Starting phenix.real_space_refine on Wed Mar 5 15:19:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol6_16952/03_2025/8ol6_16952.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol6_16952/03_2025/8ol6_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/cci-nas-00/data/ceres_data/8ol6_16952/03_2025/8ol6_16952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol6_16952/03_2025/8ol6_16952.map" model { file = "/net/cci-nas-00/data/ceres_data/8ol6_16952/03_2025/8ol6_16952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol6_16952/03_2025/8ol6_16952.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2260 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.75, per 1000 atoms: 0.77 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 - 3.00 Amino acid : True - 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: 0.52 Conformation dependent library (CDL) restraints added in 289.2 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: 0.33 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: 0.53 Time building geometry restraints manager: 0.64 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: 0.00 - 0.78: 2726 0.78 - 1.55: 314 1.55 - 2.33: 10 2.33 - 3.11: 10 3.11 - 3.88: 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 3.120 nonbonded pdb=" NZ LYS C 28 " pdb=" OXT ALA F 42 " model vdw 2.255 3.120 nonbonded pdb=" NZ LYS G 28 " pdb=" OXT ALA J 42 " model vdw 2.255 3.120 nonbonded pdb=" NZ LYS H 28 " pdb=" OXT ALA I 42 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS D 28 " pdb=" OXT ALA E 42 " model vdw 2.257 3.120 ... (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 Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.262 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: 0.1376 time to fit residues: 19.5962 Evaluate side-chains 81 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.105724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090790 restraints weight = 4894.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.093165 restraints weight = 2544.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094887 restraints weight = 1648.250| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2290 Z= 0.254 Angle : 0.580 7.070 3080 Z= 0.293 Chirality : 0.053 0.123 370 Planarity : 0.002 0.015 390 Dihedral : 9.397 64.874 310 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 7.39 % Allowed : 25.22 % Favored : 67.39 % 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: -2.26 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 13 PHE 0.004 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 111 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.251 Fit side-chains REVERT: A 39 VAL cc_start: 0.9154 (t) cc_final: 0.8914 (t) REVERT: B 22 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7601 (pt0) REVERT: C 39 VAL cc_start: 0.9425 (t) cc_final: 0.9140 (t) REVERT: D 22 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7705 (tp30) REVERT: E 22 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7897 (mm-30) REVERT: F 22 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8002 (tp30) REVERT: G 22 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7720 (mm-30) REVERT: G 39 VAL cc_start: 0.9364 (t) cc_final: 0.9118 (t) REVERT: H 22 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7935 (tp30) REVERT: I 16 LYS cc_start: 0.8141 (mttp) cc_final: 0.7319 (mmtt) REVERT: I 22 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7666 (mm-30) REVERT: I 35 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8526 (ptm) REVERT: J 14 HIS cc_start: 0.8697 (m170) cc_final: 0.6573 (p90) REVERT: J 16 LYS cc_start: 0.8499 (mttp) cc_final: 0.8113 (mmtt) outliers start: 17 outliers final: 5 residues processed: 97 average time/residue: 0.0901 time to fit residues: 10.9962 Evaluate side-chains 97 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 40 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.108466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093019 restraints weight = 4772.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095493 restraints weight = 2497.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.097368 restraints weight = 1626.381| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2290 Z= 0.173 Angle : 0.489 5.538 3080 Z= 0.252 Chirality : 0.052 0.118 370 Planarity : 0.001 0.006 390 Dihedral : 9.625 76.137 310 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 6.96 % Allowed : 28.70 % Favored : 64.35 % 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: -2.32 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 14 PHE 0.005 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 120 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9142 (t) cc_final: 0.8899 (t) REVERT: B 18 VAL cc_start: 0.9469 (t) cc_final: 0.9177 (p) REVERT: G 16 LYS cc_start: 0.7908 (mttp) cc_final: 0.7533 (mtpp) REVERT: G 22 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7739 (mm-30) REVERT: H 22 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7910 (tp30) REVERT: I 16 LYS cc_start: 0.8124 (mttp) cc_final: 0.7298 (mmtt) REVERT: I 22 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7646 (tp30) REVERT: J 14 HIS cc_start: 0.8703 (m170) cc_final: 0.6447 (p90) REVERT: J 15 GLN cc_start: 0.8583 (tm-30) cc_final: 0.7917 (tm-30) REVERT: J 16 LYS cc_start: 0.8392 (mttp) cc_final: 0.7793 (tptt) outliers start: 16 outliers final: 1 residues processed: 107 average time/residue: 0.0878 time to fit residues: 11.8845 Evaluate side-chains 95 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 9.9990 chunk 1 optimal weight: 0.3980 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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** J 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.091619 restraints weight = 4784.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094100 restraints weight = 2601.