Starting phenix.real_space_refine on Mon Feb 10 21:30:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8owj_17238/02_2025/8owj_17238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8owj_17238/02_2025/8owj_17238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8owj_17238/02_2025/8owj_17238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8owj_17238/02_2025/8owj_17238.map" model { file = "/net/cci-nas-00/data/ceres_data/8owj_17238/02_2025/8owj_17238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8owj_17238/02_2025/8owj_17238.cif" } resolution = 3.75 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= 0.001 sd= 0.005 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 1730 2.51 5 N 490 2.21 5 O 490 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: 2720 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "A" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "B" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "D" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "F" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "H" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "I" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "J" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Time building chain proxies: 2.22, per 1000 atoms: 0.82 Number of scatterers: 2720 At special positions: 0 Unit cell: (84, 116.55, 45.15, 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 490 8.00 N 490 7.00 C 1730 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: 0.64 Conformation dependent library (CDL) restraints added in 409.6 milliseconds 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.294A pdb=" N TYR A 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR E 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR G 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 23 removed outlier: 6.558A pdb=" N LYS E 16 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE C 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL E 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ALA C 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE E 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASP C 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU E 22 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 35 removed outlier: 6.809A pdb=" N LEU A 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET C 35 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY E 29 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE C 32 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE E 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 34 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY E 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU E 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET G 35 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA I 30 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE G 31 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE I 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY G 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.272A pdb=" N TYR B 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR D 10 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR F 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR H 10 " --> pdb=" O GLU J 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 23 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 35 removed outlier: 6.763A pdb=" N LEU B 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET D 35 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU D 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N MET F 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU F 34 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N MET H 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU H 34 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET J 35 " --> pdb=" O LEU H 34 " (cutoff:3.500A) 79 hydrogen bonds defined for protein. 234 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: 0.62 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 817 1.34 - 1.46: 433 1.46 - 1.58: 1500 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 2770 Sorted by residual: bond pdb=" N SER E 8 " pdb=" CA SER E 8 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.23e-02 6.61e+03 7.35e+00 bond pdb=" N SER H 8 " pdb=" CA SER H 8 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.23e-02 6.61e+03 7.20e+00 bond pdb=" N SER J 8 " pdb=" CA SER J 8 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.14e+00 bond pdb=" N SER D 8 " pdb=" CA SER D 8 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.97e+00 bond pdb=" N SER A 8 " pdb=" CA SER A 8 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.97e+00 ... (remaining 2765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 2213 1.76 - 3.53: 1035 3.53 - 5.29: 381 5.29 - 7.05: 71 7.05 - 8.81: 10 Bond angle restraints: 3710 Sorted by residual: angle pdb=" C VAL C 24 " pdb=" N GLY C 25 " pdb=" CA GLY C 25 " ideal model delta sigma weight residual 119.92 126.56 -6.64 9.60e-01 1.09e+00 4.78e+01 angle pdb=" C VAL F 24 " pdb=" N GLY F 25 " pdb=" CA GLY F 25 " ideal model delta sigma weight residual 119.92 126.52 -6.60 9.60e-01 1.09e+00 4.72e+01 angle pdb=" C VAL A 24 " pdb=" N GLY A 25 " pdb=" CA GLY A 25 " ideal model delta sigma weight residual 119.92 126.51 -6.59 9.60e-01 1.09e+00 4.71e+01 angle pdb=" C VAL B 24 " pdb=" N GLY B 25 " pdb=" CA GLY B 25 " ideal model delta sigma weight residual 119.92 126.50 -6.58 9.60e-01 1.09e+00 4.70e+01 angle