Starting phenix.real_space_refine (version: dev) on Thu Feb 16 17:27:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/02_2023/6tgp_10500.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/02_2023/6tgp_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_10500/02_2023/6tgp_10500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/02_2023/6tgp_10500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/02_2023/6tgp_10500.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgp_10500/02_2023/6tgp_10500.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 1.36, per 1000 atoms: 1.01 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: 0.45 Conformation dependent library (CDL) restraints added in 366.7 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: 0.12 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: 0.33 Time building geometry restraints manager: 0.50 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 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. 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: 0.070 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: 0.420 Check model and map are aligned: 0.020 Process input model: 9.710 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 % 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 *********************** 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 : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 44 average time/residue: 0.2672 time to fit residues: 12.5305 Evaluate side-chains 18 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.196 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2196 ------------------------------------------------------------------------------- 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: 20.0000 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 40.0000 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 50.0000 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 50.0000 chunk 10 optimal weight: 30.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 80 GLN B 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3856 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= 0.196 Angle : 0.564 5.546 1832 Z= 0.304 Chirality : 0.040 0.127 220 Planarity : 0.003 0.016 240 Dihedral : 4.925 15.903 186 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.00 % 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: -2.41 (0.58), residues: 172 helix: -2.90 (0.59), residues: 48 sheet: -0.16 (0.76), residues: 56 loop : -1.68 (0.55), residues: 68 *********************** 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 22 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2789 time to fit residues: 6.7092 Evaluate side-chains 14 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2296 ------------------------------------------------------------------------------- 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: 20.0000 chunk 1 optimal weight: 50.0000 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 50.0000 chunk 15 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 12 optimal weight: 50.0000 chunk 8 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 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 72 ASN A 80 GLN B 47 ASN B 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 1356 Z= 0.256 Angle : 0.625 6.332 1832 Z= 0.317 Chirality : 0.039 0.104 220 Planarity : 0.004 0.038 240 Dihedral : 4.818 13.987 186 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.00 % 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: -1.13 (0.62), residues: 172 helix: -1.36 (0.67), residues: 48 sheet: 0.20 (0.72), residues: 60 loop : -0.99 (0.71), residues: 64 *********************** 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 20 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.274 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2371 time to fit residues: 5.4316 Evaluate side-chains 12 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2124 ------------------------------------------------------------------------------- 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: 50.0000 chunk 6 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 70.0000 chunk 7 optimal weight: 50.0000 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 overall best weight: 8.7996 ------------------------------------------------------------------------------- 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: 0.8521 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 1356 Z= 0.143 Angle : 0.484 5.438 1832 Z= 0.258 Chirality : 0.039 0.117 220 Planarity : 0.002 0.014 240 Dihedral : 4.119 11.795 186 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.00 % 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: 0.05 (0.66), residues: 172 helix: -0.13 (0.82), residues: 40 sheet: 0.56 (0.72), residues: 60 loop : -0.17 (0.75), residues: 72 *********************** 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 22 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2395 time to fit residues: 5.7638 Evaluate side-chains 14 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1915 ------------------------------------------------------------------------------- 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: 30.0000 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 8 optimal weight: 90.0000 chunk 14 optimal weight: 30.0000 chunk 11 optimal weight: 50.0000 chunk 13 optimal weight: 40.0000 chunk 15 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 40.0000 overall best weight: 16.5994 ------------------------------------------------------------------------------- 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: 0.8528 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.020 1356 Z= 0.225 Angle : 0.570 5.034 1832 Z= 0.291 Chirality : 0.039 0.113 220 Planarity : 0.003 0.017 240 Dihedral : 4.420 13.318 186 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.00 % 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: 0.24 (0.65), residues: 172 helix: 0.24 (0.79), residues: 42 sheet: 0.57 (0.69), residues: 60 loop : -0.10 (0.77), residues: 70 *********************** 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 19 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.169 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2065 time to fit residues: 4.3995 Evaluate side-chains 13 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1966 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 50.0000 chunk 10 optimal weight: 50.0000 chunk 7 optimal weight: 50.0000 chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 50.0000 chunk 14 optimal weight: 30.0000 chunk 13 optimal weight: 30.0000 chunk 8 optimal weight: 40.0000 chunk 6 optimal weight: 2.9990 overall best weight: 13.9994 ------------------------------------------------------------------------------- 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: 