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.096009 restraints weight = 1745.545| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2290 Z= 0.214 Angle : 0.506 6.364 3080 Z= 0.258 Chirality : 0.053 0.121 370 Planarity : 0.002 0.008 390 Dihedral : 9.752 85.027 310 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 9.13 % Allowed : 28.70 % Favored : 62.17 % 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: -2.38 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.004 0.001 PHE C 19 *********************** 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 121 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9198 (t) cc_final: 0.8956 (t) REVERT: C 39 VAL cc_start: 0.9453 (t) cc_final: 0.9173 (t) REVERT: E 39 VAL cc_start: 0.9435 (t) cc_final: 0.9125 (t) REVERT: G 22 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7734 (mm-30) REVERT: H 22 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7944 (tp30) REVERT: I 16 LYS cc_start: 0.8243 (mttp) cc_final: 0.7403 (mmtt) REVERT: I 22 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7454 (tp30) REVERT: J 14 HIS cc_start: 0.8778 (m170) cc_final: 0.6423 (p90) REVERT: J 15 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8014 (tm-30) REVERT: J 16 LYS cc_start: 0.8496 (mttp) cc_final: 0.7881 (tptt) outliers start: 21 outliers final: 6 residues processed: 108 average time/residue: 0.0922 time to fit residues: 12.4091 Evaluate side-chains 101 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain G residue 41 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.103722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088834 restraints weight = 4927.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.091118 restraints weight = 2651.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092787 restraints weight = 1737.959| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 2290 Z= 0.434 Angle : 0.595 5.492 3080 Z= 0.311 Chirality : 0.052 0.117 370 Planarity : 0.002 0.011 390 Dihedral : 10.533 86.432 310 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % 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: -2.44 (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 0.004 0.001 HIS D 13 PHE 0.005 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 122 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9215 (t) cc_final: 0.8944 (t) REVERT: G 22 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8130 (tp30) REVERT: G 39 VAL cc_start: 0.9528 (t) cc_final: 0.9326 (t) REVERT: H 22 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8077 (tp30) REVERT: I 16 LYS cc_start: 0.8297 (mttp) cc_final: 0.7354 (mmtt) REVERT: I 22 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7700 (mm-30) REVERT: J 16 LYS cc_start: 0.8399 (mttp) cc_final: 0.8012 (mmtt) outliers start: 22 outliers final: 12 residues processed: 108 average time/residue: 0.0858 time to fit residues: 11.5805 Evaluate side-chains 106 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain H residue 41 ILE 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 20 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.106320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091585 restraints weight = 4839.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093951 restraints weight = 2622.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095626 restraints weight = 1725.232| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2290 Z= 0.248 Angle : 0.530 5.358 3080 Z= 0.276 Chirality : 0.053 0.126 370 Planarity : 0.002 0.022 390 Dihedral : 10.487 87.574 310 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 11.30 % Allowed : 28.70 % 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: -2.50 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.004 0.001 PHE C 19 *********************** 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 124 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9199 (t) cc_final: 0.8916 (t) REVERT: E 22 GLU cc_start: 0.8514 (tp30) cc_final: 0.7860 (tp30) REVERT: F 22 GLU cc_start: 0.8476 (tp30) cc_final: 0.7861 (tp30) REVERT: G 22 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7982 (tp30) REVERT: G 39 VAL cc_start: 0.9510 (t) cc_final: 0.9273 (t) REVERT: H 22 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7922 (tp30) REVERT: I 16 LYS cc_start: 0.8383 (mttp) cc_final: 0.7421 (mmtt) REVERT: J 16 LYS cc_start: 0.8508 (mttp) cc_final: 0.8096 (mmtt) outliers start: 26 outliers final: 13 residues processed: 108 average time/residue: 0.0840 time to fit residues: 11.4591 Evaluate side-chains 108 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL 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 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 41 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.105630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.090911 restraints weight = 4944.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093251 restraints weight = 2685.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094924 restraints weight = 1767.517| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2290 Z= 0.279 Angle : 0.547 5.137 3080 Z= 0.287 Chirality : 0.053 0.122 370 Planarity : 0.002 0.021 390 Dihedral : 10.372 81.934 310 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.97 % Favored : 90.69 % Rotamer: Outliers : 10.43 % Allowed : 30.87 % Favored : 58.70 % 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: -2.56 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.003 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 122 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9234 (t) cc_final: 0.8968 (t) REVERT: B 39 VAL cc_start: 0.9163 (t) cc_final: 0.8872 (t) REVERT: E 39 VAL cc_start: 0.9549 (t) cc_final: 0.9291 (t) REVERT: F 22 GLU cc_start: 0.8492 (tp30) cc_final: 0.7857 (tp30) REVERT: G 39 VAL cc_start: 0.9531 (t) cc_final: 0.9262 (t) REVERT: I 16 LYS cc_start: 0.8365 (mttp) cc_final: 0.7375 (mmtt) REVERT: J 15 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8174 (tm-30) REVERT: J 16 LYS cc_start: 0.8417 (mttp) cc_final: 0.7813 (mmtt) outliers start: 24 outliers final: 13 residues processed: 107 average time/residue: 0.0825 time to fit residues: 11.1425 Evaluate side-chains 108 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL 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 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089928 restraints weight = 5279.