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/7v49_31704/03_2024/7v49_31704.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/03_2024/7v49_31704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/03_2024/7v49_31704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/03_2024/7v49_31704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/03_2024/7v49_31704.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/03_2024/7v49_31704.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 765 2.51 5 N 210 2.21 5 O 246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1221 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 407 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "A" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 407 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 407 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Time building chain proxies: 1.12, per 1000 atoms: 0.92 Number of scatterers: 1221 At special positions: 0 Unit cell: (78.44, 65.72, 28.62, 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 246 8.00 N 210 7.00 C 765 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: 0.41 Conformation dependent library (CDL) restraints added in 251.5 milliseconds 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 300 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.281A pdb=" N ILE C 88 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 No hydrogen bonds 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: 0.02 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 - 1.29: 213 1.29 - 1.35: 192 1.35 - 1.42: 54 1.42 - 1.48: 207 1.48 - 1.54: 561 Bond restraints: 1227 Sorted by residual: bond pdb=" CB VAL A 82 " pdb=" CG1 VAL A 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB VAL B 82 " pdb=" CG1 VAL B 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB VAL C 82 " pdb=" CG1 VAL C 82 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB VAL C 37 " pdb=" CG1 VAL C 37 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.96e-01 bond pdb=" CB VAL B 37 " pdb=" CG1 VAL B 37 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.70e-01 ... (remaining 1222 not shown) Histogram of bond angle deviations from ideal: 106.16 - 111.18: 562 111.18 - 116.20: 315 116.20 - 121.22: 418 121.22 - 126.23: 367 126.23 - 131.25: 3 Bond angle restraints: 1665 Sorted by residual: angle pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" CG LEU C 38 " ideal model delta sigma weight residual 116.30 123.99 -7.69 3.50e+00 8.16e-02 4.83e+00 angle pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " ideal model delta sigma weight residual 116.30 123.98 -7.68 3.50e+00 8.16e-02 4.81e+00 angle pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" CG LEU B 38 " ideal model delta sigma weight residual 116.30 123.97 -7.67 3.50e+00 8.16e-02 4.80e+00 angle pdb=" N ILE B 88 " pdb=" CA ILE B 88 " pdb=" C ILE B 88 " ideal model delta sigma weight residual 106.61 110.32 -3.71 1.78e+00 3.16e-01 4.34e+00 angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 106.61 110.28 -3.67 1.78e+00 3.16e-01 4.25e+00 ... (remaining 1660 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 9.48: 557 9.48 - 18.94: 91 18.94 - 28.41: 36 28.41 - 37.88: 3 37.88 - 47.34: 15 Dihedral angle restraints: 702 sinusoidal: 222 harmonic: 480 Sorted by residual: dihedral pdb=" CA THR B 81 " pdb=" C THR B 81 " pdb=" N VAL B 82 " pdb=" CA VAL B 82 " ideal model delta harmonic sigma weight residual 180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR A 81 " pdb=" C THR A 81 " pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR C 81 " pdb=" C THR C 81 " pdb=" N VAL C 82 " pdb=" CA VAL C 82 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 68 0.028 - 0.055: 77 0.055 - 0.082: 43 0.082 - 0.109: 19 0.109 - 0.136: 15 Chirality restraints: 222 Sorted by residual: chirality pdb=" CA VAL C 40 " pdb=" N VAL C 40 " pdb=" C VAL C 40 " pdb=" CB VAL C 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL B 40 " pdb=" N VAL B 40 " pdb=" C VAL B 40 " pdb=" CB VAL B 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL A 40 " pdb=" N VAL A 40 " pdb=" C VAL A 40 " pdb=" CB VAL A 40 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 219 not shown) Planarity restraints: 207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 70 " -0.005 2.00e-02 2.50e+03 9.63e-03 9.27e-01 pdb=" C VAL B 70 " 0.017 2.00e-02 2.50e+03 pdb=" O VAL B 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL B 71 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 70 " -0.005 2.00e-02 2.50e+03 9.44e-03 8.90e-01 pdb=" C VAL A 70 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL A 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL A 71 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 70 " -0.005 2.00e-02 2.50e+03 9.16e-03 8.39e-01 pdb=" C VAL C 70 