Starting phenix.real_space_refine on Sun Mar 10 14:49:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzs_35090/03_2024/8hzs_35090.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzs_35090/03_2024/8hzs_35090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzs_35090/03_2024/8hzs_35090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzs_35090/03_2024/8hzs_35090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzs_35090/03_2024/8hzs_35090.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzs_35090/03_2024/8hzs_35090.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-dev-5265/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: 1.60, per 1000 atoms: 0.67 Number of scatterers: 2376 At special positions: 0 Unit cell: (98.58, 90.1, 30.74, 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: 0.85 Conformation dependent library (CDL) restraints added in 455.7 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: 0.31 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: 6.362A pdb=" N LYS E 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.359A 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: 6.190A 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: 0.46 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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 B 38 " pdb=" C LEU B 38 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.49e-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 9.09e-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 8.61e-01 bond pdb=" CA LEU D 38 " pdb=" C LEU D 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.61e-01 bond pdb=" CA LEU F 38 " pdb=" C LEU F 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.50e-01 ... (remaining 2383 not shown) Histogram of bond angle deviations from ideal: 106.10 - 111.11: 1027 111.11 - 116.12: 718 116.12 - 121.14: 682 121.14 - 126.15: 807 126.15 - 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 3.68e+00 angle pdb=" CA ASN C 65 " pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 112.60 114.51 -1.91 1.00e+00 1.00e+00 3.64e+00 angle pdb=" CA ASN A 65 " pdb=" CB ASN A 65 " pdb=" CG ASN A 65 " ideal model delta sigma weight residual 112.60 114.48 -1.88 1.00e+00 1.00e+00 3.55e+00 angle pdb=" CA ASN E 65 " pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 112.60 114.48 -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 112.60 114.47 -1.87 1.00e+00 1.00e+00 3.50e+00 ... (remaining 3235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.23: 1206 12.23 - 24.45: 132 24.45 - 36.67: 18 36.67 - 48.90: 12 48.90 - 61.12: 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 180.00 162.65 17.35 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 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL F 48 " pdb=" C VAL F 48 " pdb=" N VAL F 49 " pdb=" CA VAL F 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 - 0.026: 225 0.026 - 0.051: 100 0.051 - 0.076: 58 0.076 - 0.102: 35 0.102 - 0.127: 14 Chirality restraints: 432 Sorted by residual: 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 2.57 -0.13 2.00e-01 2.50e+01 4.03e-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 3.70e-01 chirality pdb=" CA VAL F 70 " pdb=" N VAL F 70 " pdb=" C VAL F 70 " pdb=" CB VAL F 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 429 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 87 " -0.006 2.00e-02 2.50e+03 1.13e-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 C 87 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+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 F 87 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+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: 2210 3.30 - 3.83: 3523 3.83 - 4.37: 3820 4.37 - 4.90: 7885 Nonbonded interactions: 17769 Sorted by model distance: nonbonded pdb=" OE1 GLU A 61 " pdb=" OG1 THR A 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 C 61 " pdb=" OG1 THR C 72 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLU F 61 " pdb=" OG1 THR F 72 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLU D 61 " pdb=" OG1 THR D 72 " model vdw 2.235 2.440 ... (remaining 17764 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 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: 0.990 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: 4.710 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.850 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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= 0.197 Angle : 0.545 3.397 3240 Z= 0.315 Chirality : 0.045 0.127 432 Planarity : 0.002 0.011 402 Dihedral : 11.889 61.125 786 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % 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 B 50 PHE 0.001 0.000 PHE F 94 TYR 0.002 0.001 TYR A 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 25 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.234 Fit side-chains REVERT: C 83 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7380 (mm-30) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0808 time to fit residues: 2.9620 Evaluate side-chains 25 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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: 7.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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: 0.7847 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2388 Z= 0.308 Angle : 0.566 4.342 3240 Z= 0.317 Chirality : 0.045 0.126 432 Planarity : 0.002 0.011 402 Dihedral : 4.943 17.373 348 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 8.33 % Allowed : 15.42 % Favored : 76.25 % 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: -5.28 (0.30), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.23), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.004 0.001 PHE B 94 TYR 0.004 0.002 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 51 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 31 time to evaluate : 0.275 Fit side-chains REVERT: C 71 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8447 (t) outliers start: 20 outliers final: 16 residues processed: 41 average time/residue: 0.0613 time to fit residues: 3.6790 Evaluate side-chains 46 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 29 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.1674 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= 0.245 Angle : 0.543 5.632 3240 Z= 0.306 Chirality : 0.046 0.156 432 Planarity : 0.002 0.011 402 Dihedral : 4.750 18.051 348 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 7.92 % Allowed : 11.25 % 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: -4.83 (0.32), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.003 0.001 PHE B 94 TYR 0.002 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 46 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 27 time to evaluate : 0.256 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 38 average time/residue: 0.0629 time to fit residues: 3.5062 Evaluate side-chains 38 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 24 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.0060 chunk 18 optimal weight: 0.0050 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.7414 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2388 Z= 0.236 Angle : 0.535 4.689 3240 Z= 0.303 Chirality : 0.046 0.147 432 Planarity : 0.002 0.011 402 Dihedral : 4.635 17.905 348 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 9.17 % Allowed : 12.92 % 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: -4.52 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 50 PHE 0.003 0.000 PHE B 94 TYR 0.002 0.001 TYR E 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 44 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 22 time to evaluate : 0.260 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 35 average time/residue: 0.0627 time to fit residues: 3.2814 Evaluate side-chains 41 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 22 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2388 Z= 0.336 Angle : 0.638 6.217 3240 Z= 0.355 Chirality : 0.047 0.142 432 Planarity : 0.002 0.012 402 Dihedral : 4.967 17.990 348 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 10.00 % Allowed : 12.08 % 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: -4.51 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.003 0.001 PHE B 94 TYR 0.004 0.001 TYR E 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 48 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 24 time to evaluate : 0.243 Fit side-chains REVERT: F 38 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8544 (tt) REVERT: E 83 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7624 (mm-30) outliers start: 24 outliers final: 21 residues processed: 44 average time/residue: 0.0668 time to fit residues: 4.1972 Evaluate side-chains 45 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 23 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2256 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= 0.179 Angle : 0.556 6.072 3240 Z= 0.304 Chirality : 0.047 0.149 432 Planarity : 0.002 0.016 402 Dihedral : 4.408 17.898 348 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 10.42 % Allowed : 12.08 % Favored : 77.50 % 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: -4.27 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.002 0.000 PHE B 94 TYR 0.002 0.001 TYR F 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 45 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 20 time to evaluate : 0.258 Fit side-chains REVERT: F 38 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8526 (tt) REVERT: E 62 GLN cc_start: 0.7826 (tt0) cc_final: 0.7303 (mt0) outliers start: 25 outliers final: 16 residues processed: 39 average time/residue: 0.0691 time to fit residues: 3.8466 Evaluate side-chains 37 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 20 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.0050 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7676 ------------------------------------------------------------------------------- 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: 0.7722 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2388 Z= 0.146 Angle : 0.531 6.734 3240 Z= 0.282 Chirality : 0.047 0.148 432 Planarity : 0.002 0.019 402 Dihedral : 4.055 17.293 348 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 5.42 % Allowed : 15.00 % 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: -4.09 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.001 0.000 PHE B 94 TYR 0.001 0.000 TYR B 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 33 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 20 time to evaluate : 0.250 Fit side-chains REVERT: F 38 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8552 (tt) REVERT: E 62 GLN cc_start: 0.7762 (tt0) cc_final: 0.7359 (mt0) REVERT: E 65 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7585 (t0) outliers start: 13 outliers final: 9 residues processed: 28 average time/residue: 0.0664 time to fit residues: 2.7830 Evaluate side-chains 27 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 16 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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: 0.7844 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 2388 Z= 0.398 Angle : 0.679 7.715 3240 Z= 0.362 Chirality : 0.048 0.156 432 Planarity : 0.003 0.017 402 Dihedral : 5.068 18.019 348 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 7.50 % Allowed : 12.08 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.002 0.000 PHE D 94 TYR 0.005 0.002 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 46 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 28 time to evaluate : 0.248 Fit side-chains REVERT: F 38 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8615 (tt) outliers start: 18 outliers final: 17 residues processed: 42 average time/residue: 0.0691 time to fit residues: 4.1089 Evaluate side-chains 46 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 28 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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: 0.7781 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2388 Z= 0.222 Angle : 0.606 6.993 3240 Z= 0.326 Chirality : 0.047 0.143 432 Planarity : 0.002 0.018 402 Dihedral : 4.627 17.669 348 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 6.67 % Allowed : 12.92 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.002 0.000 PHE B 94 TYR 0.002 0.001 TYR C 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 34 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 18 time to evaluate : 0.256 Fit side-chains REVERT: F 38 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8584 (tt) REVERT: E 62 GLN cc_start: 0.7859 (tt0) cc_final: 0.7324 (mt0) outliers start: 16 outliers final: 15 residues processed: 28 average time/residue: 0.0732 time to fit residues: 3.0583 Evaluate side-chains 34 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 18 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.7787 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2388 Z= 0.237 Angle : 0.583 7.055 3240 Z= 0.311 Chirality : 0.047 0.141 432 Planarity : 0.003 0.022 402 Dihedral : 4.597 17.485 348 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 7.50 % Allowed : 12.50 % 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: -4.16 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.002 0.000 PHE B 94 TYR 0.003 0.001 TYR A 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 36 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 18 time to evaluate : 0.246 Fit side-chains REVERT: F 38 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8609 (tt) REVERT: C 42 SER cc_start: 0.9028 (p) cc_final: 0.8730 (m) REVERT: E 62 GLN cc_start: 0.7798 (tt0) cc_final: 0.7298 (mt0) outliers start: 18 outliers final: 16 residues processed: 30 average time/residue: 0.0663 time to fit residues: 2.9433 Evaluate side-chains 35 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 18 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.0270 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- 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 = 0.4434 r_free = 0.4434 target = 0.170162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.147212 restraints weight = 2661.307| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.58 r_work: 0.4072 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2388 Z= 0.309 Angle : 0.627 7.065 3240 Z= 0.338 Chirality : 0.047 0.147 432 Planarity : 0.003 0.021 402 Dihedral : 4.944 17.609 348 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 7.50 % Allowed : 12.08 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.002 0.000 PHE B 94 TYR 0.004 0.001 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 933.41 seconds wall clock time: 17 minutes 44.70 seconds (1064.70 seconds total)