Starting phenix.real_space_refine on Sun Mar 10 14:39:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/03_2024/8ol6_16952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/03_2024/8ol6_16952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/03_2024/8ol6_16952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/03_2024/8ol6_16952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/03_2024/8ol6_16952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/03_2024/8ol6_16952.pdb" } resolution = 3.8 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= 0.428 sd= 1.733 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1470 2.51 5 N 390 2.21 5 O 390 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: 2260 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "B" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "D" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "H" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "J" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Time building chain proxies: 1.61, per 1000 atoms: 0.71 Number of scatterers: 2260 At special positions: 0 Unit cell: (73.528, 66.256, 40.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 390 8.00 N 390 7.00 C 1470 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: 0.80 Conformation dependent library (CDL) restraints added in 406.3 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.444A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.118A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU C 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU E 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET C 35 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU G 34 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET E 35 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU I 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET G 35 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.364A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 35 removed outlier: 6.955A pdb=" N LEU D 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET B 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU F 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET D 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU H 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET F 35 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU J 34 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET H 35 " --> pdb=" O LEU J 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 41 29 hydrogen bonds defined for protein. 87 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: 0.47 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 740 1.34 - 1.46: 310 1.46 - 1.57: 1220 1.57 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 2290 Sorted by residual: bond pdb=" C VAL H 36 " pdb=" O VAL H 36 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.62e-01 bond pdb=" C VAL B 36 " pdb=" O VAL B 36 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.50e-01 bond pdb=" C VAL C 36 " pdb=" O VAL C 36 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.46e-01 bond pdb=" C VAL E 36 " pdb=" O VAL E 36 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.11e-01 bond pdb=" C VAL I 36 " pdb=" O VAL I 36 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.19e-02 7.06e+03 5.08e-01 ... (remaining 2285 not shown) Histogram of bond angle deviations from ideal: 99.51 - 105.86: 10 105.86 - 112.21: 1318 112.21 - 118.56: 547 118.56 - 124.91: 1185 124.91 - 131.26: 20 Bond angle restraints: 3080 Sorted by residual: angle pdb=" C VAL A 39 " pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta sigma weight residual 122.90 120.00 2.90 1.28e+00 6.10e-01 5.14e+00 angle pdb=" C VAL D 39 " pdb=" N VAL D 40 " pdb=" CA VAL D 40 " ideal model delta sigma weight residual 122.90 120.01 2.89 1.28e+00 6.10e-01 5.10e+00 angle pdb=" C VAL J 39 " pdb=" N VAL J 40 " pdb=" CA VAL J 40 " ideal model delta sigma weight residual 122.90 120.01 2.89 1.28e+00 6.10e-01 5.10e+00 angle pdb=" C VAL I 39 " pdb=" N VAL I 40 " pdb=" CA VAL I 40 " ideal model delta