Starting phenix.real_space_refine on Thu Dec 7 16:15:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/12_2023/7v4d_31708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/12_2023/7v4d_31708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/12_2023/7v4d_31708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/12_2023/7v4d_31708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/12_2023/7v4d_31708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/12_2023/7v4d_31708.pdb" } resolution = 3.5 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= 0.002 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 1488 2.51 5 N 408 2.21 5 O 480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 2376 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "C" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "A" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Time building chain proxies: 1.71, per 1000 atoms: 0.72 Number of scatterers: 2376 At special positions: 0 Unit cell: (98.58, 87.98, 31.8, 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 480 8.00 N 408 7.00 C 1488 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: 0.87 Conformation dependent library (CDL) restraints added in 494.3 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.367A pdb=" N LYS F 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 48 through 50 Processing sheet with id=AA3, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'F' and resid 62 through 63 removed outlier: 6.128A pdb=" N GLN F 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AA6, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.361A pdb=" N LYS E 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=AA9, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'E' and resid 62 through 63 removed outlier: 6.129A pdb=" N GLN E 62 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB3, first strand: chain 'E' and resid 81 through 82 20 hydrogen bonds defined for protein. 60 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: 0.49 Time building geometry restraints manager: 0.95 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: 414 1.29 - 1.35: 373 1.35 - 1.42: 102 1.42 - 1.48: 401 1.48 - 1.55: 1098 Bond restraints: 2388 Sorted by residual: bond pdb=" CA LEU D 38 " pdb=" C LEU D 38 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.42e-01 bond pdb=" CA LEU F 38 " pdb=" C LEU F 38 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.17e-01 bond pdb=" CA LEU A 38 " pdb=" C LEU A 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 9.07e-01 bond pdb=" CA LEU E 38 " pdb=" C LEU E 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 9.04e-01 bond pdb=" CA LEU C 38 " pdb=" C LEU C 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.62e-01 ... (remaining 2383 not shown) Histogram of bond angle deviations from ideal: 106.13 - 111.14: 1035 111.14 - 116.14: 716 116.14 - 121.15: 679 121.15 - 126.16: 804 126.16 - 131.16: 6 Bond angle restraints: 3240 Sorted by residual: angle pdb=" CA ASN B 65 " pdb=" CB ASN B 65 " pdb=" CG ASN B 65 " ideal model delta sigma weight residual 112.60 114.52 -1.92 1.00e+00 1.00e+00 3.70e+00 angle pdb=" CA ASN A 65 " pdb=" CB ASN A 65 " pdb=" CG ASN A 65 " ideal model delta sigma weight residual 112.60 114.49 -1.89 1.00e+00 1.00e+00 3.58e+00 angle pdb=" CA ASN E 65 " pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 112.60 114.49 -1.89 1.00e+00 1.00e+00 3.58e+00 angle pdb=" CA ASN C 65 " pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 112.60 114.48 -1.88 1.00e+00 1.00e+00 3.54e+00 angle pdb=" CA ASN F 65 " pdb=" CB ASN F 65 " pdb=" CG ASN F 65 " ideal model delta sigma weight residual 112.60 114.48 -1.88 1.00e+00 1.00e+00 3.52e+00 ... (remaining 3235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.21: 1206 12.21 - 24.43: 132 24.43 - 36.64: 18 36.64 - 48.85: 12 48.85 - 61.07: 6 Dihedral angle restraints: 1374 sinusoidal: 438 harmonic: 936 Sorted by residual: dihedral pdb=" CA VAL A 48 " pdb=" C VAL A 48 " pdb=" N VAL A 49 " pdb=" CA VAL A 49 " ideal model delta harmonic sigma weight residual 180.00 162.67 17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL B 48 " pdb=" C VAL B 48 " pdb=" N VAL B 49 " pdb=" CA VAL B 49 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL C 48 " pdb=" C VAL C 48 " pdb=" N VAL C 49 " pdb=" CA VAL C 49 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 1371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 214 0.025 - 0.049: 108 0.049 - 0.074: 52 0.074 - 0.099: 34 0.099 - 0.124: 24 Chirality restraints: 432 Sorted by residual: chirality pdb=" CA VAL A 70 " pdb=" N VAL A 70 " pdb=" C VAL A 70 " pdb=" CB VAL A 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL D 70 " pdb=" N VAL D 70 " pdb=" C VAL D 70 " pdb=" CB VAL D 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA VAL C 70 " pdb=" N VAL C 70 " pdb=" C VAL C 70 " pdb=" CB VAL C 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 429 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 87 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C SER C 87 " -0.020 2.00e-02 2.50e+03 pdb=" O SER C 87 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 88 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 87 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.29e+00 pdb=" C SER E 87 " 0.020 2.00e-02 2.50e+03 pdb=" O SER E 87 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE E 88 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 87 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C SER F 87 " -0.019 2.00e-02 2.50e+03 pdb=" O SER F 87 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE F 88 " 0.006 2.00e-02 2.50e+03 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 331 2.77 - 3.30: 2209 3.30 - 3.83: 3524 3.83 - 4.37: 3821 4.37 - 4.90: 7885 Nonbonded interactions: 17770 Sorted by model distance: nonbonded pdb=" OE1 GLU A 61 " pdb=" OG1 THR A 72 " model vdw 2.234 2.440 nonbonded pdb=" OE1 GLU E 61 " pdb=" OG1 THR E 72 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLU C 61 " pdb=" OG1 THR C 72 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLU B 61 " pdb=" OG1 THR B 72 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLU F 61 " pdb=" OG1 THR F 72 " model vdw 2.235 2.440 ... (remaining 17765 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' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.090 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: 4.720 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.730 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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 : 0.003 0.024 2388 Z= 0.196 Angle : 0.544 3.405 3240 Z= 0.315 Chirality : 0.045 0.124 432 Planarity : 0.002 0.011 402 Dihedral : 11.888 61.066 786 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % 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: -5.68 (0.26), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.20), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.001 0.000 PHE F 94 TYR 0.002 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.266 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0810 time to fit residues: 4.3542 Evaluate side-chains 35 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2388 Z= 0.309 Angle : 0.618 4.988 3240 Z= 0.340 Chirality : 0.046 0.132 432 Planarity : 0.003 0.012 402 Dihedral : 5.200 17.145 348 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 7.50 % Allowed : 12.92 % Favored : 79.58 % 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: -5.30 (0.29), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.22), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.005 0.001 PHE D 94 TYR 0.003 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 35 time to evaluate : 0.262 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 50 average time/residue: 0.0848 time to fit residues: 5.6008 Evaluate side-chains 49 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 34 time to evaluate : 0.264 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0257 time to fit residues: 1.0104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.0470 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2388 Z= 0.152 Angle : 0.532 4.284 3240 Z= 0.299 Chirality : 0.046 0.149 432 Planarity : 0.002 0.013 402 Dihedral : 4.665 17.790 348 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.58 % Allowed : 16.25 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.000 PHE D 94 TYR 0.001 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.257 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 47 average time/residue: 0.0717 time to fit residues: 4.6471 Evaluate side-chains 40 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0350 time to fit residues: 0.6029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.0040 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 0.0020 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 2388 Z= 0.382 Angle : 0.672 5.991 3240 Z= 0.368 Chirality : 0.048 0.209 432 Planarity : 0.003 0.014 402 Dihedral : 5.301 18.172 348 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 5.42 % Allowed : 16.25 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.006 0.001 PHE D 94 TYR 0.004 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 0.237 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.0768 time to fit residues: 4.6763 Evaluate side-chains 43 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.264 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0258 time to fit residues: 0.8164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2388 Z= 0.263 Angle : 0.636 6.867 3240 Z= 0.351 Chirality : 0.047 0.170 432 Planarity : 0.002 0.015 402 Dihedral : 5.078 17.531 348 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.33 % Allowed : 18.75 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.004 0.001 PHE D 94 TYR 0.002 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.257 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 40 average time/residue: 0.0715 time to fit residues: 4.0983 Evaluate side-chains 35 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0321 time to fit residues: 0.5372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.5140 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2388 Z= 0.137 Angle : 0.537 5.885 3240 Z= 0.294 Chirality : 0.047 0.168 432 Planarity : 0.002 0.019 402 Dihedral : 4.357 16.949 348 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.33 % Allowed : 17.92 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.002 0.000 PHE D 94 TYR 0.002 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.240 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 35 average time/residue: 0.0718 time to fit residues: 3.5606 Evaluate side-chains 34 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0301 time to fit residues: 0.5746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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: 0.7810 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2388 Z= 0.367 Angle : 0.684 7.838 3240 Z= 0.372 Chirality : 0.048 0.155 432 Planarity : 0.003 0.016 402 Dihedral : 5.238 17.908 348 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 2.92 % Allowed : 16.25 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 PHE 0.005 0.001 PHE D 94 TYR 0.004 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.251 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 39 average time/residue: 0.0640 time to fit residues: 3.5261 Evaluate side-chains 36 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.192 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0213 time to fit residues: 0.4893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2388 Z= 0.197 Angle : 0.616 7.385 3240 Z= 0.334 Chirality : 0.048 0.162 432 Planarity : 0.003 0.021 402 Dihedral : 4.753 16.883 348 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.67 % Allowed : 18.75 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.003 0.001 PHE D 94 TYR 0.002 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.241 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 35 average time/residue: 0.0754 time to fit residues: 3.7223 Evaluate side-chains 32 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0328 time to fit residues: 0.5629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2388 Z= 0.174 Angle : 0.568 6.835 3240 Z= 0.305 Chirality : 0.047 0.160 432 Planarity : 0.003 0.020 402 Dihedral : 4.499 17.445 348 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.42 % Allowed : 19.58 % Favored : 80.00 % 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: -3.91 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.003 0.001 PHE B 94 TYR 0.002 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.411 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.0766 time to fit residues: 3.1563 Evaluate side-chains 28 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.217 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0262 time to fit residues: 0.3912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7697 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2388 Z= 0.176 Angle : 0.558 6.564 3240 Z= 0.298 Chirality : 0.046 0.159 432 Planarity : 0.003 0.019 402 Dihedral : 4.427 16.627 348 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.42 % Allowed : 20.42 % Favored : 79.17 % 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: -3.70 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.002 0.001 PHE C 94 TYR 0.002 0.001 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.254 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.0799 time to fit residues: 2.9896 Evaluate side-chains 26 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.253 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0253 time to fit residues: 0.3810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.173985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.146731 restraints weight = 2549.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.149950 restraints weight = 1295.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.152183 restraints weight = 896.276| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2388 Z= 0.180 Angle : 0.552 6.474 3240 Z= 0.295 Chirality : 0.046 0.159 432 Planarity : 0.003 0.021 402 Dihedral : 4.420 17.183 348 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 20.42 % Favored : 79.58 % 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: -3.61 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.003 0.001 PHE D 94 TYR 0.002 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 938.25 seconds wall clock time: 17 minutes 49.70 seconds (1069.70 seconds total)