pdb=" C VAL J 24 " pdb=" N GLY J 25 " pdb=" CA GLY J 25 " ideal model delta sigma weight residual 119.92 126.50 -6.58 9.60e-01 1.09e+00 4.70e+01 ... (remaining 3705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 1408 17.79 - 35.57: 102 35.57 - 53.35: 30 53.35 - 71.14: 0 71.14 - 88.92: 10 Dihedral angle restraints: 1550 sinusoidal: 590 harmonic: 960 Sorted by residual: dihedral pdb=" C HIS G 13 " pdb=" N HIS G 13 " pdb=" CA HIS G 13 " pdb=" CB HIS G 13 " ideal model delta harmonic sigma weight residual -122.60 -131.42 8.82 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" C HIS A 13 " pdb=" N HIS A 13 " pdb=" CA HIS A 13 " pdb=" CB HIS A 13 " ideal model delta harmonic sigma weight residual -122.60 -131.40 8.80 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C HIS E 13 " pdb=" N HIS E 13 " pdb=" CA HIS E 13 " pdb=" CB HIS E 13 " ideal model delta harmonic sigma weight residual -122.60 -131.37 8.77 0 2.50e+00 1.60e-01 1.23e+01 ... (remaining 1547 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.050: 83 0.050 - 0.100: 153 0.100 - 0.150: 93 0.150 - 0.200: 41 0.200 - 0.250: 30 Chirality restraints: 400 Sorted by residual: chirality pdb=" CA HIS G 13 " pdb=" N HIS G 13 " pdb=" C HIS G 13 " pdb=" CB HIS G 13 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA HIS A 13 " pdb=" N HIS A 13 " pdb=" C HIS A 13 " pdb=" CB HIS A 13 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA HIS D 13 " pdb=" N HIS D 13 " pdb=" C HIS D 13 " pdb=" CB HIS D 13 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 397 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 13 " 0.045 2.00e-02 2.50e+03 3.52e-02 1.86e+01 pdb=" CG HIS C 13 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS C 13 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS C 13 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 HIS C 13 " 0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS C 13 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 13 " 0.045 2.00e-02 2.50e+03 3.50e-02 1.84e+01 pdb=" CG HIS H 13 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS H 13 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS H 13 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS H 13 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS H 13 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 13 " 0.045 2.00e-02 2.50e+03 3.49e-02 1.83e+01 pdb=" CG HIS G 13 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS G 13 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS G 13 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 HIS G 13 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS G 13 " 0.022 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1682 3.07 - 3.53: 2845 3.53 - 3.98: 4140 3.98 - 4.44: 4971 4.44 - 4.90: 9197 Nonbonded interactions: 22835 Sorted by model distance: nonbonded pdb=" OD2 ASP G 23 " pdb=" NZ LYS G 28 " model vdw 2.610 3.120 nonbonded pdb=" OD2 ASP F 23 " pdb=" NZ LYS F 28 " model vdw 2.610 3.120 nonbonded pdb=" OD2 ASP B 23 " pdb=" NZ LYS B 28 " model vdw 2.610 3.120 nonbonded pdb=" OD2 ASP C 23 " pdb=" NZ LYS C 28 " model vdw 2.610 3.120 nonbonded pdb=" OD2 ASP H 23 " pdb=" NZ LYS H 28 " model vdw 2.610 3.120 ... (remaining 22830 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: 0.680 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.370 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 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 : 0.012 0.033 2770 Z= 0.834 Angle : 2.256 8.813 3710 Z= 1.604 Chirality : 0.112 0.250 400 Planarity : 0.015 0.048 480 Dihedral : 15.837 88.923 950 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.57 % Allowed : 14.29 % Favored : 82.14 % 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: -1.73 (0.36), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.010 HIS D 14 PHE 0.041 0.014 PHE B 20 TYR 0.004 0.001 TYR E 10 ARG 0.001 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6681 (ptpt) cc_final: 0.6209 (tptp) REVERT: G 11 GLU cc_start: 0.6215 (tt0) cc_final: 0.5480 (tm-30) REVERT: G 35 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.7026 (ptp) REVERT: H 11 GLU cc_start: 0.6450 (tt0) cc_final: 0.6104 (tm-30) REVERT: J 35 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7718 (ptp) outliers start: 10 outliers final: 0 residues processed: 110 average time/residue: 0.1171 time to fit residues: 15.6937 Evaluate side-chains 61 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 HIS E 27 ASN A 6 HIS D 14 HIS H 27 ASN I 14 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.101335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.091513 restraints weight = 8809.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.092708 restraints weight = 5038.