Starting phenix.real_space_refine on Sun Mar 10 14:49:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/03_2024/7v4d_31708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/03_2024/7v4d_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_31708/03_2024/7v4d_31708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/03_2024/7v4d_31708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/03_2024/7v4d_31708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/03_2024/7v4d_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-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: 1.72, 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: 0.93 Conformation dependent library (CDL) restraints added in 492.5 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: 0.32 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: 0.46 Time building geometry restraints manager: 1.01 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.760 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.400 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- 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 : 0.253 Fit side-chains REVERT: F 83 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7835 (pm20) REVERT: C 46 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8023 (mt-10) REVERT: C 83 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7843 (mm-30) REVERT: B 62 GLN cc_start: 0.8139 (tt0) cc_final: 0.7757 (tt0) REVERT: B 83 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7599 (mm-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0796 time to fit residues: 4.2327 Evaluate side-chains 35 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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: 3.9990 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: 3.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1289 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= 0.329 Angle : 0.622 5.056 3240 Z= 0.342 Chirality : 0.046 0.130 432 Planarity : 0.003 0.012 402 Dihedral : 5.284 16.880 348 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 8.33 % Allowed : 11.67 % 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: -5.35 (0.29), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (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 B 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 56 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 36 time to evaluate : 0.256 Fit side-chains REVERT: F 83 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7654 (pm20) REVERT: C 46 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7964 (mt-10) REVERT: C 83 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7903 (mm-30) REVERT: B 62 GLN cc_start: 0.8211 (tt0) cc_final: 0.7771 (tt0) outliers start: 20 outliers final: 15 residues processed: 52 average time/residue: 0.0929 time to fit residues: 6.3597 Evaluate side-chains 50 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 35 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 64 THR 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: 2.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7769 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2388 Z= 0.176 Angle : 0.541 4.345 3240 Z= 0.303 Chirality : 0.046 0.127 432 Planarity : 0.002 0.014 402 Dihedral : 4.794 17.396 348 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 10.00 % Allowed : 12.92 % Favored : 77.08 % 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: -4.83 (0.32), 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 A 50 PHE 0.003 0.001 PHE D 94 TYR 0.001 0.000 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 61 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 37 time to evaluate : 0.257 Fit side-chains REVERT: F 83 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7660 (pm20) REVERT: C 46 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7996 (mt-10) REVERT: C 83 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7819 (mm-30) outliers start: 24 outliers final: 19 residues processed: 53 average time/residue: 0.0703 time to fit residues: 5.1118 Evaluate side-chains 55 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 36 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 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 88 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 46 GLU 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: 0.0770 chunk 13 optimal weight: 0.0870 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.6322 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 2388 Z= 0.441 Angle : 0.704 5.693 3240 Z= 0.384 Chirality : 0.046 0.132 432 Planarity : 0.003 0.014 402 Dihedral : 5.567 17.775 348 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 10.42 % Allowed : 12.50 % Favored : 77.08 % 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: -5.05 (0.32), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.006 0.001 PHE D 94 TYR 0.005 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 58 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 33 time to evaluate : 0.317 Fit side-chains REVERT: F 83 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7745 (pm20) REVERT: C 83 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7983 (mm-30) REVERT: D 83 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7742 (mm-30) REVERT: E 62 GLN cc_start: 0.7673 (tt0) cc_final: 0.7444 (tt0) REVERT: B 62 GLN cc_start: 0.8284 (tt0) cc_final: 0.7827 (tt0) outliers start: 25 outliers final: 21 residues processed: 52 average time/residue: 0.0754 time to fit residues: 5.3661 Evaluate side-chains 54 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 33 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 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 88 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 46 GLU 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: 0.7980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7776 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2388 Z= 0.181 Angle : 0.572 5.013 3240 Z= 0.321 Chirality : 0.046 0.122 432 Planarity : 0.002 0.013 402 Dihedral : 4.891 16.825 348 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 10.00 % Allowed : 12.92 % Favored : 77.08 % 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: -4.68 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.003 0.001 PHE D 94 TYR 0.002 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 59 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 35 time to evaluate : 0.252 Fit side-chains REVERT: F 62 GLN cc_start: 0.7777 (tt0) cc_final: 0.6934 (mt0) REVERT: F 83 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7721 (pm20) REVERT: C 83 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7908 (mm-30) REVERT: D 83 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7714 (mm-30) outliers start: 24 outliers final: 18 residues processed: 54 average time/residue: 0.0708 time to fit residues: 5.2336 Evaluate side-chains 52 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 34 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 88 ILE 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 E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 46 GLU 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: 8.