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL C 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL C 71 " -0.005 2.00e-02 2.50e+03 ... (remaining 204 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 356 2.80 - 3.33: 1111 3.33 - 3.85: 1702 3.85 - 4.38: 1838 4.38 - 4.90: 3934 Nonbonded interactions: 8941 Sorted by model distance: nonbonded pdb=" O SER A 42 " pdb=" OG SER A 42 " model vdw 2.279 2.440 nonbonded pdb=" O SER B 42 " pdb=" OG SER B 42 " model vdw 2.279 2.440 nonbonded pdb=" O SER C 42 " pdb=" OG SER C 42 " model vdw 2.280 2.440 nonbonded pdb=" O LYS B 80 " pdb=" OG1 THR B 81 " model vdw 2.498 2.440 nonbonded pdb=" O LYS C 80 " pdb=" OG1 THR C 81 " model vdw 2.499 2.440 ... (remaining 8936 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 'C' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.390 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.540 Find NCS groups from input model: 0.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.007 0.048 1227 Z= 0.293 Angle : 1.014 7.691 1665 Z= 0.570 Chirality : 0.057 0.136 222 Planarity : 0.004 0.010 207 Dihedral : 13.695 47.342 402 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 39.66 % Favored : 60.34 % Rotamer: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % 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: -7.67 (0.34), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.84 (0.26), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.007 0.002 PHE A 94 TYR 0.014 0.004 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.132 Fit side-chains REVERT: C 43 LYS cc_start: 0.7224 (mttt) cc_final: 0.5716 (tttt) REVERT: C 94 PHE cc_start: 0.7455 (t80) cc_final: 0.6889 (t80) REVERT: A 43 LYS cc_start: 0.7146 (mttt) cc_final: 0.5842 (tttt) REVERT: A 57 GLU cc_start: 0.7923 (tp30) cc_final: 0.7141 (tp30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1062 time to fit residues: 3.0017 Evaluate side-chains 13 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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: 5.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.6953 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1227 Z= 0.124 Angle : 0.769 6.802 1665 Z= 0.417 Chirality : 0.058 0.128 222 Planarity : 0.003 0.012 207 Dihedral : 6.372 18.283 180 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.41 % Favored : 77.59 % Rotamer: Outliers : 2.44 % Allowed : 18.70 % Favored : 78.86 % 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: -6.92 (0.36), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.27 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.013 0.003 PHE B 94 TYR 0.007 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.130 Fit side-chains REVERT: C 43 LYS cc_start: 0.7052 (mttt) cc_final: 0.5581 (tttt) REVERT: C 94 PHE cc_start: 0.7317 (t80) cc_final: 0.6787 (t80) REVERT: A 43 LYS cc_start: 0.7027 (mttt) cc_final: 0.5879 (tttt) REVERT: A 77 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7746 (t) outliers start: 3 outliers final: 1 residues processed: 23 average time/residue: 0.0974 time to fit residues: 2.6771 Evaluate side-chains 20 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A 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: 4.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.0060 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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: 0.6841 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1227 Z= 0.104 Angle : 0.663 5.521 1665 Z= 0.360 Chirality : 0.056 0.132 222 Planarity : 0.003 0.017 207 Dihedral : 5.435 15.472 180 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 5.69 % Allowed : 17.89 % Favored : 76.42 % 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: -6.53 (0.37), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.97 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.011 0.002 PHE A 94 TYR 0.007 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.127 Fit side-chains REVERT: C 37 VAL cc_start: 0.7983 (p) cc_final: 0.7739 (t) REVERT: C 43 LYS cc_start: 0.6745 (mttt) cc_final: 0.5315 (tttt) REVERT: C 94 PHE cc_start: 0.7250 (t80) cc_final: 0.6807 (t80) REVERT: A 43 LYS cc_start: 0.6919 (mttt) cc_final: 0.5755 (tttt) REVERT: A 77 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7767 (t) REVERT: B 43 LYS cc_start: 0.7055 (mttt) cc_final: 0.5827 (tttt) outliers start: 7 outliers final: 5 residues processed: 26 average time/residue: 0.1055 time to fit residues: 3.2121 Evaluate side-chains 25 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 0.0470 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 0.0870 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 overall best weight: 0.8058 ------------------------------------------------------------------------------- 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: 