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.093421 restraints weight = 3570.599| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2770 Z= 0.357 Angle : 0.798 7.316 3710 Z= 0.441 Chirality : 0.049 0.133 400 Planarity : 0.003 0.011 480 Dihedral : 7.285 18.990 376 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.43 % Allowed : 23.21 % Favored : 75.36 % 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: -2.36 (0.36), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.28), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 6 PHE 0.013 0.002 PHE B 19 TYR 0.012 0.003 TYR D 10 ARG 0.003 0.001 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.316 Fit side-chains REVERT: E 11 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6076 (tm-30) REVERT: E 22 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7574 (tm-30) REVERT: A 11 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7107 (pm20) REVERT: B 19 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: C 11 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6527 (tm-30) REVERT: F 11 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7090 (tm-30) REVERT: G 19 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.6449 (m-80) REVERT: G 22 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7465 (tm-30) REVERT: I 35 MET cc_start: 0.7920 (ptp) cc_final: 0.7476 (ptt) REVERT: J 11 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6735 (tm-30) REVERT: J 22 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7855 (tm-30) REVERT: J 35 MET cc_start: 0.7593 (ptp) cc_final: 0.7350 (ptt) outliers start: 4 outliers final: 0 residues processed: 49 average time/residue: 0.1078 time to fit residues: 6.8662 Evaluate side-chains 30 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain G residue 19 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.097001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.088041 restraints weight = 9401.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.089115 restraints weight = 5414.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.089888 restraints weight = 3855.876| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2770 Z= 0.387 Angle : 0.771 7.352 3710 Z= 0.434 Chirality : 0.049 0.129 400 Planarity : 0.004 0.015 480 Dihedral : 6.838 18.571 370 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.07 % Allowed : 25.71 % Favored : 73.21 % 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 (0.37), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 6 PHE 0.021 0.003 PHE G 20 TYR 0.017 0.004 TYR D 10 ARG 0.002 0.001 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.334 Fit side-chains REVERT: E 11 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6612 (tm-30) REVERT: E 22 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 19 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: B 22 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7482 (tm-30) REVERT: C 11 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6915 (tm-30) REVERT: D 22 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7447 (tm-30) REVERT: G 19 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.6874 (m-80) REVERT: H 11 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7025 (tm-30) REVERT: I 35 MET cc_start: 0.7640 (ptp) cc_final: 0.7030 (ptt) REVERT: J 11 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6603 (tm-30) REVERT: J 35 MET cc_start: 0.7522 (ptp) cc_final: 0.7160 (ptt) outliers start: 3 outliers final: 0 residues processed: 38 average time/residue: 0.1171 time to fit residues: 5.7839 Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain G residue 19 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.094907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.085973 restraints weight = 9555.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.087016 restraints weight = 5541.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.087711 restraints weight = 4011.381| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2770 Z= 0.417 Angle : 0.757 5.561 3710 Z= 0.433 Chirality : 0.050 0.134 400 Planarity : 0.003 0.015 480 Dihedral : 6.854 19.031 370 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.86 % Allowed : 23.57 % Favored : 73.57 % 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: -2.58 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 6 PHE 0.020 0.003 PHE G 20 TYR 0.015 0.004 TYR F 10 ARG 0.003 0.001 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.361 Fit side-chains REVERT: E 11 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6805 (tm-30) REVERT: E 22 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 28 LYS cc_start: 0.8195 (ptpt) cc_final: 0.7103 (tptp) REVERT: B 19 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: B 22 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7361 (tm-30) REVERT: C 11 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6581 (tm-30) REVERT: C 19 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.6888 (m-10) REVERT: D 35 MET cc_start: 0.7602 (ptp) cc_final: 0.7332 (ttm) REVERT: F 11 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6977 (tm-30) REVERT: G 19 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6793 (m-80) REVERT: H 11 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6731 (tm-30) REVERT: H 19 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7013 (m-10) REVERT: I 11 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6598 (tm-30) REVERT: I 22 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7984 (tm-30) REVERT: I 35 MET cc_start: 0.8026 (ptp) cc_final: 0.7445 (ptt) REVERT: J 11 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6651 (tm-30) REVERT: J 35 MET cc_start: 0.7429 (ptp) cc_final: 0.6957 (ptt) outliers start: 8 outliers final: 1 residues processed: 46 average time/residue: 0.1191 time to fit residues: 7.5895 Evaluate side-chains 37 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 19 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN D 15 GLN I 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.096185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.088198 restraints weight = 9848.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.089325 restraints weight = 5329.