sigma weight residual 122.90 120.01 2.89 1.28e+00 6.10e-01 5.09e+00 angle pdb=" C VAL B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 122.90 120.02 2.88 1.28e+00 6.10e-01 5.06e+00 ... (remaining 3075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.06: 1040 7.06 - 14.12: 140 14.12 - 21.18: 60 21.18 - 28.23: 40 28.23 - 35.29: 10 Dihedral angle restraints: 1290 sinusoidal: 470 harmonic: 820 Sorted by residual: dihedral pdb=" N MET I 35 " pdb=" CA MET I 35 " pdb=" CB MET I 35 " pdb=" CG MET I 35 " ideal model delta sinusoidal sigma weight residual 60.00 86.58 -26.58 3 1.50e+01 4.44e-03 3.90e+00 dihedral pdb=" N MET D 35 " pdb=" CA MET D 35 " pdb=" CB MET D 35 " pdb=" CG MET D 35 " ideal model delta sinusoidal sigma weight residual 60.00 86.58 -26.58 3 1.50e+01 4.44e-03 3.90e+00 dihedral pdb=" N MET E 35 " pdb=" CA MET E 35 " pdb=" CB MET E 35 " pdb=" CG MET E 35 " ideal model delta sinusoidal sigma weight residual 60.00 86.56 -26.56 3 1.50e+01 4.44e-03 3.89e+00 ... (remaining 1287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 189 0.023 - 0.046: 71 0.046 - 0.069: 51 0.069 - 0.092: 17 0.092 - 0.115: 42 Chirality restraints: 370 Sorted by residual: chirality pdb=" CA ILE E 32 " pdb=" N ILE E 32 " pdb=" C ILE E 32 " pdb=" CB ILE E 32 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA ILE I 32 " pdb=" N ILE I 32 " pdb=" C ILE I 32 " pdb=" CB ILE I 32 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA ILE C 32 " pdb=" N ILE C 32 " pdb=" C ILE C 32 " pdb=" CB ILE C 32 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 367 not shown) Planarity restraints: 390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 39 " 0.003 2.00e-02 2.50e+03 5.75e-03 3.30e-01 pdb=" C VAL A 39 " -0.010 2.00e-02 2.50e+03 pdb=" O VAL A 39 " 0.004 2.00e-02 2.50e+03 pdb=" N VAL A 40 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 39 " -0.003 2.00e-02 2.50e+03 5.68e-03 3.23e-01 pdb=" C VAL D 39 " 0.010 2.00e-02 2.50e+03 pdb=" O VAL D 39 " -0.004 2.00e-02 2.50e+03 pdb=" N VAL D 40 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 39 " 0.003 2.00e-02 2.50e+03 5.67e-03 3.21e-01 pdb=" C VAL I 39 " -0.010 2.00e-02 2.50e+03 pdb=" O VAL I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N VAL I 40 " 0.003 2.00e-02 2.50e+03 ... (remaining 387 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 451 2.78 - 3.31: 1967 3.31 - 3.84: 3629 3.84 - 4.37: 3971 4.37 - 4.90: 7939 Nonbonded interactions: 17957 Sorted by model distance: nonbonded pdb=" NZ LYS E 28 " pdb=" OXT ALA H 42 " model vdw 2.255 2.520 nonbonded pdb=" NZ LYS C 28 " pdb=" OXT ALA F 42 " model vdw 2.255 2.520 nonbonded pdb=" NZ LYS G 28 " pdb=" OXT ALA J 42 " model vdw 2.255 2.520 nonbonded pdb=" NZ LYS H 28 " pdb=" OXT ALA I 42 " model vdw 2.257 2.520 nonbonded pdb=" NZ LYS D 28 " pdb=" OXT ALA E 42 " model vdw 2.257 2.520 ... (remaining 17952 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.910 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: 0.020 Extract box with map and model: 3.920 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.800 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.011 2290 Z= 0.240 Angle : 0.560 3.884 3080 Z= 0.354 Chirality : 0.048 0.115 370 Planarity : 0.001 0.006 390 Dihedral : 9.684 35.293 770 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 13 PHE 0.004 0.001 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.259 Fit side-chains REVERT: B 18 VAL cc_start: 0.9485 (t) cc_final: 0.9191 (p) REVERT: C 39 VAL cc_start: 0.9441 (t) cc_final: 0.9160 (t) REVERT: D 15 GLN cc_start: 0.8563 (tt0) cc_final: 0.8333 (tm-30) REVERT: E 22 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7935 (mm-30) REVERT: F 15 GLN cc_start: 0.8632 (tt0) cc_final: 0.8385 (tm-30) REVERT: G 22 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7722 (mm-30) REVERT: H 15 GLN cc_start: 0.8679 (tt0) cc_final: 0.8357 (tm-30) REVERT: I 22 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7677 (mm-30) REVERT: I 40 VAL cc_start: 0.9100 (t) cc_final: 0.8892 (p) REVERT: J 14 HIS cc_start: 0.8525 (m170) cc_final: 0.6694 (p-80) REVERT: J 16 LYS cc_start: 0.8538 (mttp) cc_final: 0.8223 (mmtt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1354 time to fit residues: 19.2908 Evaluate side-chains 81 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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: 10.0000 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2290 Z= 0.415 Angle : 0.619 6.880 3080 Z= 0.318 Chirality : 0.051 0.121 370 Planarity : 0.003 0.017 390 Dihedral : 10.185 72.282 310 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 11.74 % Allowed : 24.78 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 13 PHE 0.006 0.001 PHE C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 0.252 Fit side-chains REVERT: B 23 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7541 (p0) REVERT: C 39 VAL cc_start: 0.9488 (t) cc_final: 0.9230 (t) REVERT: D 23 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7899 (p0) REVERT: E 22 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7974 (mm-30) REVERT: F 23 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7941 (p0) REVERT: G 22 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7772 (mm-30) REVERT: H 22 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7983 (tp30) REVERT: I 15 GLN cc_start: 0.8152 (mt0) cc_final: 0.7946 (mt0) REVERT: I 16 LYS cc_start: 0.8196 (mttp) cc_final: 0.7401 (mmtt) REVERT: I 22 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7664 (mm-30) REVERT: J 14 HIS cc_start: 0.8770 (m170) cc_final: 0.6790 (p-80) REVERT: J 16 LYS cc_start: 0.8484 (mttp) cc_final: 0.8191 (mmtt) outliers start: 27 outliers final: 9 residues processed: 113 average time/residue: 0.0940 time to fit residues: 12.9746 Evaluate side-chains 105 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain I residue 35 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2290 Z= 0.154 Angle : 0.481 5.010 3080 Z= 0.247 Chirality : 0.053 0.118 370 Planarity : 0.002 0.017 390 Dihedral : 10.503 80.297 310 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 9.57 % Allowed : 30.43 % Favored : 60.00 % 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: -2.38 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 13 PHE 0.004 0.001 PHE E 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.301 Fit side-chains REVERT: A 39 VAL cc_start: 0.9190 (t) cc_final: 0.8938 (t) REVERT: E 22 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7861 (mm-30) REVERT: G 22 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7681 (mm-30) REVERT: H 22 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7879 (tp30) REVERT: I 16 LYS cc_start: 0.8290 (mttp) cc_final: 0.7446 (mmtt) REVERT: I 22 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7599 (mm-30) REVERT: J 14 HIS cc_start: 0.8752 (m170) cc_final: 0.6601 (p-80) REVERT: J 15 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7925 (tm-30) REVERT: J 16 LYS cc_start: 0.8597 (mttp) cc_final: 0.7922 (tptt) outliers start: 22 outliers final: 6 residues processed: 108 average time/residue: 0.0826 time to fit residues: 11.2137 Evaluate side-chains 101 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain I residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2290 Z= 0.372 Angle : 0.557 5.808 3080 Z= 0.289 Chirality : 0.052 0.116 370 Planarity : 0.002 0.010 390 Dihedral : 10.812 84.190 310 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 11.30 % Allowed : 27.39 % Favored : 61.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.005 0.001 PHE E 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9247 (t) cc_final: 0.8989 (t) REVERT: B 15 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 23 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7460 (p0) REVERT: G 22 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8016 (tp30) REVERT: H 22 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7995 (tp30) REVERT: I 16 LYS cc_start: 0.8311 (mttp) cc_final: 0.7414 (mmtt) REVERT: I 22 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7692 (mm-30) REVERT: J 16 LYS cc_start: 0.8509 (mttp) cc_final: 0.8145 (mmtt) outliers start: 26 outliers