Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/03_2024/6tgp_10500.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/03_2024/6tgp_10500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/03_2024/6tgp_10500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/03_2024/6tgp_10500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/03_2024/6tgp_10500.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/03_2024/6tgp_10500.pdb" } resolution = 4.4 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= 1.000 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 2 5.16 5 C 850 2.51 5 N 230 2.21 5 O 262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1344 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 672 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "B" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 672 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Time building chain proxies: 1.28, per 1000 atoms: 0.95 Number of scatterers: 1344 At special positions: 0 Unit cell: (54.054, 62.37, 76.23, 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 2 16.00 O 262 8.00 N 230 7.00 C 850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 285.2 milliseconds 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 328 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 22.7% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.814A pdb=" N GLU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.923A pdb=" N ASN A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 removed outlier: 3.832A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.920A pdb=" N ASN B 79 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.589A pdb=" N VAL A 17 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 14 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.589A pdb=" N VAL A 17 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 14 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 13 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A 89 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.674A pdb=" N TYR B 14 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.674A pdb=" N TYR B 14 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 13 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL B 89 " --> pdb=" O SER B 13 " (cutoff:3.500A) 36 hydrogen bonds defined for protein. 81 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.24 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 280 1.33 - 1.45: 345 1.45 - 1.58: 724 1.58 - 1.70: 2 1.70 - 1.83: 5 Bond restraints: 1356 Sorted by residual: bond pdb=" CD ARG A 19 " pdb=" NE ARG A 19 " ideal model delta sigma weight residual 1.458 1.603 -0.145 1.40e-02 5.10e+03 1.08e+02 bond pdb=" CG ARG A 19 " pdb=" CD ARG A 19 " ideal model delta sigma weight residual 1.520 1.810 -0.290 3.00e-02 1.11e+03 9.36e+01 bond pdb=" NE ARG A 19 " pdb=" CZ ARG A 19 " ideal model delta sigma weight residual 1.326 1.391 -0.065 1.10e-02 8.26e+03 3.48e+01 bond pdb=" C VAL A 9 " pdb=" O VAL A 9 " ideal model delta sigma weight residual 1.237 1.201 0.036 9.90e-03 1.02e+04 1.30e+01 bond pdb=" CZ ARG A 19 " pdb=" NH2 ARG A 19 " ideal model delta sigma weight residual 1.330 1.376 -0.046 1.30e-02 5.92e+03 1.23e+01 ... (remaining 1351 not shown) Histogram of bond angle deviations from ideal: 101.57 - 107.41: 37 107.41 - 113.25: 644 113.25 - 119.08: 465 119.08 - 124.92: 652 124.92 - 130.75: 34 Bond angle restraints: 1832 Sorted by residual: angle pdb=" C ALA B 5 " pdb=" CA ALA B 5 " pdb=" CB ALA B 5 " ideal model delta sigma weight residual 110.50 125.65 -15.15 1.50e+00 4.44e-01 1.02e+02 angle pdb=" NE ARG A 19 " pdb=" CZ ARG A 19 " pdb=" NH2 ARG A 19 " ideal model delta sigma weight residual 119.20 125.66 -6.46 9.00e-01 1.23e+00 5.15e+01 angle pdb=" NE ARG A 19 " pdb=" CZ ARG A 19 " pdb=" NH1 ARG A 19 " ideal model delta sigma weight residual 121.50 115.97 5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" C ASP A 32 " pdb=" CA ASP A 32 " pdb=" CB ASP A 32 " ideal model delta sigma weight residual 111.14 117.89 -6.75 1.39e+00 5.18e-01 2.36e+01 angle pdb=" CD ARG A 19 " pdb=" NE ARG A 19 " pdb=" CZ ARG A 19 " ideal model delta sigma weight residual 124.40 130.75 -6.35 1.40e+00 5.10e-01 2.06e+01 ... (remaining 1827 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.57: 659 10.57 - 21.14: 120 21.14 - 31.71: 30 31.71 - 42.27: 10 42.27 - 52.84: 5 Dihedral angle restraints: 824 sinusoidal: 318 harmonic: 506 Sorted by residual: dihedral pdb=" C ALA B 5 " pdb=" N ALA B 5 " pdb=" CA ALA B 5 " pdb=" CB ALA B 5 " ideal model delta harmonic sigma weight residual -122.60 -137.10 14.50 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" CA ASP A 62 " pdb=" C ASP A 62 " pdb=" N GLY A 63 " pdb=" CA GLY A 63 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ALA B 5 " pdb=" C ALA B 5 " pdb=" N ASN