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.090015 restraints weight = 3616.424| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2770 Z= 0.317 Angle : 0.674 5.680 3710 Z= 0.385 Chirality : 0.049 0.134 400 Planarity : 0.003 0.014 480 Dihedral : 6.305 17.279 370 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.07 % Allowed : 26.07 % Favored : 72.86 % 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: -2.73 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 6 PHE 0.021 0.003 PHE G 20 TYR 0.012 0.003 TYR C 10 ARG 0.001 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.365 Fit side-chains REVERT: E 11 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6701 (tm-30) REVERT: E 22 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 28 LYS cc_start: 0.8206 (ptpt) cc_final: 0.7044 (tptp) REVERT: A 35 MET cc_start: 0.8451 (ttp) cc_final: 0.7968 (ttm) REVERT: C 11 GLU cc_start: 0.7576 (tm-30) cc_final: 0.6520 (tm-30) REVERT: D 11 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7104 (tm-30) REVERT: D 35 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7322 (ttm) REVERT: F 11 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6850 (tm-30) REVERT: G 11 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6836 (tm-30) REVERT: G 19 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.6596 (m-80) REVERT: H 11 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6384 (tm-30) REVERT: I 22 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7229 (tm-30) REVERT: I 35 MET cc_start: 0.8150 (ptp) cc_final: 0.7612 (ptt) REVERT: J 11 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6604 (tm-30) REVERT: J 35 MET cc_start: 0.7408 (ptp) cc_final: 0.7015 (ptt) outliers start: 3 outliers final: 0 residues processed: 45 average time/residue: 0.1180 time to fit residues: 7.0448 Evaluate side-chains 36 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain G residue 19 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.093720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.086237 restraints weight = 10387.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.087323 restraints weight = 5688.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.087976 restraints weight = 3865.194| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.7556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 2770 Z= 0.466 Angle : 0.791 7.190 3710 Z= 0.448 Chirality : 0.050 0.130 400 Planarity : 0.004 0.013 480 Dihedral : 6.891 20.204 370 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.86 % Allowed : 27.14 % Favored : 70.00 % 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: -2.98 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS J 6 PHE 0.020 0.003 PHE G 20 TYR 0.018 0.004 TYR I 10 ARG 0.003 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.246 Fit side-chains REVERT: E 11 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6881 (tm-30) REVERT: E 22 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 28 LYS cc_start: 0.8299 (ptpt) cc_final: 0.7234 (mmtm) REVERT: A 35 MET cc_start: 0.8421 (ttp) cc_final: 0.7991 (ttm) REVERT: B 19 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: C 11 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6459 (tm-30) REVERT: C 19 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6973 (m-10) REVERT: D 11 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6938 (tm-30) REVERT: D 35 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7249 (ttm) REVERT: F 11 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6455 (tm-30) REVERT: G 19 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: G 22 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7884 (tm-30) REVERT: H 11 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6785 (tm-30) REVERT: H 19 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: I 22 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7736 (tm-30) outliers start: 8 outliers final: 1 residues processed: 45 average time/residue: 0.1134 time to fit residues: 6.5729 Evaluate side-chains 40 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain J residue 19 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 0.0670 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.094990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.087047 restraints weight = 10325.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.088141 restraints weight = 5530.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.088831 restraints weight = 3758.510| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.7737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2770 Z= 0.339 Angle : 0.752 7.389 3710 Z= 0.415 Chirality : 0.050 0.136 400 Planarity : 0.003 0.015 480 Dihedral : 6.317 19.560 370 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.43 % Allowed : 28.93 % Favored : 69.64 % 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: -3.08 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 6 PHE 0.018 0.002 PHE C 20 TYR 0.013 0.003 TYR C 10 ARG 0.002 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.300 Fit side-chains REVERT: E 11 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6957 (tm-30) REVERT: E 22 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8302 (tm-30) REVERT: A 28 LYS cc_start: 0.8341 (ptpt) cc_final: 0.7303 (mmtm) REVERT: B 35 MET cc_start: 0.6983 (ttt) cc_final: 0.6736 (ttt) REVERT: C 11 GLU cc_start: 0.7489 (tm-30) cc_final: 0.6591 (tm-30) REVERT: D 35 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7508 (ttm) REVERT: F 11 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6458 (tm-30) REVERT: G 19 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: G 22 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7886 (tm-30) REVERT: G 35 MET cc_start: 0.7518 (ttm) cc_final: 0.7114 (ttt) REVERT: H 11 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6720 (tm-30) REVERT: I 22 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7534 (tm-30) outliers start: 4 outliers final: 1 residues processed: 46 average time/residue: 0.1114 time to fit residues: 6.5935 Evaluate side-chains 42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.095461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.087547 restraints weight = 9864.