0.8508 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 1356 Z= 0.196 Angle : 0.544 6.264 1832 Z= 0.280 Chirality : 0.038 0.106 220 Planarity : 0.002 0.016 240 Dihedral : 4.289 11.832 186 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.00 % 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: 0.35 (0.67), residues: 172 helix: -0.23 (0.74), residues: 42 sheet: 0.70 (0.69), residues: 60 loop : 0.32 (0.84), residues: 70 *********************** 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 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.152 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.2161 time to fit residues: 4.1021 Evaluate side-chains 11 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.150 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1986 ------------------------------------------------------------------------------- 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: 50.0000 chunk 4 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 chunk 13 optimal weight: 50.0000 chunk 14 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 7 optimal weight: 40.0000 chunk 10 optimal weight: 40.0000 chunk 1 optimal weight: 40.0000 chunk 3 optimal weight: 9.9990 overall best weight: 23.9998 ------------------------------------------------------------------------------- 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: 0.8525 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 1356 Z= 0.309 Angle : 0.721 7.463 1832 Z= 0.363 Chirality : 0.042 0.158 220 Planarity : 0.003 0.019 240 Dihedral : 4.821 15.911 186 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.00 % 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: 0.01 (0.67), residues: 172 helix: -1.01 (0.67), residues: 42 sheet: 0.67 (0.69), residues: 60 loop : 0.30 (0.86), residues: 70 *********************** 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 : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2181 time to fit residues: 4.5872 Evaluate side-chains 12 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.148 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1957 ------------------------------------------------------------------------------- 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: 50.0000 chunk 1 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 50.0000 chunk 5 optimal weight: 50.0000 chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 14 optimal weight: 50.0000 chunk 8 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 72 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.7509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 1356 Z= 0.179 Angle : 0.530 7.846 1832 Z= 0.281 Chirality : 0.038 0.136 220 Planarity : 0.003 0.017 240 Dihedral : 4.419 12.925 186 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % 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: 0.55 (0.67), residues: 172 helix: -0.56 (0.71), residues: 42 sheet: 1.02 (0.68), residues: 60 loop : 0.59 (0.87), residues: 70 *********************** 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 : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2136 time to fit residues: 4.7346 Evaluate side-chains 13 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.149 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1979 ------------------------------------------------------------------------------- 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: 5.9990 chunk 0 optimal weight: 90.0000 chunk 9 optimal weight: 30.0000 chunk 6 optimal weight: 40.0000 chunk 5 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 40.0000 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- 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: 0.8488 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 1356 Z= 0.166 Angle : 0.536 8.907 1832 Z= 0.281 Chirality : 0.038 0.128 220 Planarity : 0.003 0.019 240 Dihedral : 4.219 12.085 186 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % 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: 0.89 (0.68), residues: 172 helix: -0.20 (0.76), residues: 42 sheet: 1.24 (0.68), residues: 60 loop : 0.72 (0.87), residues: 70 *********************** 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 20 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2200 time to fit residues: 4.9129 Evaluate side-chains 13 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.168 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1927 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 20.0000 chunk 4 optimal weight: 50.0000 chunk 3 optimal weight: 40.0000 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 8 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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: 0.8470 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 1356 Z= 0.145 Angle : 0.522 9.362 1832 Z= 0.276 Chirality : 0.038 0.132 220 Planarity : 0.002 0.019 240 Dihedral : 4.015 10.143 186 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % 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: 1.16 (0.68), residues: 172 helix: -0.07 (0.80), residues: 42 sheet: 1.47 (0.68), residues: 60 loop : 0.87 (0.86), residues: 70 ********************** 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 18 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.2401 time to fit residues: 4.7700 Evaluate side-chains 13 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1945 ------------------------------------------------------------------------------- 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: 50.0000 chunk 14 optimal weight: 20.0000 chunk 2 optimal weight: 50.0000 chunk 10 optimal weight: 40.0000 chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 80.0000 chunk 5 optimal weight: 50.0000 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 40.0000 chunk 7 optimal weight: 40.0000 chunk 6 optimal weight: 8.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.054191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046889 restraints weight = 13011.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.047612 restraints weight = 9567.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.048206 restraints weight = 7814.932| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.8027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 1356 Z= 0.235 Angle : 0.609 9.148 1832 Z= 0.312 Chirality : 0.038 0.124 220 Planarity : 0.003 0.020 240 Dihedral : 4.443 14.075 186 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % 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: 0.85 (0.67), residues: 172 helix: -0.45 (0.75), residues: 42 sheet: 1.35 (0.68), residues: 60 loop : 0.71 (0.85), residues: 70 =============================================================================== Job complete usr+sys time: 553.55 seconds wall clock time: 10 minutes 49.15 seconds (649.15 seconds total)