B 6 " pdb=" CA ASN B 6 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 821 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.097: 123 0.097 - 0.191: 70 0.191 - 0.286: 21 0.286 - 0.381: 5 0.381 - 0.475: 1 Chirality restraints: 220 Sorted by residual: chirality pdb=" CB VAL B 9 " pdb=" CA VAL B 9 " pdb=" CG1 VAL B 9 " pdb=" CG2 VAL B 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CG LEU B 8 " pdb=" CB LEU B 8 " pdb=" CD1 LEU B 8 " pdb=" CD2 LEU B 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB VAL B 77 " pdb=" CA VAL B 77 " pdb=" CG1 VAL B 77 " pdb=" CG2 VAL B 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 217 not shown) Planarity restraints: 240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 14 " 0.052 2.00e-02 2.50e+03 3.29e-02 2.16e+01 pdb=" CG TYR B 14 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 14 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR B 14 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 14 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR B 14 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 14 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 14 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 14 " -0.051 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR A 14 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 14 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR A 14 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 14 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 14 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 14 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR A 14 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 19 " 0.016 2.00e-02 2.50e+03 3.11e-02 9.67e+00 pdb=" C ARG A 19 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG A 19 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 20 " 0.018 2.00e-02 2.50e+03 ... (remaining 237 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 181 2.76 - 3.30: 1165 3.30 - 3.83: 1865 3.83 - 4.37: 2293 4.37 - 4.90: 3751 Nonbonded interactions: 9255 Sorted by model distance: nonbonded pdb=" OD1 ASP A 60 " pdb=" N GLU A 61 " model vdw 2.228 2.520 nonbonded pdb=" OD1 ASP B 60 " pdb=" N GLU B 61 " model vdw 2.236 2.520 nonbonded pdb=" O PHE A 46 " pdb=" OD1 ASN B 28 " model vdw 2.294 3.040 nonbonded pdb=" N ASP A 60 " pdb=" O ASP A 60 " model vdw 2.579 2.496 nonbonded pdb=" N ASP B 60 " pdb=" O ASP B 60 " model vdw 2.582 2.496 ... (remaining 9250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.300 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.013 0.290 1356 Z= 0.737 Angle : 1.899 15.148 1832 Z= 1.215 Chirality : 0.126 0.475 220 Planarity : 0.010 0.067 240 Dihedral : 12.884 52.842 496 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.08 % Allowed : 4.86 % Favored : 93.06 % Cbeta Deviations : 0.61 % 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: -3.36 (0.53), residues: 172 helix: -4.65 (0.23), residues: 36 sheet: -1.04 (0.72), residues: 56 loop : -1.79 (0.50), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.042 0.010 PHE B 46 TYR 0.059 0.020 TYR B 14 ARG 0.029 0.005 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9449 (mmm) cc_final: 0.9185 (mmm) REVERT: B 72 ASN cc_start: 0.9548 (m-40) cc_final: 0.9120 (t0) REVERT: B 82 LEU cc_start: 0.9166 (tp) cc_final: 0.8930 (mt) REVERT: B 83 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9002 (tptt) outliers start: 3 outliers final: 0 residues processed: 44 average time/residue: 0.2482 time to fit residues: 11.6685 Evaluate side-chains 21 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 50.0000 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 50.0000 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1356 Z= 0.175 Angle : 0.557 5.582 1832 Z= 0.301 Chirality : 0.041 0.115 220 Planarity : 0.003 0.019 240 Dihedral : 4.993 15.934 186 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: -2.27 (0.59), residues: 172 helix: -2.80 (0.60), residues: 48 sheet: -0.05 (0.77), residues: 56 loop : -1.61 (0.56), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE B 21 TYR 0.007 0.001 TYR A 14 ARG 0.002 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 MET cc_start: 0.9771 (tpp) cc_final: 0.9006 (tpp) REVERT: B 72 ASN cc_start: 0.9544 (m-40) cc_final: 0.8915 (t0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2254 time to fit residues: 5.9206 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 50.0000 chunk 1 optimal weight: 50.0000 chunk 6 optimal weight: 50.0000 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 13 optimal weight: 30.0000 chunk 4 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 chunk 8 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 overall best weight: 31.