Starting phenix.real_space_refine on Mon Nov 13 16:20:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdc_22136/11_2023/6xdc_22136.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdc_22136/11_2023/6xdc_22136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdc_22136/11_2023/6xdc_22136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdc_22136/11_2023/6xdc_22136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdc_22136/11_2023/6xdc_22136.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdc_22136/11_2023/6xdc_22136.pdb" } resolution = 2.9 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= -0.001 sd= 0.101 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 16 5.16 5 C 2094 2.51 5 N 490 2.21 5 O 550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 3150 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Time building chain proxies: 2.24, per 1000 atoms: 0.71 Number of scatterers: 3150 At special positions: 0 Unit cell: (55.713, 62.535, 94.371, 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 16 16.00 O 550 8.00 N 490 7.00 C 2094 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: 1.19 Conformation dependent library (CDL) restraints added in 616.9 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 2 sheets defined 50.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.806A pdb=" N ILE A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 100 Processing helix chain 'A' and resid 102 through 134 removed outlier: 3.618A pdb=" N LEU A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.881A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 4.067A pdb=" N THR A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.825A pdb=" N ILE B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 100 Processing helix chain 'B' and resid 102 through 133 removed outlier: 3.716A pdb=" N LEU B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.831A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.074A pdb=" N THR B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 160 removed outlier: 5.422A pdb=" N LEU A 214 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN A 234 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 216 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 172 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP A 183 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 160 removed outlier: 5.387A pdb=" N LEU B 214 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASN B 234 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 216 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 172 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP B 183 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 585 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: 0.82 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 912 1.34 - 1.46: 719 1.46 - 1.57: 1595 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3244 Sorted by residual: bond pdb=" CB GLN A 185 " pdb=" CG GLN A 185 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" CB CYS B 157 " pdb=" SG CYS B 157 " ideal model delta sigma weight residual 1.808 1.760 0.048 3.30e-02 9.18e+02 2.09e+00 bond pdb=" CB GLN B 185 " pdb=" CG GLN B 185 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" C ALA A 103 " pdb=" N PRO A 104 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.28e-02 6.10e+03 2.05e+00 bond pdb=" CB CYS A 157 " pdb=" SG CYS A 157 " ideal model delta sigma weight residual 1.808 1.762 0.046 3.30e-02 9.18e+02 1.96e+00 ... (remaining 3239 not shown) Histogram of bond angle deviations from ideal: 100.97 - 107.59: 114 107.59 - 114.21: 1802 114.21 - 120.84: 1460 120.84 - 127.46: 1006 127.46 - 134.08: 42 Bond angle restraints: 4424 Sorted by residual: angle pdb=" CA TYR A 107 " pdb=" CB TYR A 107 " pdb=" CG TYR A 107 " ideal model delta sigma weight residual 113.90 120.12 -6.22 1.80e+00 3.09e-01 1.19e+01 angle pdb=" CA TYR B 107 " pdb=" CB TYR B 107 " pdb=" CG TYR B 107 " ideal model delta sigma weight residual 113.90 120.05 -6.15 1.80e+00 3.09e-01 1.17e+01 angle pdb=" N ASN A 137 " pdb=" CA ASN A 137 " pdb=" C ASN A 137 " ideal model delta sigma weight residual 109.81 117.09 -7.28 2.21e+00 2.05e-01 1.08e+01 angle pdb=" N ASN B 137 " pdb=" CA ASN B 137 " pdb=" C ASN B 137 " ideal model delta sigma weight residual 109.81 117.00 -7.19 2.21e+00 2.05e-01 1.06e+01 angle pdb=" OG1 THR A 170 " pdb=" CB THR A 170 " pdb=" CG2 THR A 170 " ideal model delta sigma weight residual 109.30 102.79 6.51 2.00e+00 2.50e-01 1.06e+01 ... (remaining 4419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.27: 1544 12.27 - 24.53: 191 24.53 - 36.80: 67 36.80 - 49.07: 18 49.07 - 61.34: 10 Dihedral angle restraints: 1830 sinusoidal: 684 harmonic: 1146 Sorted by residual: dihedral pdb=" CA LEU B 140 " pdb=" C LEU B 140 " pdb=" N TYR B 141 " pdb=" CA TYR B 141 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LEU A 140 " pdb=" C LEU A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual 180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR B 189 " pdb=" C TYR B 189 " pdb=" N THR B 190 " pdb=" CA THR B 190 " ideal model delta harmonic sigma weight residual -180.00 -163.99 -16.01 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 1827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 407 0.071 - 0.141: 83 0.141 - 0.212: 8 0.212 - 0.282: 3 0.282 - 0.353: 1 Chirality restraints: 502 Sorted by residual: chirality pdb=" CB ILE B 236 " pdb=" CA ILE B 236 " pdb=" CG1 ILE B 236 " pdb=" CG2 ILE B 236 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB VAL B 197 " pdb=" CA VAL B 197 " pdb=" CG1 VAL B 197 " pdb=" CG2 VAL B 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL A 197 " pdb=" CA VAL A 197 " pdb=" CG1 VAL A 197 " pdb=" CG2 VAL A 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 499 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 137 " -0.053 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO B 138 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 137 " 0.053 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO A 138 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 103 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO B 104 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 104 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 104 " -0.034 5.00e-02 4.00e+02 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 831 2.80 - 3.33: 2598 3.33 - 3.85: 5072 3.85 - 4.38: 5521 4.38 - 4.90: 9971 Nonbonded interactions: 23993 Sorted by model distance: nonbonded pdb=" OG1 THR B 151 " pdb=" O TYR B 154 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR A 151 " pdb=" O TYR A 154 " model vdw 2.284 2.440 nonbonded pdb=" O PHE B 114 " pdb=" OG SER B 117 " model vdw 2.375 2.440 nonbonded pdb=" O PHE A 114 " pdb=" OG SER A 117 " model vdw 2.378 2.440 nonbonded pdb=" N ASP A 238 " pdb=" OD1 ASP A 238 " model vdw 2.381 2.520 ... (remaining 23988 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 3.850 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.490 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.006 0.065 3244 Z= 0.365 Angle : 0.788 8.610 4424 Z= 0.444 Chirality : 0.062 0.353 502 Planarity : 0.008 0.079 528 Dihedral : 13.654 61.336 1098 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.15 % Allowed : 15.23 % Favored : 83.62 % 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: -2.72 (0.34), residues: 378 helix: -1.09 (0.30), residues: 168 sheet: -1.40 (0.42), residues: 106 loop : -3.07 (0.45), residues: 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.350 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 66 average time/residue: 0.6761 time to fit residues: 46.8819 Evaluate side-chains 46 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1937 time to fit residues: 0.6927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 93 HIS B 185 GLN B 204 HIS B 234 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3244 Z= 0.208 Angle : 0.564 9.218 4424 Z= 0.311 Chirality : 0.044 0.143 502 Planarity : 0.006 0.063 528 Dihedral : 4.843 18.812 422 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.60 % Allowed : 18.39 % Favored : 77.01 % 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: -0.52 (0.40), residues: 378 helix: 1.49 (0.38), residues: 168 sheet: -0.77 (0.47), residues: 96 loop : -2.79 (0.44), residues: 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.361 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 61 average time/residue: 0.6608 time to fit residues: 42.3827 Evaluate side-chains 58 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 5 average time/residue: 0.1245 time to fit residues: 1.2193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 11 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3244 Z= 0.168 Angle : 0.528 9.103 4424 Z= 0.290 Chirality : 0.043 0.134 502 Planarity : 0.005 0.056 528 Dihedral : 4.478 16.921 422 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.02 % Allowed : 21.26 % Favored : 74.71 % 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: 0.20 (0.43), residues: 378 helix: 2.32 (0.40), residues: 170 sheet: -0.70 (0.48), residues: 96 loop : -2.65 (0.47), residues: 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.321 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.6651 time to fit residues: 41.9110 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.0913 time to fit residues: 0.8208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3244 Z= 0.227 Angle : 0.579 10.254 4424 Z= 0.313 Chirality : 0.044 0.136 502 Planarity : 0.005 0.055 528 Dihedral : 4.567 16.940 422 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.74 % Allowed : 22.99 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.43), residues: 378 helix: 2.62 (0.40), residues: 170 sheet: -0.85 (0.48), residues: 96 loop : -2.59 (0.48), residues: 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.358 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 52 average time/residue: 0.7293 time to fit residues: 39.7995 Evaluate