cc_final: 0.7570 (t80) REVERT: B 128 PHE cc_start: 0.7846 (p90) cc_final: 0.7100 (p90) REVERT: B 242 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.6117 (m-10) REVERT: B 264 LYS cc_start: 0.9148 (ttmt) cc_final: 0.8828 (ttmt) outliers start: 18 outliers final: 13 residues processed: 107 average time/residue: 0.7219 time to fit residues: 83.6026 Evaluate side-chains 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 51 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6396 Z= 0.168 Angle : 0.489 7.797 8698 Z= 0.251 Chirality : 0.036 0.117 1032 Planarity : 0.004 0.051 1042 Dihedral : 3.356 17.998 846 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.24 % Allowed : 27.31 % 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: 3.71 (0.30), residues: 754 helix: 3.12 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -1.97 (0.54), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.003 0.001 HIS B 551 PHE 0.011 0.001 PHE A 332 TYR 0.009 0.001 TYR B 548 ARG 0.001 0.000 ARG B 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 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.661 Fit side-chains REVERT: A 124 TYR cc_start: 0.8052 (t80) cc_final: 0.7735 (t80) REVERT: B 242 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.6146 (m-10) REVERT: B 264 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8823 (ttmt) outliers start: 15 outliers final: 13 residues processed: 102 average time/residue: 0.6947 time to fit residues: 76.8158 Evaluate side-chains 102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 404 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 chunk 57 optimal weight: 0.0670 chunk 9 optimal weight: 0.4980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6396 Z= 0.142 Angle : 0.482 8.451 8698 Z= 0.246 Chirality : 0.035 0.112 1032 Planarity : 0.004 0.050 1042 Dihedral : 3.316 18.455 846 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.94 % Allowed : 27.76 % Favored : 70.30 % 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: 3.80 (0.30), residues: 754 helix: 3.12 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -1.72 (0.54), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.003 0.000 HIS B 551 PHE 0.010 0.001 PHE B 332 TYR 0.008 0.001 TYR A 548 ARG 0.001 0.000 ARG B 170 ********************** 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 106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.588 Fit side-chains REVERT: A 264 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8740 (tttt) REVERT: B 242 PHE cc_start: 0.6753 (p90) cc_final: 0.6160 (m-10) REVERT: B 264 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8752 (tttt) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.7434 time to fit residues: 84.5636 Evaluate side-chains 99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 404 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.088472 restraints weight = 9983.756| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.07 r_work: 0.2908 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6396 Z= 0.182 Angle : 0.499 8.201 8698 Z= 0.256 Chirality : 0.036 0.121 1032 Planarity : 0.004 0.051 1042 Dihedral : 3.332 18.322 846 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.64 % Allowed : 27.91 % 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: 3.73 (0.30), residues: 754 helix: 3.11 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -1.84 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 76 HIS 0.003 0.001 HIS B 551 PHE 0.012 0.001 PHE A 63 TYR 0.009 0.001 TYR A 548 ARG 0.001 0.000 ARG A 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.45 seconds wall clock time: 40 minutes 24.67 seconds (2424.67 seconds total)