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 72 ASN A 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 1356 Z= 0.420 Angle : 0.857 9.460 1832 Z= 0.423 Chirality : 0.043 0.143 220 Planarity : 0.005 0.043 240 Dihedral : 5.984 17.858 186 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.65), residues: 172 helix: -0.90 (0.76), residues: 46 sheet: 0.12 (0.71), residues: 60 loop : -0.61 (0.75), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE A 21 TYR 0.012 0.003 TYR A 58 ARG 0.007 0.002 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.154 Fit side-chains REVERT: A 35 MET cc_start: 0.9483 (mmm) cc_final: 0.9276 (mmm) REVERT: A 53 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7389 (tm-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2151 time to fit residues: 4.5853 Evaluate side-chains 12 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 40.0000 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 40.0000 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 7 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 50.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1356 Z= 0.173 Angle : 0.491 5.578 1832 Z= 0.266 Chirality : 0.039 0.122 220 Planarity : 0.002 0.018 240 Dihedral : 4.520 12.728 186 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.66), residues: 172 helix: -0.37 (0.81), residues: 42 sheet: 0.50 (0.71), residues: 60 loop : -0.12 (0.77), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 75 TYR 0.008 0.001 TYR B 58 ARG 0.001 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.9386 (mmm) cc_final: 0.9132 (mmm) REVERT: A 53 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7310 (tm-30) REVERT: A 85 LEU cc_start: 0.9419 (tp) cc_final: 0.9195 (mp) REVERT: B 22 ARG cc_start: 0.8630 (mtp-110) cc_final: 0.7962 (mtt90) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2818 time to fit residues: 6.3866 Evaluate side-chains 15 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 50.0000 chunk 1 optimal weight: 50.0000 chunk 5 optimal weight: 50.0000 chunk 8 optimal weight: 90.0000 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 50.0000 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 40.0000 chunk 9 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1356 Z= 0.157 Angle : 0.483 5.754 1832 Z= 0.259 Chirality : 0.038 0.116 220 Planarity : 0.002 0.017 240 Dihedral : 4.323 11.736 186 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.66), residues: 172 helix: -0.34 (0.75), residues: 48 sheet: 0.75 (0.70), residues: 60 loop : -0.13 (0.80), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE A 46 TYR 0.006 0.001 TYR B 58 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.9371 (mmm) cc_final: 0.9137 (mmm) REVERT: A 53 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7321 (tm-30) REVERT: A 85 LEU cc_start: 0.9373 (tp) cc_final: 0.9149 (mp) REVERT: B 22 ARG cc_start: 0.8744 (mtp-110) cc_final: 0.8149 (mtt90) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2393 time to fit residues: 5.2639 Evaluate side-chains 15 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 12 optimal weight: 50.0000 chunk 14 optimal weight: 50.0000 chunk 13 optimal weight: 50.0000 chunk 8 optimal weight: 20.0000 chunk 6 optimal weight: 40.0000 overall best weight: 9.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1356 Z= 0.142 Angle : 0.462 6.527 1832 Z= 0.243 Chirality : 0.037 0.105 220 Planarity : 0.002 0.014 240 Dihedral : 4.135 11.330 186 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.70), residues: 172 helix: 0.27 (0.83), residues: 40 sheet: 0.99 (0.70), residues: 60 loop : 1.00 (0.86), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE B 84 TYR 0.006 0.001 TYR B 58 ARG 0.001 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9359 (mmm) cc_final: 0.9129 (mmm) REVERT: A 53 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7402 (tm-30) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2410 time to fit residues: 5.5643 Evaluate side-chains 11 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 50.0000 chunk 12 optimal weight: 40.0000 chunk 13 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 1 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 overall best weight: 17.