Starting phenix.real_space_refine on Mon Feb 10 20:25:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol6_16952/02_2025/8ol6_16952.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol6_16952/02_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_16952/02_2025/8ol6_16952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol6_16952/02_2025/8ol6_16952.map" model { file = "/net/cci-nas-00/data/ceres_data/8ol6_16952/02_2025/8ol6_16952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol6_16952/02_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-5592/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: 1.28, per 1000 atoms: 0.57 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: 0.47 Conformation dependent library (CDL) restraints added in 266.9 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: 0.31 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: 0.57 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- 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 : 0.288 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: 0.1407 time to fit residues: 20.0564 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 : 0.248 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.104978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.090411 restraints weight = 4899.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092688 restraints weight = 2569.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094419 restraints weight = 1670.113| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3370 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= 0.302 Angle : 0.587 6.719 3080 Z= 0.300 Chirality : 0.051 0.122 370 Planarity : 0.002 0.015 390 Dihedral : 9.865 69.292 310 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 7.39 % Allowed : 26.09 % Favored : 66.52 % 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: -2.29 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 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 116 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.244 Fit side-chains REVERT: A 39 VAL cc_start: 0.9253 (t) cc_final: 0.9013 (t) REVERT: C 39 VAL cc_start: 0.9516 (t) cc_final: 0.9244 (t) REVERT: D 22 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7742 (tp30) REVERT: E 22 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7887 (mm-30) REVERT: F 22 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8000 (tp30) REVERT: G 16 LYS cc_start: 0.8090 (mttp) cc_final: 0.7782 (mtpp) REVERT: G 22 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7690 (mm-30) REVERT: G 39 VAL cc_start: 0.9456 (t) cc_final: 0.9216 (t) REVERT: H 22 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7905 (tp30) REVERT: I 16 LYS cc_start: 0.8305 (mttp) cc_final: 0.7504 (mmtt) REVERT: I 22 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7621 (mm-30) REVERT: I 35 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8538 (ptm) REVERT: J 14 HIS cc_start: 0.8682 (m170) cc_final: 0.6717 (p-80) REVERT: J 16 LYS cc_start: 0.8630 (mttp) cc_final: 0.8235 (mmtt) outliers start: 17 outliers final: 3 residues processed: 102 average time/residue: 0.0910 time to fit residues: 11.4834 Evaluate side-chains 97 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 8.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 28 optimal weight: 7.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.105499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090492 restraints weight = 4894.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092784 restraints weight = 2532.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094733 restraints weight = 1650.248| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3880 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= 0.276 Angle : 0.529 5.770 3080 Z= 0.275 Chirality : 0.052 0.116 370 Planarity : 0.002 0.019 390 Dihedral : 10.205 75.895 310 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 7.83 % Allowed : 28.70 % 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: -2.34 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 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: 18 poor density : 102 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9178 (t) cc_final: 0.8915 (t) REVERT: C 39 VAL cc_start: 0.9440 (t) cc_final: 0.9162 (t) REVERT: G 22 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8035 (tp30) REVERT: G 39 VAL cc_start: 0.9426 (t) cc_final: 0.9187 (t) REVERT: H 18 VAL cc_start: 0.9472 (t) cc_final: 0.9067 (p) REVERT: H 22 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7996 (tp30) REVERT: I 16 LYS cc_start: 0.8106 (mttp) cc_final: 0.7335 (mmtt) REVERT: I 22 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7666 (mm-30) REVERT: J 14 HIS cc_start: 0.8806 (m170) cc_final: 0.6724 (p-80) REVERT: J 15 GLN cc_start: 0.8606 (tm-30) cc_final: 0.7939 (tm-30) REVERT: J 16 LYS cc_start: 0.8453 (mttp) cc_final: 0.7848 (tptt) outliers start: 18 outliers final: 4 residues processed: 106 average time/residue: 0.0950 time to fit residues: 12.4732 Evaluate side-chains 99 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain H residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090994 restraints weight = 4782.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093429 restraints weight = 2576.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095365 restraints weight = 1702.321| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4263 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= 0.278 Angle : 0.525 4.901 3080 Z= 0.271 Chirality : 0.052 0.115 370 Planarity : 0.002 0.014 390 Dihedral : 10.490 84.487 310 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 9.13 % Allowed : 27.39 % 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: -2.42 (0.47), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.36), 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 : 0.261 Fit side-chains revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9253 (t) cc_final: 0.8989 (t) REVERT: G 22 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8059 (tp30) REVERT: H 22 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8010 (tp30) REVERT: I 16 LYS cc_start: 0.8249 (mttp) cc_final: 0.7383 (mmtt) REVERT: I 22 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7733 (mm-30) REVERT: J 14 HIS cc_start: 0.8733 (m170) cc_final: 0.6581 (p-80) REVERT: J 16 LYS cc_start: 0.8498 (mttp) cc_final: 0.8095 (mmtt) outliers start: 21 outliers final: 7 residues processed: 107 average time/residue: 0.0917 time to fit residues: 12.1617 Evaluate side-chains 102 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 8.