Starting phenix.real_space_refine on Thu Dec 7 15:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/12_2023/7v4c_31707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/12_2023/7v4c_31707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/12_2023/7v4c_31707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/12_2023/7v4c_31707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/12_2023/7v4c_31707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/12_2023/7v4c_31707.pdb" } resolution = 3.3 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= 0.007 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: 3 Type Number sf(0) Gaussians C 807 2.51 5 N 222 2.21 5 O 258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 1287 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 429 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "A" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 429 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "B" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 429 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Time building chain proxies: 1.09, per 1000 atoms: 0.85 Number of scatterers: 1287 At special positions: 0 Unit cell: (75.26, 66.78, 33.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 258 8.00 N 222 7.00 C 807 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 408.3 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 318 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 68 through 71 removed outlier: 6.792A pdb=" N ALA F 69 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 74 through 76 removed outlier: 6.774A pdb=" N VAL F 74 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 74 " --> pdb=" O THR B 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 91 through 92 Processing sheet with id=AA4, first strand: chain 'F' and resid 95 through 96 4 hydrogen bonds defined for protein. 12 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: 0.35 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 225 1.28 - 1.35: 198 1.35 - 1.41: 54 1.41 - 1.48: 210 1.48 - 1.54: 606 Bond restraints: 1293 Sorted by residual: bond pdb=" C SER A 87 " pdb=" N ILE A 88 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.42e-02 4.96e+03 2.61e+00 bond pdb=" C SER B 87 " pdb=" N ILE B 88 " ideal model delta sigma weight residual 1.330 1.308 0.023 1.42e-02 4.96e+03 2.55e+00 bond pdb=" C SER F 87 " pdb=" N ILE F 88 " ideal model delta sigma weight residual 1.330 1.308 0.023 1.42e-02 4.96e+03 2.54e+00 bond pdb=" CB VAL A 48 " pdb=" CG1 VAL A 48 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" CB VAL F 48 " pdb=" CG1 VAL F 48 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.69e+00 ... (remaining 1288 not shown) Histogram of bond angle deviations from ideal: 106.15 - 111.17: 594 111.17 - 116.20: 352 116.20 - 121.22: 407 121.22 - 126.24: 393 126.24 - 131.26: 3 Bond angle restraints: 1749 Sorted by residual: angle pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" N PHE A 94 " ideal model delta sigma weight residual 114.86 117.14 -2.28 1.01e+00 9.80e-01 5.07e+00 angle pdb=" C ASN A 65 " pdb=" N VAL A 66 " pdb=" CA VAL A 66 " ideal model delta sigma weight residual 122.36 119.75 2.61 1.16e+00 7.43e-01 5.07e+00 angle pdb=" CA GLY B 93 " pdb=" C GLY B 93 " pdb=" N PHE B 94 " ideal model delta sigma weight residual 114.86 117.13 -2.27 1.01e+00 9.80e-01 5.06e+00 angle pdb=" C VAL B 66 " pdb=" N GLY B 67 " pdb=" CA GLY B 67 " ideal model delta sigma weight residual 121.41 117.02 4.39 1.96e+00 2.60e-01 5.01e+00 angle pdb=" CA GLY F 93 " pdb=" C GLY F 93 " pdb=" N PHE F 94 " ideal model delta sigma weight residual 114.86 117.11 -2.25 1.01e+00 9.80e-01 4.98e+00 ... (remaining 1744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.06: 594 10.06 - 20.12: 111 20.12 - 30.18: 39 30.18 - 40.24: 9 40.24 - 50.30: 3 Dihedral angle restraints: 756 sinusoidal: 252 harmonic: 504 Sorted by residual: dihedral pdb=" CA GLU B 57 " pdb=" CB GLU B 57 " pdb=" CG GLU B 57 " pdb=" CD GLU B 57 " ideal model delta sinusoidal sigma weight residual -60.00 -110.30 50.30 3 1.50e+01 4.44e-03 8.88e+00 dihedral pdb=" CA GLU F 57 " pdb=" CB GLU F 57 " pdb=" CG GLU F 57 " pdb=" CD GLU F 57 " ideal model delta sinusoidal sigma weight residual -60.00 -110.29 50.29 3 1.50e+01 4.44e-03 8.88e+00 dihedral pdb=" CA GLU A 57 " pdb=" CB GLU A 57 " pdb=" CG GLU A 57 " pdb=" CD GLU A 57 " ideal model delta sinusoidal sigma weight residual -60.00 -110.26 50.26 3 1.50e+01 4.44e-03 8.88e+00 ... (remaining 753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 94 0.032 - 0.065: 83 0.065 - 0.097: 33 0.097 - 0.130: 12 0.130 - 0.162: 9 Chirality restraints: 231 Sorted by residual: chirality pdb=" CB VAL F 77 " pdb=" CA VAL F 77 " pdb=" CG1 VAL F 77 " pdb=" CG2 VAL F 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.57e-01 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 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB VAL A 77 " pdb=" CA VAL A 77 " pdb=" CG1 VAL A 77 " pdb=" CG2 VAL A 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 228 not shown) Planarity restraints: 216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 67 " -0.003 2.00e-02 2.50e+03 6.98e-03 4.87e-01 pdb=" C GLY B 67 " 0.012 2.00e-02 2.50e+03 pdb=" O GLY B 67 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY B 68 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 67 " -0.003 2.00e-02 2.50e+03 6.64e-03 4.41e-01 pdb=" C GLY A 67 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY A 67 " -0.004 2.00e-02 2.50e+03 pdb=" N GLY A 68 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 67 " -0.003 2.00e-02 2.50e+03 6.61e-03 4.37e-01 pdb=" C GLY F 67 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY F 67 " -0.004 2.00e-02 2.50e+03 pdb=" N GLY F 68 " -0.004 2.00e-02 2.50e+03 ... (remaining 213 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 417 2.82 - 3.34: 1087 3.34 - 3.86: 1957 3.86 - 4.38: 2068 4.38 - 4.90: 3876 Nonbonded interactions: 9405 Sorted by model distance: nonbonded pdb=" OG1 THR A 81 " pdb=" O LYS B 80 " model vdw 2.305 2.440 nonbonded pdb=" OG1 THR F 81 " pdb=" O LYS A 80 " model vdw 2.340 2.440 nonbonded pdb=" OG1 THR B 72 " pdb=" N GLY B 73 " model vdw 2.622 2.520 nonbonded pdb=" OG1 THR A 72 " pdb=" N GLY A 73 " model vdw 2.622 2.520 nonbonded pdb=" OG1 THR F 72 " pdb=" N GLY F 73 " model vdw 2.623 2.520 ... (remaining 9400 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' selection = chain 'F' } 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.980 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.730 Find NCS groups from input model: 0.090 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.008 0.043 1293 Z= 0.534 Angle : 0.745 4.388 1749 Z= 0.456 Chirality : 0.058 0.162 231 Planarity : 0.002 0.007 216 Dihedral : 12.467 50.301 438 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 0.00 % Allowed : 20.45 % Favored : 79.55 % 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: -6.54 (0.37), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.98 (0.28), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE B 94 TYR 0.007 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.150 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1358 time to fit residues: 5.1330 Evaluate side-chains 23 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS A 50 HIS B 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1293 Z= 0.143 Angle : 0.501 3.385 1749 Z= 0.290 Chirality : 0.052 0.125 231 Planarity : 0.002 0.009 216 Dihedral : 4.472 13.389 186 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.30 % Allowed : 24.24 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.86 (0.38), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.46 (0.29), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.003 0.001 PHE F 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.152 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 34 average time/residue: 0.1115 time to fit residues: 4.3700 Evaluate side-chains 28 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.135 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0168 time to fit residues: 0.2376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.0020 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- 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: 0.7973 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1293 Z= 0.206 Angle : 0.496 3.182 1749 Z= 0.291 Chirality : 0.052 0.122 231 Planarity : 0.002 0.012 216 Dihedral : 4.297 12.340 186 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 9.09 % Allowed : 16.67 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.53 (0.40), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.30), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.005 0.001 PHE F 94 TYR 0.002 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 26 time to evaluate : 0.129 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 36 average time/residue: 0.1062 time to fit residues: 4.4173 Evaluate side-chains 33 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 23 time to evaluate : 0.125 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0163 time to fit residues: 0.4369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 0.2980 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.0060 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.6602 ------------------------------------------------------------------------------- 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: 0.7965 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 1293 Z= 0.248 Angle : 0.515 3.922 1749 Z= 0.300 Chirality : 0.053 0.128 231 Planarity : 0.002 0.013 216 Dihedral : 4.359 13.017 186 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 3.79 % Allowed : 19.70 % Favored : 76.52 % 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: -5.24 (0.42), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.004 0.001 PHE F 94 TYR 0.003 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.117 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 31 average time/residue: 0.1060 time to fit residues: 3.8452 Evaluate side-chains 29 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.125 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0156 time to fit residues: 0.2301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.0030 