0.6812 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 0.018 1227 Z= 0.099 Angle : 0.627 6.404 1665 Z= 0.343 Chirality : 0.054 0.128 222 Planarity : 0.003 0.016 207 Dihedral : 5.280 14.762 180 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 6.50 % Allowed : 18.70 % Favored : 74.80 % 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: -6.40 (0.36), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.87 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.009 0.001 PHE A 94 TYR 0.008 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 15 time to evaluate : 0.127 Fit side-chains REVERT: C 43 LYS cc_start: 0.6692 (mttt) cc_final: 0.5296 (tttt) REVERT: C 94 PHE cc_start: 0.7273 (t80) cc_final: 0.6843 (t80) REVERT: A 43 LYS cc_start: 0.6909 (mttt) cc_final: 0.5673 (tttt) REVERT: A 62 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: B 43 LYS cc_start: 0.7048 (mttt) cc_final: 0.6670 (mptt) outliers start: 8 outliers final: 7 residues processed: 22 average time/residue: 0.1173 time to fit residues: 3.0101 Evaluate side-chains 21 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 13 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 0.0030 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.2946 ------------------------------------------------------------------------------- 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: 0.6668 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1227 Z= 0.085 Angle : 0.561 4.794 1665 Z= 0.307 Chirality : 0.052 0.137 222 Planarity : 0.002 0.018 207 Dihedral : 4.572 13.019 180 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 6.50 % Allowed : 19.51 % Favored : 73.98 % 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: -6.12 (0.37), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.66 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.007 0.001 PHE A 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 17 time to evaluate : 0.125 Fit side-chains REVERT: C 43 LYS cc_start: 0.6593 (mttt) cc_final: 0.5231 (tttt) REVERT: A 43 LYS cc_start: 0.6952 (mttt) cc_final: 0.5823 (tttt) REVERT: A 61 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: A 77 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7546 (t) REVERT: B 43 LYS cc_start: 0.7001 (mttt) cc_final: 0.6709 (mptt) outliers start: 8 outliers final: 4 residues processed: 24 average time/residue: 0.1172 time to fit residues: 3.2600 Evaluate side-chains 20 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 14 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 11 optimal weight: 7.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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: 0.6858 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1227 Z= 0.124 Angle : 0.620 4.712 1665 Z= 0.344 Chirality : 0.051 0.130 222 Planarity : 0.002 0.014 207 Dihedral : 5.524 15.172 180 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.26 % Favored : 78.74 % Rotamer: Outliers : 7.32 % Allowed : 20.33 % Favored : 72.36 % 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: -6.17 (0.37), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.006 0.001 PHE B 94 TYR 0.012 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 16 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: C 43 LYS cc_start: 0.6695 (mttt) cc_final: 0.5203 (tttt) REVERT: C 94 PHE cc_start: 0.7481 (t80) cc_final: 0.6902 (t80) REVERT: A 43 LYS cc_start: 0.6987 (mttt) cc_final: 0.6473 (mptt) REVERT: A 77 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7627 (t) REVERT: B 43 LYS cc_start: 0.7090 (mttt) cc_final: 0.6708 (mptt) outliers start: 9 outliers final: 7 residues processed: 25 average time/residue: 0.1236 time to fit residues: 3.5510 Evaluate side-chains 22 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 14 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.6913 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1227 Z= 0.151 Angle : 0.689 5.223 1665 Z= 0.384 Chirality : 0.053 0.141 222 Planarity : 0.003 0.010 207 Dihedral : 6.072 16.454 180 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.84 % Favored : 78.16 % Rotamer: Outliers : 5.69 % Allowed : 22.76 % Favored : 71.54 % 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: -6.15 (0.38), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.68 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.007 0.001 PHE A 94 TYR 0.012 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 14 time to evaluate : 0.132 Fit side-chains REVERT: C 43 LYS cc_start: 0.6816 (mttt) cc_final: 0.5261 (tttt) REVERT: C 94 PHE cc_start: 0.7571 (t80) cc_final: 0.6976 (t80) REVERT: A 43 LYS cc_start: 0.6988 (mttt) cc_final: 0.5618 (tttt) REVERT: A 77 VAL cc_start: 0.7871 (OUTLIER) cc_final: 0.7617 (t) REVERT: B 43 LYS cc_start: 0.7181 (mttt) cc_final: 0.6744 (mptt) outliers start: 7 