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.7081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1356 Z= 0.232 Angle : 0.609 6.598 1832 Z= 0.311 Chirality : 0.039 0.111 220 Planarity : 0.003 0.015 240 Dihedral : 4.379 13.488 186 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.69), residues: 172 helix: 0.27 (0.78), residues: 40 sheet: 1.05 (0.70), residues: 60 loop : 0.89 (0.88), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 46 TYR 0.005 0.002 TYR B 14 ARG 0.003 0.001 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.9414 (mmm) cc_final: 0.9177 (mmm) REVERT: A 53 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7189 (tm-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2284 time to fit residues: 4.8069 Evaluate side-chains 12 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 50.0000 chunk 5 optimal weight: 40.0000 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 50.0000 chunk 14 optimal weight: 0.0970 chunk 8 optimal weight: 50.0000 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.7088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1356 Z= 0.114 Angle : 0.457 5.989 1832 Z= 0.249 Chirality : 0.039 0.132 220 Planarity : 0.002 0.013 240 Dihedral : 3.975 13.568 186 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.07 (0.66), residues: 172 helix: 0.07 (0.75), residues: 44 sheet: 1.44 (0.69), residues: 60 loop : 0.67 (0.82), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE A 75 TYR 0.009 0.001 TYR B 58 ARG 0.001 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9282 (mmm) cc_final: 0.9068 (mmm) REVERT: A 53 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7660 (tm-30) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2301 time to fit residues: 5.1204 Evaluate side-chains 13 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 10 optimal weight: 50.0000 chunk 0 optimal weight: 80.0000 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 40.0000 chunk 5 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 2 optimal weight: 50.0000 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 50.0000 chunk 14 optimal weight: 50.0000 overall best weight: 13.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.7237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1356 Z= 0.187 Angle : 0.567 6.078 1832 Z= 0.293 Chirality : 0.038 0.125 220 Planarity : 0.002 0.015 240 Dihedral : 4.172 12.433 186 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.47 (0.68), residues: 172 helix: 0.24 (0.75), residues: 42 sheet: 1.53 (0.68), residues: 60 loop : 1.17 (0.88), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 46 TYR 0.005 0.001 TYR B 14 ARG 0.003 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9376 (mmm) cc_final: 0.9126 (mmm) REVERT: A 53 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7466 (tm-30) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.2087 time to fit residues: 4.2065 Evaluate side-chains 12 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 0 optimal weight: 80.0000 chunk 6 optimal weight: 40.0000 chunk 1 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 3 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 8 optimal weight: 50.0000 chunk 15 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 overall best weight: 17.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 72 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.7688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1356 Z= 0.225 Angle : 0.617 6.211 1832 Z= 0.314 Chirality : 0.038 0.129 220 Planarity : 0.003 0.019 240 Dihedral : 4.481 15.517 186 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 1.32 (0.68), residues: 172 helix: -0.17 (0.72), residues: 42 sheet: 1.51 (0.67), residues: 60 loop : 1.21 (0.89), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 46 TYR 0.004 0.001 TYR B 58 ARG 0.004 0.001 ARG B 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 344 Ramachandran restraints generated. 172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9381 (mmm) cc_final: 0.9156 (mmm) REVERT: A 53 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7456 (tm-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.2163 time to fit residues: 4.1288 Evaluate side-chains 12 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 40.0000 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 5 optimal weight: 50.0000 chunk 4 optimal weight: 50.0000 chunk 9 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.0870 overall best weight: 3.8566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 72 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.055501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.047807 restraints weight = 12582.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.048741 restraints weight = 9131.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.049413 restraints weight = 7196.669| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.7617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1356 Z= 0.112 Angle : 0.489 6.105 1832 Z= 0.258 Chirality : 0.039 0.125 220 Planarity : 0.002 0.013 240 Dihedral : 3.876 11.952 186 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 1.45 (0.69), residues: 172 helix: -0.25 (0.73), residues: 48 sheet: 1.53 (0.62), residues: 72 loop : 1.65 (1.07), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE B 84 TYR 0.008 0.001 TYR B 58 ARG 0.001 0.000 ARG A 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 618.38 seconds wall clock time: 12 minutes 6.25 seconds (726.25 seconds total)