final: 13 residues processed: 107 average time/residue: 0.1090 time to fit residues: 14.7824 Evaluate side-chains 108 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2290 Z= 0.180 Angle : 0.493 5.616 3080 Z= 0.253 Chirality : 0.052 0.122 370 Planarity : 0.002 0.020 390 Dihedral : 10.691 84.759 310 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 9.57 % Allowed : 29.57 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 13 PHE 0.004 0.001 PHE C 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9163 (t) cc_final: 0.8888 (t) REVERT: B 15 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8175 (tm-30) REVERT: B 23 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7474 (p0) REVERT: G 22 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7946 (tp30) REVERT: H 22 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7921 (tp30) REVERT: I 16 LYS cc_start: 0.8369 (mttp) cc_final: 0.7420 (mmtt) REVERT: I 22 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7725 (mm-30) REVERT: J 15 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7804 (tm-30) REVERT: J 16 LYS cc_start: 0.8593 (mttp) cc_final: 0.7841 (tptt) outliers start: 22 outliers final: 12 residues processed: 107 average time/residue: 0.0855 time to fit residues: 11.5115 Evaluate side-chains 106 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 40 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2290 Z= 0.366 Angle : 0.540 5.053 3080 Z= 0.282 Chirality : 0.052 0.123 370 Planarity : 0.002 0.021 390 Dihedral : 10.480 79.154 310 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.66 % Favored : 90.00 % Rotamer: Outliers : 15.65 % Allowed : 24.35 % Favored : 60.00 % 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: -2.44 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.004 0.001 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9244 (t) cc_final: 0.8987 (t) REVERT: B 23 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7399 (p0) REVERT: B 39 VAL cc_start: 0.9144 (t) cc_final: 0.8875 (t) REVERT: C 39 VAL cc_start: 0.9483 (t) cc_final: 0.9235 (t) REVERT: G 22 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8049 (tp30) REVERT: H 22 GLU cc_start: 0.8219 (mm-30) cc_final: 0.8002 (tp30) REVERT: H 39 VAL cc_start: 0.9457 (t) cc_final: 0.9175 (t) REVERT: I 16 LYS cc_start: 0.8329 (mttp) cc_final: 0.7402 (mmtt) REVERT: I 22 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7757 (mm-30) REVERT: J 15 GLN cc_start: 0.8539 (tm-30) cc_final: 0.7830 (tm-30) REVERT: J 16 LYS cc_start: 0.8557 (mttp) cc_final: 0.7850 (tptt) outliers start: 36 outliers final: 19 residues processed: 114 average time/residue: 0.0830 time to fit residues: 11.8776 Evaluate side-chains 112 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2290 Z= 0.206 Angle : 0.541 7.175 3080 Z= 0.265 Chirality : 0.053 0.124 370 Planarity : 0.002 0.020 390 Dihedral : 10.105 70.259 310 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.55 % Favored : 93.10 % Rotamer: Outliers : 11.74 % Allowed : 29.13 % Favored : 59.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 13 PHE 0.004 0.001 PHE A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9166 (t) cc_final: 0.8902 (t) REVERT: B 23 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7431 (p0) REVERT: B 39 VAL cc_start: 0.9116 (t) cc_final: 0.8844 (t) REVERT: G 22 GLU cc_start: 0.8234 (mm-30) cc_final: 0.8010 (tp30) REVERT: G 39 VAL cc_start: 0.9441 (t) cc_final: 0.9199 (t) REVERT: H 39 VAL cc_start: 0.9400 (t) cc_final: 0.9129 (t) REVERT: I 16 LYS cc_start: 0.8374 (mttp) cc_final: 0.7433 (mmtt) REVERT: I 22 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7714 (mm-30) REVERT: J 16 LYS cc_start: 0.8551 (mttp) cc_final: 0.8120 (mmtt) outliers start: 27 outliers final: 16 residues processed: 111 average time/residue: 0.0864 time to fit residues: 11.9945 Evaluate side-chains 112 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 23 ASP 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: 9.