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 0.0170 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.105977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.091139 restraints weight = 4877.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.093629 restraints weight = 2589.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.095452 restraints weight = 1669.643| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4498 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= 0.370 Angle : 0.560 4.625 3080 Z= 0.293 Chirality : 0.052 0.115 370 Planarity : 0.002 0.012 390 Dihedral : 10.780 88.440 310 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 9.57 % Allowed : 27.39 % Favored : 63.04 % 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: -2.41 (0.47), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.004 0.001 PHE E 20 *********************** 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 121 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 22 GLU cc_start: 0.8501 (tp30) cc_final: 0.7846 (tp30) REVERT: G 22 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8117 (tp30) REVERT: G 39 VAL cc_start: 0.9507 (t) cc_final: 0.9245 (t) REVERT: H 22 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7951 (tp30) REVERT: I 16 LYS cc_start: 0.8112 (mttp) cc_final: 0.7183 (mmtt) REVERT: I 22 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7716 (mm-30) REVERT: J 15 GLN cc_start: 0.8628 (tm-30) cc_final: 0.7839 (tm-30) REVERT: J 16 LYS cc_start: 0.8440 (mttp) cc_final: 0.7736 (tptt) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 0.0928 time to fit residues: 12.2818 Evaluate side-chains 108 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 35 MET 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: 10.0000 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.108140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.092967 restraints weight = 4829.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.095313 restraints weight = 2675.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097111 restraints weight = 1793.019| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2290 Z= 0.185 Angle : 0.514 4.607 3080 Z= 0.267 Chirality : 0.053 0.120 370 Planarity : 0.002 0.021 390 Dihedral : 10.494 81.458 310 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 11.74 % Allowed : 25.22 % Favored : 63.04 % 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: -2.52 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 13 PHE 0.003 0.001 PHE A 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 126 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9182 (t) cc_final: 0.8916 (t) REVERT: B 39 VAL cc_start: 0.9110 (t) cc_final: 0.8827 (t) REVERT: F 22 GLU cc_start: 0.8477 (tp30) cc_final: 0.7881 (tp30) REVERT: G 39 VAL cc_start: 0.9458 (t) cc_final: 0.9193 (t) REVERT: H 22 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7875 (tp30) REVERT: I 16 LYS cc_start: 0.8238 (mttp) cc_final: 0.7350 (mmtt) REVERT: J 15 GLN cc_start: 0.8612 (tm-30) cc_final: 0.7956 (tm-30) REVERT: J 16 LYS cc_start: 0.8485 (mttp) cc_final: 0.7773 (tptt) outliers start: 27 outliers final: 13 residues processed: 110 average time/residue: 0.0869 time to fit residues: 12.2020 Evaluate side-chains 107 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 26 SER 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 35 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 12 VAL 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 14 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.105967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.091219 restraints weight = 4942.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093527 restraints weight = 2621.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095329 restraints weight = 1701.454| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2290 Z= 0.321 Angle : 0.553 5.180 3080 Z= 0.288 Chirality : 0.052 0.123 370 Planarity : 0.002 0.018 390 Dihedral : 10.335 75.277 310 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.69 % Favored : 88.97 % Rotamer: Outliers : 10.87 % Allowed : 25.65 % 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: -2.55 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (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 E 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: 25 poor density : 97 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9283 (t) cc_final: 0.9043 (t) REVERT: B 39 VAL cc_start: 0.9192 (t) cc_final: 0.8917 (t) REVERT: F 22 GLU cc_start: 0.8479 (tp30) cc_final: 0.7852 (tp30) REVERT: G 22 GLU cc_start: 0.8291 (tp30) cc_final: 0.7621 (tp30) REVERT: G 39 VAL cc_start: 0.9501 (t) cc_final: 0.9259 (t) REVERT: I 16 LYS cc_start: 0.8161 (mttp) cc_final: 0.7255 (mmtt) REVERT: J 16 LYS cc_start: 0.8423 (mttp) cc_final: 0.7980 (mmtt) outliers start: 25 outliers final: 14 residues processed: 106 average time/residue: 0.0888 time to fit residues: 11.8970 Evaluate side-chains 108 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 C residue 26 SER 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 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 12 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain H residue 41 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.106928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092244 restraints weight = 5148.