chunk 3 optimal weight: 0.0570 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 1 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.0712 ------------------------------------------------------------------------------- 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: 0.7906 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1293 Z= 0.118 Angle : 0.421 3.043 1749 Z= 0.248 Chirality : 0.049 0.119 231 Planarity : 0.002 0.009 216 Dihedral : 3.932 12.141 186 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.76 % Allowed : 23.48 % Favored : 75.76 % 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: -4.76 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE F 94 TYR 0.001 0.000 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.137 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.1351 time to fit residues: 3.8884 Evaluate side-chains 24 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.144 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1293 Z= 0.238 Angle : 0.494 3.616 1749 Z= 0.289 Chirality : 0.051 0.127 231 Planarity : 0.002 0.011 216 Dihedral : 4.164 10.934 186 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 5.30 % Allowed : 20.45 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.003 0.001 PHE F 94 TYR 0.003 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.149 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 34 average time/residue: 0.1383 time to fit residues: 5.2817 Evaluate side-chains 34 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.141 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0169 time to fit residues: 0.3788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1293 Z= 0.223 Angle : 0.507 3.425 1749 Z= 0.293 Chirality : 0.051 0.121 231 Planarity : 0.002 0.011 216 Dihedral : 4.193 11.354 186 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 22.73 % Favored : 77.27 % 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: -4.73 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.004 0.001 PHE F 94 TYR 0.003 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1475 time to fit residues: 4.3456 Evaluate side-chains 26 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.146 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1293 Z= 0.135 Angle : 0.448 3.189 1749 Z= 0.258 Chirality : 0.048 0.119 231 Planarity : 0.002 0.010 216 Dihedral : 3.939 10.385 186 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 24.24 % Favored : 75.76 % 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: -4.49 (0.47), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.36), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.004 0.001 PHE F 94 TYR 0.002 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.147 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1734 time to fit residues: 4.7212 Evaluate side-chains 23 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1293 Z= 0.275 Angle : 0.535 3.819 1749 Z= 0.308 Chirality : 0.051 0.125 231 Planarity : 0.002 0.011 216 Dihedral : 4.235 10.974 186 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 1.52 % Allowed : 21.97 % Favored : 76.52 % 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: -4.70 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.003 0.001 PHE F 94 TYR 0.004 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.143 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.1814 time to fit residues: 5.3477 Evaluate side-chains 24 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.182 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0278 time to fit residues: 0.3510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.7986 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 1293 Z= 0.358 Angle : 0.629 5.411 1749 Z= 0.360 Chirality : 0.055 0.169 231 Planarity : 0.002 0.012 216 Dihedral : 4.519 12.021 186 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 21.97 % Favored : 78.03 % 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: -4.85 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.003 0.001 PHE F 94 TYR 0.004 0.002 TYR F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.143 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1458 time to fit residues: 3.8417 Evaluate side-chains 23 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.0060 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.136121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.110983 restraints weight = 1591.928| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.81 r_work: 0.3462 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1293 Z= 0.097 Angle : 0.467 4.548 1749 Z= 0.268 Chirality : 0.049 0.118 231 Planarity : 0.002 0.010 216 Dihedral : 3.923 10.664 186 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.76 % Allowed : 21.97 % Favored : 77.27 % 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: -4.30 (0.48), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.37), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.004 0.001 PHE F 94 TYR 0.001 0.001 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 822.99 seconds wall clock time: 21 minutes 23.13 seconds (1283.13 seconds total)