Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/03_2024/7v4c_31707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/03_2024/7v4c_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_31707/03_2024/7v4c_31707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/03_2024/7v4c_31707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/03_2024/7v4c_31707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4c_31707/03_2024/7v4c_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-dev-5265/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: 1.03, per 1000 atoms: 0.80 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: 0.39 Conformation dependent library (CDL) restraints added in 407.0 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: 0.15 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: 0.30 Time building geometry restraints manager: 0.45 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: 0.210 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: 0.970 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.110 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.600 ------------------------------------------------------------------------------- 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 : 0.176 Fit side-chains REVERT: F 45 LYS cc_start: 0.8437 (tttt) cc_final: 0.7848 (mttp) REVERT: F 83 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7929 (mm-30) REVERT: B 43 LYS cc_start: 0.8913 (mttt) cc_final: 0.8664 (mttt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1197 time to fit residues: 4.5368 Evaluate side-chains 24 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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: 0.0570 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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: 0.7947 moved from start: 0.1473 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= 0.145 Angle : 0.498 3.301 1749 Z= 0.289 Chirality : 0.051 0.127 231 Planarity : 0.002 0.008 216 Dihedral : 4.449 13.322 186 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.30 % Allowed : 23.48 % Favored : 71.21 % 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 0.000 HIS A 50 PHE 0.003 0.001 PHE F 94 TYR 0.002 0.001 TYR A 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 39 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.132 Fit side-chains REVERT: F 43 LYS cc_start: 0.8593 (mttp) cc_final: 0.8385 (mttm) REVERT: F 83 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7932 (mm-30) REVERT: A 71 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.8839 (t) outliers start: 7 outliers final: 2 residues processed: 36 average time/residue: 0.1118 time to fit residues: 4.6484 Evaluate side-chains 30 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 0.0070 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- 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: 0.7978 moved from start: 0.1748 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= 0.208 Angle : 0.493 3.111 1749 Z= 0.290 Chirality : 0.052 0.122 231 Planarity : 0.002 0.012 216 Dihedral : 4.290 11.973 186 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 9.85 % Allowed : 17.42 % Favored : 72.73 % 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 (0.39), 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 0.004 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 42 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 29 time to evaluate : 0.143 Fit side-chains REVERT: F 83 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7754 (mm-30) REVERT: A 83 GLU cc_start: 0.8226 (tt0) cc_final: 0.7831 (mm-30) REVERT: B 45 LYS cc_start: 0.8327 (tttt) cc_final: 0.8007 (mtpp) outliers start: 13 outliers final: 10 residues processed: 40 average time/residue: 0.1205 time to fit residues: 5.5180 Evaluate side-chains 37 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 27 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 0.0000 chunk 17 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.3590 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 1293 Z= 0.303 Angle : 0.551 4.497 1749 Z= 0.322 Chirality : 0.053 0.135 231 Planarity : 0.002 0.014 216 Dihedral : 4.495 12.502 186 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 10.61 % Allowed : 18.18 % Favored : 71.21 % 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: -5.37 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.31), 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 0.003 0.001 TYR A 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 41 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 27 time to evaluate : 0.142 Fit side-chains REVERT: F 43 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8463 (mttp) REVERT: F 83 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7770 (mm-30) REVERT: A 83 GLU cc_start: 0.8229 (tt0) cc_final: 0.7880 (mm-30) REVERT: B 45 LYS cc_start: 0.8294 (tttt) cc_final: 0.8007 (mtpp) outliers start: 14 outliers final: 12 residues processed: 38 average time/residue: 0.1171 time to fit residues: 5.0738 Evaluate side-chains 39 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 26 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.7944 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1293 Z= 0.166 Angle : 0.458 2.875 1749 Z= 0.270 Chirality : 0.050 0.121 231 Planarity : 0.002 0.010 216 Dihedral : 4.174 12.560 186 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 12.12 % Allowed : 17.42 % 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: -5.01 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.33), 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 0.002 0.001 TYR A 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 42 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 26 time to evaluate : 0.148 Fit side-chains REVERT: A 71 VAL cc_start: 0.9162 (p) cc_final: 0.8872 (t) REVERT: A 83 GLU cc_start: 0.8206 (tt0) cc_final: 0.7875 (mm-30) REVERT: B 43 LYS cc_start: 0.8855 (mttp) cc_final: 0.8651 (mttm) REVERT: B 83 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8050 (tt0) outliers start: 16 outliers final: 13 residues processed: 37 average time/residue: 0.1056 time to fit residues: 4.5399 Evaluate side-chains 39 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 25 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU 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: 10.0000 chunk 12 optimal weight: 0.0870 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- 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: 0.7962 moved from start: 0.2167 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= 0.208 Angle : 0.473 3.304 1749 Z= 0.279 Chirality : 0.050 0.121 231 Planarity : 0.002 0.011 216 Dihedral : 4.176 12.549 186 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 13.64 % Allowed : 17.42 % Favored : 68.94 % 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: -4.96 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.34), 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 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 45 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 27 time to evaluate : 0.149 Fit side-chains REVERT: A 71 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8853 (t) REVERT: A 83 GLU cc_start: 0.8264 (tt0) cc_final: 0.7934 (mm-30) REVERT: B 43 LYS cc_start: 0.8830 (mttp) cc_final: 0.8603 (mttt) REVERT: B 45 LYS cc_start: 0.8222 (tttt) cc_final: 0.7921 (mtpp) REVERT: B 83 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7815 (mm-30) outliers start: 18 outliers final: 14 residues processed: 41 average time/residue: 0.1035 time to fit residues: 4.9014 Evaluate side-chains 43 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 27 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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: 0.7981 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1293 Z= 0.271 Angle : 0.513 3.825 1749 Z= 0.302 Chirality : 0.051 0.127 231 Planarity : 0.002 0.011 216 Dihedral : 4.316 12.962 186 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 12.12 % Allowed : 18.94 % Favored : 68.94 % 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: -5.05 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.33), 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 0.004 0.001 TYR A 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 41 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 25 time to evaluate : 0.127 Fit side-chains REVERT: A 83 GLU cc_start: 0.8161 (tt0) cc_final: 0.7841 (mm-30) REVERT: B 43 LYS cc_start: 0.8843 (mttp) cc_final: 0.8590 (mttt) REVERT: B 45 LYS cc_start: 0.8251 (tttt) cc_final: 0.8012 (mtpp) REVERT: B 83 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7853 (mm-30) outliers start: 16 outliers final: 14 residues processed: 39 average time/residue: 0.0977 time to fit residues: 4.4157 Evaluate side-chains 40 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 25 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7951 moved from start: 0.2238 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= 0.191 Angle : 0.463 3.206 1749 Z= 0.273 Chirality : 0.050 0.122 231 Planarity : 0.002 0.010 216 Dihedral : 4.166 12.865 186 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 11.36 % Allowed : 18.18 % 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: -4.87 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.34), 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 0.002 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 40 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 25 time to evaluate : 0.138 Fit side-chains REVERT: A 71 VAL cc_start: 0.9128 (p) cc_final: 0.8812 (t) REVERT: A 83 GLU cc_start: 0.8252 (tt0) cc_final: 0.7944 (mm-30) REVERT: B 43 LYS cc_start: 0.8845 (mttp) cc_final: 0.8583 (mttt) REVERT: B 83 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7832 (mm-30) outliers start: 15 outliers final: 14 residues processed: 38 average time/residue: 0.0924 time to fit residues: 4.1330 Evaluate side-chains 40 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 25 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 overall best weight: 2.1742 ------------------------------------------------------------------------------- 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: 0.7955 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1293 Z= 0.205 Angle : 0.470 3.419 1749 Z= 0.278 Chirality : 0.050 0.120 231 Planarity : 0.002 0.010 216 Dihedral : 4.151 12.921 186 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 12.88 % Allowed : 17.42 % Favored : 69.70 % 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 0.002 0.001 HIS A 50 PHE 0.004 0.001 PHE F 94 TYR 0.003 0.001 TYR A 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 42 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 25 time to evaluate : 0.156 Fit side-chains REVERT: A 83 GLU cc_start: 0.8252 (tt0) cc_final: 0.7979 (mm-30) REVERT: B 43 LYS cc_start: 0.8826 (mttp) cc_final: 0.8602 (mttt) REVERT: B 45 LYS cc_start: 0.8202 (tttt) cc_final: 0.7967 (mtpp) REVERT: B 62 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7315 (mt0) REVERT: B 83 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7829 (mm-30) outliers start: 17 outliers final: 14 residues processed: 40 average time/residue: 0.1113 time to fit residues: 5.1374 Evaluate side-chains 41 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 25 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1293 Z= 0.230 Angle : 0.487 3.526 1749 Z= 0.287 Chirality : 0.050 0.127 231 Planarity : 0.002 0.011 216 Dihedral : 4.220 13.084 186 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 11.36 % Allowed : 19.70 % Favored : 68.94 % 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: -4.87 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.34), 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 A 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 39 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 24 time to evaluate : 0.152 Fit side-chains REVERT: A 83 GLU cc_start: 0.8251 (tt0) cc_final: 0.7937 (mm-30) REVERT: B 43 LYS cc_start: 0.8844 (mttp) cc_final: 0.8614 (mttt) REVERT: B 45 LYS cc_start: 0.8216 (tttt) cc_final: 0.7977 (mtpp) REVERT: B 83 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7834 (mm-30) outliers start: 15 outliers final: 14 residues processed: 37 average time/residue: 0.1081 time to fit residues: 4.6371 Evaluate side-chains 39 residues out of total 132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 24 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.125750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.099819 restraints weight = 1582.736| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.90 r_work: 0.3369 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2224 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= 0.239 Angle : 0.494 3.581 1749 Z= 0.291 Chirality : 0.051 0.127 231 Planarity : 0.002 0.011 216 Dihedral : 4.255 13.361 186 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 11.36 % Allowed : 19.70 % Favored : 68.94 % 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: -4.89 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.34), 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 A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 797.36 seconds wall clock time: 15 minutes 57.53 seconds (957.53 seconds total)