side-chains 48 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1771 time to fit residues: 0.8778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3244 Z= 0.218 Angle : 0.561 9.210 4424 Z= 0.305 Chirality : 0.044 0.133 502 Planarity : 0.005 0.054 528 Dihedral : 4.486 15.961 422 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.31 % Allowed : 22.70 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.43), residues: 378 helix: 2.75 (0.40), residues: 170 sheet: -0.97 (0.47), residues: 96 loop : -2.48 (0.48), residues: 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.357 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 52 average time/residue: 0.7159 time to fit residues: 39.0690 Evaluate side-chains 48 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.0340 time to fit residues: 0.6266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3244 Z= 0.224 Angle : 0.564 8.708 4424 Z= 0.307 Chirality : 0.044 0.136 502 Planarity : 0.005 0.054 528 Dihedral : 4.534 16.294 422 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.74 % Allowed : 23.85 % Favored : 72.41 % 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: 0.60 (0.44), residues: 378 helix: 2.84 (0.40), residues: 170 sheet: -0.86 (0.48), residues: 96 loop : -2.44 (0.48), residues: 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.324 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 0.7343 time to fit residues: 38.5257 Evaluate side-chains 46 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.4913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3244 Z= 0.231 Angle : 0.569 8.545 4424 Z= 0.309 Chirality : 0.044 0.136 502 Planarity : 0.005 0.053 528 Dihedral : 4.544 15.938 422 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.16 % Allowed : 23.85 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.44), residues: 378 helix: 2.90 (0.40), residues: 170 sheet: -0.84 (0.47), residues: 96 loop : -2.41 (0.49), residues: 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.349 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.7572 time to fit residues: 38.1333 Evaluate side-chains 47 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.0060 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3244 Z= 0.167 Angle : 0.543 8.563 4424 Z= 0.294 Chirality : 0.042 0.134 502 Planarity : 0.004 0.053 528 Dihedral : 4.305 14.617 422 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.45 % Allowed : 23.56 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.44), residues: 378 helix: 3.03 (0.39), residues: 170 sheet: -0.73 (0.48), residues: 96 loop : -2.37 (0.49), residues: 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.354 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 47 average time/residue: 0.7793 time to fit residues: 38.3725 Evaluate side-chains 48 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.0318 time to fit residues: 0.5796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3244 Z= 0.209 Angle : 0.569 8.433 4424 Z= 0.310 Chirality : 0.043 0.136 502 Planarity : 0.005 0.053 528 Dihedral : 4.458 15.220 422 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.59 % Allowed : 24.43 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.44), residues: 378 helix: 3.08 (0.39), residues: 170 sheet: -0.72 (0.49), residues: 96 loop : -2.33 (0.50), residues: 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.371 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.6881 time to fit residues: 34.8108 Evaluate side-chains 43 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.0270 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3244 Z= 0.169 Angle : 0.573 12.567 4424 Z= 0.305 Chirality : 0.042 0.132 502 Planarity : 0.004 0.053 528 Dihedral : 4.275 13.854 422 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.01 % Allowed : 25.57 % Favored : 72.41 % 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: 0.96 (0.44), residues: 378 helix: 3.09 (0.39), residues: 170 sheet: -0.55 (0.50), residues: 96 loop : -2.29 (0.50), residues: 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.371 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 0.6885 time to fit residues: 34.1295 Evaluate side-chains 44 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.166899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139111 restraints weight = 4161.633| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.92 r_work: 0.3652 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3244 Z= 0.186 Angle : 0.576 12.073 4424 Z= 0.307 Chirality : 0.043 0.134 502 Planarity : 0.005 0.052 528 Dihedral : 4.332 14.181 422 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.59 % Allowed : 25.00 % Favored : 72.41 % 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: 0.98 (0.44), residues: 378 helix: 3.12 (0.39), residues: 170 sheet: -0.57 (0.50), residues: 96 loop : -2.27 (0.50), residues: 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1415.97 seconds wall clock time: 25 minutes 58.78 seconds (1558.78 seconds total)