Starting phenix.real_space_refine on Thu Dec 7 17:09:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/12_2023/6wkt_21708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/12_2023/6wkt_21708.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/6wkt_21708/12_2023/6wkt_21708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/12_2023/6wkt_21708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/12_2023/6wkt_21708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/12_2023/6wkt_21708.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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 1884 2.51 5 N 556 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 6": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3152 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "B" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "C" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "D" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Time building chain proxies: 2.29, per 1000 atoms: 0.73 Number of scatterers: 3152 At special positions: 0 Unit cell: (79.056, 63.504, 55.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 620 8.00 N 556 7.00 C 1884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 639.1 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 58 Processing helix chain 'A' and resid 62 through 82 Processing helix chain 'A' and resid 86 through 107 Processing helix chain 'B' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 58 Processing helix chain 'B' and resid 62 through 82 Processing helix chain 'B' and resid 86 through 107 Processing helix chain 'C' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 58 Processing helix chain 'C' and resid 62 through 82 Processing helix chain 'C' and resid 86 through 107 Processing helix chain 'D' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 58 Processing helix chain 'D' and resid 62 through 82 Processing helix chain 'D' and resid 86 through 107 296 hydrogen bonds defined for protein. 888 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: 0.86 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 884 1.34 - 1.46: 504 1.46 - 1.58: 1696 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 3192 Sorted by residual: bond pdb=" C ILE B 39 " pdb=" N ARG B 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE A 39 " pdb=" N ARG A 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE D 39 " pdb=" N ARG D 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE C 39 " pdb=" N ARG C 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C THR C 24 " pdb=" O THR C 24 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.08e+00 ... (remaining 3187 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.37: 56 106.37 - 112.61: 1616 112.61 - 118.85: 1004 118.85 - 125.09: 1568 125.09 - 131.33: 40 Bond angle restraints: 4284 Sorted by residual: angle pdb=" C GLN D 32 " pdb=" N HIS D 33 " pdb=" CA HIS D 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN B 32 " pdb=" N HIS B 33 " pdb=" CA HIS B 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN A 32 " pdb=" N HIS A 33 " pdb=" CA HIS A 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN C 32 " pdb=" N HIS C 33 " pdb=" CA HIS C 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" O ILE D 39 " pdb=" C ILE D 39 " pdb=" N ARG D 40 " ideal model delta sigma weight residual 121.90 118.01 3.89 1.04e+00 9.25e-01 1.40e+01 ... (remaining 4279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 1820 17.75 - 35.49: 136 35.49 - 53.23: 24 53.23 - 70.97: 0 70.97 - 88.72: 8 Dihedral angle restraints: 1988 sinusoidal: 740 harmonic: 1248 Sorted by residual: dihedral pdb=" CA SER A 36 " pdb=" C SER A 36 " pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER B 36 " pdb=" C SER B 36 " pdb=" N GLY B 37 " pdb=" CA GLY B 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER D 36 " pdb=" C SER D 36 " pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 280 0.034 - 0.068: 148 0.068 - 0.102: 36 0.102 - 0.136: 12 0.136 - 0.170: 4 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA THR D 24 " pdb=" N THR D 24 " pdb=" C THR D 24 " pdb=" CB THR D 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA THR C 24 " pdb=" N THR C 24 " pdb=" C THR C 24 " pdb=" CB THR C 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA THR B 24 " pdb=" N THR B 24 " pdb=" C THR B 24 " pdb=" CB THR B 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 477 not shown) Planarity restraints: 568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 84 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS B 84 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS B 84 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP B 85 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 84 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS D 84 " -0.049 2.00e-02 2.50e+03 pdb=" O HIS D 84 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP D 85 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 84 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS C 84 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS C 84 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP C 85 " -0.016 2.00e-02 2.50e+03 ... (remaining 565 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1012 2.84 - 3.36: 3094 3.36 - 3.87: 5334 3.87 - 4.39: 5872 4.39 - 4.90: 10766 Nonbonded interactions: 26078 Sorted by model distance: nonbonded pdb=" O LYS D 54 " pdb=" OG1 THR D 58 " model vdw 2.329 2.440 nonbonded pdb=" O LYS B 54 " pdb=" OG1 THR B 58 " model vdw 2.329 2.440 nonbonded pdb=" O LYS A 54 " pdb=" OG1 THR A 58 " model vdw 2.329 2.440 nonbonded pdb=" O LYS C 54 " pdb=" OG1 THR C 58 " model vdw 2.329 2.440 nonbonded pdb=" O GLU B 75 " pdb=" OG1 THR B 79 " model vdw 2.426 2.440 ... (remaining 26073 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' selection = chain 'D' } 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: 0.030 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.690 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.004 0.037 3192 Z= 0.298 Angle : 0.808 8.085 4284 Z= 0.490 Chirality : 0.046 0.170 480 Planarity : 0.006 0.029 568 Dihedral : 13.975 88.716 1164 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % 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: -3.42 (0.29), residues: 416 helix: -1.91 (0.19), residues: 368 sheet: None (None), residues: 0 loop : -3.11 (0.74), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 34 PHE 0.016 0.003 PHE A 23 TYR 0.006 0.002 TYR A 4 ARG 0.001 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.353 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2420 time to fit residues: 20.9754 Evaluate side-chains 64 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.7316 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3192 Z= 0.166 Angle : 0.462 4.156 4284 Z= 0.255 Chirality : 0.033 0.098 480 Planarity : 0.003 0.022 568 Dihedral : 4.157 12.678 440 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.36), residues: 416 helix: 0.83 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -2.63 (0.65), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 88 PHE 0.007 0.002 PHE B 62 TYR 0.004 0.001 TYR A 4 ARG 0.005 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.368 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1661 time to fit residues: 15.1373 Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.7369 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3192 Z= 0.286 Angle : 0.535 4.468 4284 Z= 0.293 Chirality : 0.036 0.107 480 Planarity : 0.003 0.021 568 Dihedral : 4.156 13.718 440 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.38), residues: 416 helix: 1.51 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.93 (0.68), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 88 PHE 0.014 0.002 PHE C 62 TYR 0.005 0.001 TYR A 4 ARG 0.005 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.333 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1924 time to fit residues: 18.0538 Evaluate side-chains 80 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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: 0.7330 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3192 Z= 0.210 Angle : 0.487 4.164 4284 Z= 0.268 Chirality : 0.035 0.099 480 Planarity : 0.003 0.017 568 Dihedral : 4.098 13.484 440 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.38), residues: 416 helix: 1.93 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.61 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 88 PHE 0.011 0.002 PHE A 62 TYR 0.006 0.001 TYR B 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.328 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1618 time to fit residues: 14.7414 Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.7311 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3192 Z= 0.216 Angle : 0.501 4.162 4284 Z= 0.278 Chirality : 0.036 0.101 480 Planarity : 0.003 0.016 568 Dihedral : 4.088 13.400 440 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 18.39 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.38), residues: 416 helix: 2.18 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.38 (0.77), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 34 PHE 0.013 0.002 PHE A 62 TYR 0.005 0.001 TYR C 4 ARG 0.006 0.001 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.384 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1706 time to fit residues: 15.5758 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.7288 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3192 Z= 0.179 Angle : 0.490 4.286 4284 Z= 0.266 Chirality : 0.035 0.100 480 Planarity : 0.003 0.022 568 Dihedral : 3.953 12.996 440 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 21.55 % Favored : 78.45 % 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: 3.16 (0.38), residues: 416 helix: 2.55 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.17 (0.78), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 34 PHE 0.009 0.002 PHE C 62 TYR 0.005 0.001 TYR D 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.463 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1685 time to fit residues: 14.5563 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0050 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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: 0.7215 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3192 Z= 0.142 Angle : 0.464 4.058 4284 Z= 0.263 Chirality : 0.033 0.095 480 Planarity : 0.003 0.019 568 Dihedral : 3.795 12.166 440 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 20.98 % Favored : 79.02 % 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: 3.65 (0.39), residues: 416 helix: 2.90 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.23 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 34 PHE 0.010 0.002 PHE B 23 TYR 0.004 0.001 TYR C 4 ARG 0.004 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.392 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1764 time to fit residues: 14.3496 Evaluate side-chains 68 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.7302 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3192 Z= 0.229 Angle : 0.521 4.480 4284 Z= 0.285 Chirality : 0.036 0.100 480 Planarity : 0.002 0.014 568 Dihedral : 3.985 13.179 440 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 21.84 % Favored : 78.16 % 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: 3.27 (0.38), residues: 416 helix: 2.65 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.32 (0.68), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 88 PHE 0.012 0.003 PHE D 62 TYR 0.005 0.001 TYR B 4 ARG 0.006 0.001 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.333 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1730 time to fit residues: 14.8828 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.7288 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3192 Z= 0.195 Angle : 0.502 4.068 4284 Z= 0.277 Chirality : 0.035 0.101 480 Planarity : 0.003 0.017 568 Dihedral : 3.946 13.128 440 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.15 % Allowed : 20.69 % Favored : 78.16 % 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: 3.34 (0.38), residues: 416 helix: 2.69 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.27 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 34 PHE 0.012 0.002 PHE B 62 TYR 0.005 0.001 TYR C 4 ARG 0.007 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.383 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.1671 time to fit residues: 15.3766 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7226 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3192 Z= 0.149 Angle : 0.529 7.184 4284 Z= 0.270 Chirality : 0.034 0.093 480 Planarity : 0.003 0.021 568 Dihedral : 3.653 11.556 440 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 20.69 % Favored : 79.31 % 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: 3.75 (0.38), residues: 416 helix: 2.98 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.24 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 34 PHE 0.009 0.002 PHE B 23 TYR 0.004 0.001 TYR A 4 ARG 0.007 0.001 ARG B 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1649 time to fit residues: 14.2863 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4452 r_free = 0.4452 target = 0.226884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.199725 restraints weight = 3093.744| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.16 r_work: 0.3997 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3192 Z= 0.158 Angle : 0.511 6.915 4284 Z= 0.262 Chirality : 0.034 0.097 480 Planarity : 0.003 0.018 568 Dihedral : 3.612 11.969 440 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 19.54 % Favored : 80.46 % 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: 3.85 (0.38), residues: 416 helix: 3.05 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -1.21 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 34 PHE 0.010 0.002 PHE A 62 TYR 0.004 0.001 TYR B 4 ARG 0.006 0.001 ARG B 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 984.69 seconds wall clock time: 20 minutes 5.46 seconds (1205.46 seconds total)