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2290 Z= 0.177 Angle : 0.539 7.079 3080 Z= 0.265 Chirality : 0.053 0.127 370 Planarity : 0.002 0.018 390 Dihedral : 9.521 61.566 310 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.55 % Favored : 93.10 % Rotamer: Outliers : 10.43 % Allowed : 29.13 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 14 PHE 0.004 0.001 PHE A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9185 (t) cc_final: 0.8927 (t) REVERT: B 39 VAL cc_start: 0.9114 (t) cc_final: 0.8848 (t) REVERT: C 39 VAL cc_start: 0.9437 (t) cc_final: 0.9186 (t) REVERT: G 22 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7977 (tp30) REVERT: H 22 GLU cc_start: 0.8192 (tp30) cc_final: 0.7527 (tp30) REVERT: I 16 LYS cc_start: 0.8341 (mttp) cc_final: 0.7379 (mmtt) REVERT: I 22 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7669 (mm-30) REVERT: J 15 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8065 (tm-30) outliers start: 24 outliers final: 16 residues processed: 110 average time/residue: 0.0847 time to fit residues: 11.7386 Evaluate side-chains 112 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 23 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2290 Z= 0.339 Angle : 0.590 7.010 3080 Z= 0.296 Chirality : 0.053 0.145 370 Planarity : 0.002 0.017 390 Dihedral : 9.155 62.312 310 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.66 % Favored : 90.00 % Rotamer: Outliers : 10.43 % Allowed : 30.43 % Favored : 59.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.006 0.001 PHE A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9245 (t) cc_final: 0.9010 (t) REVERT: B 39 VAL cc_start: 0.9170 (t) cc_final: 0.8910 (t) REVERT: G 22 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8034 (tp30) REVERT: G 39 VAL cc_start: 0.9488 (t) cc_final: 0.9271 (t) REVERT: H 22 GLU cc_start: 0.8302 (tp30) cc_final: 0.7572 (tp30) REVERT: I 16 LYS cc_start: 0.8305 (mttp) cc_final: 0.7340 (mmtt) REVERT: I 22 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7668 (mm-30) REVERT: J 15 GLN cc_start: 0.8597 (tm-30) cc_final: 0.7848 (tm-30) outliers start: 24 outliers final: 19 residues processed: 105 average time/residue: 0.0832 time to fit residues: 11.0306 Evaluate side-chains 113 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2290 Z= 0.141 Angle : 0.554 7.346 3080 Z= 0.271 Chirality : 0.054 0.126 370 Planarity : 0.002 0.015 390 Dihedral : 9.222 67.578 310 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.45 % Favored : 96.21 % Rotamer: Outliers : 8.70 % Allowed : 33.04 % Favored : 58.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.44), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 14 PHE 0.004 0.000 PHE C 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9158 (t) cc_final: 0.8912 (t) REVERT: G 22 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7941 (tp30) REVERT: H 22 GLU cc_start: 0.8190 (tp30) cc_final: 0.7568 (tp30) REVERT: I 16 LYS cc_start: 0.8331 (mttp) cc_final: 0.7382 (mmtt) REVERT: I 22 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7597 (mm-30) outliers start: 20 outliers final: 15 residues processed: 108 average time/residue: 0.0820 time to fit residues: 11.2304 Evaluate side-chains 109 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 23 ASP 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: 9.9990 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.107945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.093123 restraints weight = 5007.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095566 restraints weight = 2687.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097257 restraints weight = 1758.508| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2290 Z= 0.254 Angle : 0.553 7.079 3080 Z= 0.273 Chirality : 0.053 0.141 370 Planarity : 0.002 0.015 390 Dihedral : 8.726 64.973 310 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.24 % Favored : 92.41 % Rotamer: Outliers : 10.87 % Allowed : 30.00 % Favored : 59.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 13 PHE 0.005 0.001 PHE A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 892.77 seconds wall clock time: 16 minutes 51.87 seconds (1011.87 seconds total)