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS C 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 2388 Z= 0.400 Angle : 0.684 6.755 3240 Z= 0.375 Chirality : 0.047 0.128 432 Planarity : 0.003 0.014 402 Dihedral : 5.405 17.474 348 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 8.75 % Allowed : 13.33 % 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: -4.83 (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 0.005 0.001 PHE D 94 TYR 0.004 0.002 TYR B 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 51 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 30 time to evaluate : 0.241 Fit side-chains REVERT: F 83 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7736 (pm20) REVERT: C 83 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7984 (mm-30) REVERT: D 83 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7719 (mm-30) outliers start: 21 outliers final: 20 residues processed: 47 average time/residue: 0.0740 time to fit residues: 4.8236 Evaluate side-chains 51 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 31 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 46 GLU 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: 4.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2388 Z= 0.184 Angle : 0.600 7.638 3240 Z= 0.332 Chirality : 0.048 0.126 432 Planarity : 0.002 0.020 402 Dihedral : 4.822 16.737 348 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 8.75 % Allowed : 14.58 % Favored : 76.67 % 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: -4.47 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (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 D 94 TYR 0.003 0.001 TYR D 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 53 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 32 time to evaluate : 0.261 Fit side-chains REVERT: F 83 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7697 (pm20) REVERT: C 83 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7929 (mm-30) outliers start: 21 outliers final: 19 residues processed: 49 average time/residue: 0.0717 time to fit residues: 4.8454 Evaluate side-chains 51 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 32 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU 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: 6.9990 chunk 22 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.2213 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= 0.157 Angle : 0.544 7.024 3240 Z= 0.296 Chirality : 0.047 0.124 432 Planarity : 0.003 0.021 402 Dihedral : 4.414 16.454 348 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 7.92 % Allowed : 14.17 % 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: -4.18 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.002 0.001 PHE D 94 TYR 0.003 0.001 TYR B 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 49 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 30 time to evaluate : 0.259 Fit side-chains REVERT: F 83 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7666 (pm20) REVERT: C 83 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7898 (mm-30) outliers start: 19 outliers final: 18 residues processed: 47 average time/residue: 0.0728 time to fit residues: 4.7034 Evaluate side-chains 50 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 32 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU 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: 2.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 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: 1.2784 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2388 Z= 0.235 Angle : 0.593 7.744 3240 Z= 0.322 Chirality : 0.046 0.127 432 Planarity : 0.003 0.019 402 Dihedral : 4.735 16.818 348 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 7.92 % Allowed : 12.92 % 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: -4.07 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.003 0.001 PHE D 94 TYR 0.003 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 50 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 31 time to evaluate : 0.272 Fit side-chains REVERT: F 83 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7710 (pm20) outliers start: 19 outliers final: 19 residues processed: 46 average time/residue: 0.0769 time to fit residues: 4.8984 Evaluate side-chains 50 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 31 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU 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: 6.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2388 Z= 0.299 Angle : 0.642 7.537 3240 Z= 0.348 Chirality : 0.046 0.130 432 Planarity : 0.003 0.020 402 Dihedral : 5.008 16.934 348 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 7.92 % Allowed : 13.33 % 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: -4.15 (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 E 50 PHE 0.005 0.001 PHE D 94 TYR 0.003 0.001 TYR B 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 49 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 30 time to evaluate : 0.262 Fit side-chains outliers start: 19 outliers final: 19 residues processed: 46 average time/residue: 0.0710 time to fit residues: 4.5416 Evaluate side-chains 48 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 29 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU 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: 4.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.166764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.140184 restraints weight = 2707.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.143308 restraints weight = 1438.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.144996 restraints weight = 1008.574| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2388 Z= 0.339 Angle : 0.689 7.494 3240 Z= 0.375 Chirality : 0.047 0.134 432 Planarity : 0.003 0.019 402 Dihedral : 5.322 16.981 348 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 7.92 % Allowed : 12.08 % 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: -4.21 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.005 0.001 PHE D 94 TYR 0.004 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 959.57 seconds wall clock time: 18 minutes 6.81 seconds (1086.81 seconds total)