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094676 restraints weight = 2715.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096333 restraints weight = 1751.823| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2290 Z= 0.319 Angle : 0.571 6.144 3080 Z= 0.295 Chirality : 0.053 0.128 370 Planarity : 0.002 0.019 390 Dihedral : 10.262 65.597 310 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.86 % Favored : 93.79 % Rotamer: Outliers : 10.43 % Allowed : 26.52 % Favored : 63.04 % 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 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (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 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 117 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9262 (t) cc_final: 0.9024 (t) REVERT: B 39 VAL cc_start: 0.9223 (t) cc_final: 0.8967 (t) REVERT: F 22 GLU cc_start: 0.8445 (tp30) cc_final: 0.7848 (tp30) REVERT: F 39 VAL cc_start: 0.9538 (t) cc_final: 0.9280 (t) REVERT: G 22 GLU cc_start: 0.8303 (tp30) cc_final: 0.7627 (tp30) REVERT: G 39 VAL cc_start: 0.9524 (t) cc_final: 0.9272 (t) REVERT: I 16 LYS cc_start: 0.8201 (mttp) cc_final: 0.7298 (mmtt) REVERT: J 15 GLN cc_start: 0.8544 (tm-30) cc_final: 0.7903 (tm-30) REVERT: J 16 LYS cc_start: 0.8404 (mttp) cc_final: 0.7682 (tptt) outliers start: 24 outliers final: 18 residues processed: 102 average time/residue: 0.0839 time to fit residues: 10.8048 Evaluate side-chains 108 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 35 MET 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 18 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain H residue 40 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.106460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091345 restraints weight = 5048.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093703 restraints weight = 2786.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.095455 restraints weight = 1860.111| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2290 Z= 0.332 Angle : 0.594 7.071 3080 Z= 0.302 Chirality : 0.053 0.139 370 Planarity : 0.002 0.018 390 Dihedral : 10.154 64.768 310 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.28 % Favored : 91.38 % Rotamer: Outliers : 10.43 % Allowed : 27.39 % 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: -2.61 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.005 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 115 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9246 (t) cc_final: 0.8995 (t) REVERT: B 39 VAL cc_start: 0.9210 (t) cc_final: 0.8955 (t) REVERT: F 39 VAL cc_start: 0.9553 (t) cc_final: 0.9288 (t) REVERT: G 22 GLU cc_start: 0.8378 (tp30) cc_final: 0.7682 (tp30) REVERT: G 39 VAL cc_start: 0.9541 (t) cc_final: 0.9300 (t) REVERT: H 39 VAL cc_start: 0.9508 (t) cc_final: 0.9196 (t) REVERT: I 16 LYS cc_start: 0.8128 (mttp) cc_final: 0.7233 (mmtt) REVERT: J 15 GLN cc_start: 0.8539 (tm-30) cc_final: 0.7890 (tm-30) REVERT: J 16 LYS cc_start: 0.8315 (mttp) cc_final: 0.7605 (tptt) outliers start: 24 outliers final: 16 residues processed: 100 average time/residue: 0.0838 time to fit residues: 10.5735 Evaluate side-chains 106 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 26 SER 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 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 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 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092328 restraints weight = 4990.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094725 restraints weight = 2772.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096497 restraints weight = 1853.689| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2290 Z= 0.246 Angle : 0.594 7.578 3080 Z= 0.301 Chirality : 0.053 0.134 370 Planarity : 0.002 0.023 390 Dihedral : 10.038 66.774 310 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.69 % Allowed : 4.48 % Favored : 94.83 % Rotamer: Outliers : 9.57 % Allowed : 30.00 % 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: -2.66 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 13 PHE 0.005 0.001 PHE A 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 119 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9227 (t) cc_final: 0.8986 (t) REVERT: B 39 VAL cc_start: 0.9204 (t) cc_final: 0.8954 (t) REVERT: F 22 GLU cc_start: 0.8518 (tp30) cc_final: 0.7821 (tp30) REVERT: G 22 GLU cc_start: 0.8368 (tp30) cc_final: 0.7658 (tp30) REVERT: G 39 VAL cc_start: 0.9511 (t) cc_final: 0.9267 (t) REVERT: H 39 VAL cc_start: 0.9482 (t) cc_final: 0.9201 (t) REVERT: I 16 LYS cc_start: 0.8197 (mttp) cc_final: 0.7328 (mmtt) REVERT: J 15 GLN cc_start: 0.8558 (tm-30) cc_final: 0.7993 (tm-30) REVERT: J 16 LYS cc_start: 0.8341 (mttp) cc_final: 0.7624 (tptt) outliers start: 22 outliers final: 15 residues processed: 106 average time/residue: 0.0758 time to fit residues: 10.2143 Evaluate side-chains 111 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 26 SER 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 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 H residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.107557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092731 restraints weight = 4966.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.095142 restraints weight = 2687.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096870 restraints weight = 1771.500| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2290 Z= 0.293 Angle : 0.607 7.564 3080 Z= 0.307 Chirality : 0.053 0.140 370 Planarity : 0.002 0.021 390 Dihedral : 9.955 67.635 310 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.28 % Favored : 91.03 % Rotamer: Outliers : 7.83 % Allowed : 31.74 % 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: -2.68 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 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: 1000.78 seconds wall clock time: 18 minutes 36.89 seconds (1116.89 seconds total)