outliers final: 6 residues processed: 21 average time/residue: 0.1239 time to fit residues: 3.0257 Evaluate side-chains 21 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 14 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.6854 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1227 Z= 0.109 Angle : 0.635 5.443 1665 Z= 0.352 Chirality : 0.053 0.152 222 Planarity : 0.002 0.009 207 Dihedral : 5.513 15.539 180 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 5.69 % Allowed : 23.58 % Favored : 70.73 % 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: -5.99 (0.40), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.31), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.011 0.002 PHE A 94 TYR 0.008 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 13 time to evaluate : 0.133 Fit side-chains REVERT: C 43 LYS cc_start: 0.6831 (mttt) cc_final: 0.5354 (tttt) REVERT: C 94 PHE cc_start: 0.7461 (t80) cc_final: 0.6902 (t80) REVERT: A 43 LYS cc_start: 0.7006 (mttt) cc_final: 0.6585 (mptt) REVERT: A 77 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7606 (t) REVERT: B 43 LYS cc_start: 0.7177 (mttt) cc_final: 0.6787 (mptt) outliers start: 7 outliers final: 6 residues processed: 20 average time/residue: 0.1311 time to fit residues: 3.0195 Evaluate side-chains 20 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 13 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.0030 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- 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: 0.6914 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1227 Z= 0.149 Angle : 0.695 5.603 1665 Z= 0.388 Chirality : 0.054 0.166 222 Planarity : 0.002 0.010 207 Dihedral : 6.013 16.639 180 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.41 % Favored : 77.59 % Rotamer: Outliers : 5.69 % Allowed : 23.58 % Favored : 70.73 % 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: -6.00 (0.41), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.57 (0.32), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.010 0.002 PHE A 94 TYR 0.012 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 14 time to evaluate : 0.128 Fit side-chains REVERT: C 43 LYS cc_start: 0.6947 (mttt) cc_final: 0.5353 (tttt) REVERT: C 94 PHE cc_start: 0.7596 (t80) cc_final: 0.7049 (t80) REVERT: A 43 LYS cc_start: 0.7007 (mttt) cc_final: 0.5713 (tttt) REVERT: A 77 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7649 (t) REVERT: B 43 LYS cc_start: 0.7179 (mttt) cc_final: 0.6758 (mptt) outliers start: 7 outliers final: 6 residues processed: 21 average time/residue: 0.1043 time to fit residues: 2.5621 Evaluate side-chains 21 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 14 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.6831 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1227 Z= 0.107 Angle : 0.639 5.773 1665 Z= 0.354 Chirality : 0.053 0.162 222 Planarity : 0.002 0.009 207 Dihedral : 5.395 15.343 180 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 5.69 % Allowed : 23.58 % Favored : 70.73 % 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: -5.88 (0.42), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.32), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.010 0.002 PHE A 94 TYR 0.008 0.002 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 13 time to evaluate : 0.130 Fit side-chains REVERT: C 43 LYS cc_start: 0.6827 (mttt) cc_final: 0.5334 (tttt) REVERT: C 94 PHE cc_start: 0.7445 (t80) cc_final: 0.6910 (t80) REVERT: A 43 LYS cc_start: 0.7061 (mttt) cc_final: 0.5766 (tttt) REVERT: A 77 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7645 (t) REVERT: B 43 LYS cc_start: 0.7205 (mttt) cc_final: 0.6804 (mptt) REVERT: B 61 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6590 (mp0) outliers start: 7 outliers final: 6 residues processed: 20 average time/residue: 0.1299 time to fit residues: 3.0123 Evaluate side-chains 20 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 13 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.102554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.085466 restraints weight = 2077.403| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.57 r_work: 0.3753 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1227 Z= 0.096 Angle : 0.609 5.770 1665 Z= 0.339 Chirality : 0.053 0.157 222 Planarity : 0.002 0.010 207 Dihedral : 5.048 14.232 180 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 4.88 % Allowed : 24.39 % Favored : 70.73 % 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: -5.73 (0.43), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.36 (0.33), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.009 0.001 PHE A 94 TYR 0.007 0.002 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 894.66 seconds wall clock time: 17 minutes 11.00 seconds (1031.00 seconds total)