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.092198 restraints weight = 2833.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093874 restraints weight = 1864.546| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 2290 Z= 0.553 Angle : 0.665 6.118 3080 Z= 0.354 Chirality : 0.053 0.140 370 Planarity : 0.003 0.021 390 Dihedral : 10.957 79.000 310 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.10 % Favored : 86.55 % Rotamer: Outliers : 10.00 % Allowed : 30.43 % Favored : 59.57 % 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 0.004 0.002 HIS D 13 PHE 0.005 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 119 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 39 VAL cc_start: 0.9244 (t) cc_final: 0.8991 (t) REVERT: G 22 GLU cc_start: 0.8406 (tp30) cc_final: 0.7692 (tp30) REVERT: H 39 VAL cc_start: 0.9568 (t) cc_final: 0.9284 (t) REVERT: I 16 LYS cc_start: 0.8357 (mttp) cc_final: 0.7366 (mmtt) REVERT: I 22 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7535 (mm-30) REVERT: J 16 LYS cc_start: 0.8362 (mttp) cc_final: 0.7931 (mmtt) outliers start: 23 outliers final: 18 residues processed: 103 average time/residue: 0.0886 time to fit residues: 11.4051 Evaluate side-chains 111 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL 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 35 MET Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain H residue 41 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.110096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094706 restraints weight = 4747.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097144 restraints weight = 2587.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098945 restraints weight = 1713.578| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2290 Z= 0.169 Angle : 0.603 7.407 3080 Z= 0.309 Chirality : 0.055 0.131 370 Planarity : 0.002 0.021 390 Dihedral : 10.933 70.799 310 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.79 % Favored : 95.86 % Rotamer: Outliers : 7.83 % Allowed : 31.30 % 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: -2.68 (0.45), 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 0.002 0.001 HIS B 14 PHE 0.003 0.001 PHE F 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 119 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9228 (t) cc_final: 0.8977 (t) REVERT: B 39 VAL cc_start: 0.9122 (t) cc_final: 0.8854 (t) REVERT: E 16 LYS cc_start: 0.7875 (mmtp) cc_final: 0.7663 (mmtt) REVERT: F 22 GLU cc_start: 0.8496 (tp30) cc_final: 0.7831 (tp30) REVERT: G 22 GLU cc_start: 0.8273 (tp30) cc_final: 0.7771 (tp30) REVERT: G 39 VAL cc_start: 0.9421 (t) cc_final: 0.9152 (t) REVERT: H 22 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7922 (tp30) REVERT: I 16 LYS cc_start: 0.8371 (mttp) cc_final: 0.7443 (mmtt) REVERT: I 23 ASP cc_start: 0.7346 (p0) cc_final: 0.6204 (m-30) REVERT: J 15 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8088 (tm-30) outliers start: 18 outliers final: 9 residues processed: 108 average time/residue: 0.0891 time to fit residues: 12.0284 Evaluate side-chains 107 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.0670 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.1922 ------------------------------------------------------------------------------- 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** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095845 restraints weight = 4835.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.098299 restraints weight = 2630.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100094 restraints weight = 1743.050| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2290 Z= 0.177 Angle : 0.612 8.092 3080 Z= 0.304 Chirality : 0.054 0.130 370 Planarity : 0.002 0.020 390 Dihedral : 10.663 71.824 310 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.17 % Favored : 94.14 % Rotamer: Outliers : 6.09 % Allowed : 34.35 % Favored : 59.57 % 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: -2.67 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 13 PHE 0.005 0.001 PHE F 20 ********************** 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 115 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9274 (t) cc_final: 0.9035 (t) REVERT: B 39 VAL cc_start: 0.9201 (t) cc_final: 0.8943 (t) REVERT: E 16 LYS cc_start: 0.7948 (mmtp) cc_final: 0.7655 (mttm) REVERT: F 22 GLU cc_start: 0.8450 (tp30) cc_final: 0.7819 (tp30) REVERT: G 22 GLU cc_start: 0.8226 (tp30) cc_final: 0.7731 (tp30) REVERT: H 39 VAL cc_start: 0.9427 (t) cc_final: 0.9141 (t) REVERT: I 16 LYS cc_start: 0.8419 (mttp) cc_final: 0.7540 (mmtt) REVERT: I 23 ASP cc_start: 0.7156 (p0) cc_final: 0.6106 (m-30) REVERT: J 15 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8265 (tm-30) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.0890 time to fit residues: 12.0465 Evaluate side-chains 106 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 19 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.093623 restraints weight = 4874.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.095998 restraints weight = 2679.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097747 restraints weight = 1789.872| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2290 Z= 0.229 Angle : 0.612 7.646 3080 Z= 0.303 Chirality : 0.053 0.133 370 Planarity : 0.002 0.019 390 Dihedral : 10.257 69.348 310 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.86 % Favored : 93.45 % Rotamer: Outliers : 6.52 % Allowed : 34.78 % Favored : 58.70 % 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: -2.66 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.005 0.001 PHE F 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1080.72 seconds wall clock time: 19 minutes 30.04 seconds (1170.04 seconds total)