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.088700 restraints weight = 5270.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.089392 restraints weight = 3541.556| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.7913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2770 Z= 0.288 Angle : 0.737 7.696 3710 Z= 0.400 Chirality : 0.049 0.136 400 Planarity : 0.002 0.012 480 Dihedral : 5.911 18.248 370 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.36 % Allowed : 31.43 % Favored : 68.21 % 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: -3.14 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 6 PHE 0.017 0.003 PHE C 20 TYR 0.010 0.002 TYR I 10 ARG 0.001 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.300 Fit side-chains REVERT: E 11 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6862 (tm-30) REVERT: E 22 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8277 (tm-30) REVERT: A 28 LYS cc_start: 0.8356 (ptpt) cc_final: 0.7318 (mmtm) REVERT: B 35 MET cc_start: 0.7081 (ttt) cc_final: 0.6857 (ttt) REVERT: C 11 GLU cc_start: 0.7573 (tm-30) cc_final: 0.6580 (tm-30) REVERT: F 11 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6480 (tm-30) REVERT: G 22 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7834 (tm-30) REVERT: H 11 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6513 (tm-30) REVERT: I 22 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7508 (tm-30) REVERT: J 11 GLU cc_start: 0.7230 (tm-30) cc_final: 0.7027 (tm-30) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1027 time to fit residues: 6.7794 Evaluate side-chains 46 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.093151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.085925 restraints weight = 10262.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.086998 restraints weight = 5420.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.087781 restraints weight = 3654.611| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.8229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 2770 Z= 0.446 Angle : 0.826 6.893 3710 Z= 0.453 Chirality : 0.050 0.132 400 Planarity : 0.003 0.011 480 Dihedral : 6.511 20.672 370 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 1.07 % Allowed : 32.86 % Favored : 66.07 % 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: -3.36 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 6 PHE 0.022 0.003 PHE C 20 TYR 0.017 0.004 TYR C 10 ARG 0.002 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.328 Fit side-chains REVERT: E 11 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6892 (tm-30) REVERT: E 22 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 28 LYS cc_start: 0.8475 (ptpt) cc_final: 0.7361 (mmtm) REVERT: B 19 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: C 11 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6396 (tm-30) REVERT: F 11 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6475 (tm-30) REVERT: G 19 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: G 22 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7984 (tm-30) REVERT: H 11 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6724 (tm-30) REVERT: I 22 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7644 (tm-30) outliers start: 3 outliers final: 0 residues processed: 52 average time/residue: 0.1004 time to fit residues: 6.8064 Evaluate side-chains 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain G residue 19 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.095892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.087870 restraints weight = 9850.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.089082 restraints weight = 5218.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.089826 restraints weight = 3486.241| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.8273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2770 Z= 0.268 Angle : 0.759 7.949 3710 Z= 0.405 Chirality : 0.050 0.133 400 Planarity : 0.002 0.011 480 Dihedral : 5.807 18.857 370 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 34.29 % Favored : 65.71 % 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: -3.27 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 6 PHE 0.018 0.002 PHE C 20 TYR 0.009 0.002 TYR J 10 ARG 0.001 0.000 ARG F 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.327 Fit side-chains REVERT: E 11 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6784 (tm-30) REVERT: E 22 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 28 LYS cc_start: 0.8425 (ptpt) cc_final: 0.7363 (mmtm) REVERT: C 11 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6517 (tm-30) REVERT: F 11 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6381 (tm-30) REVERT: G 22 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7827 (tm-30) REVERT: H 11 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6427 (tm-30) REVERT: I 22 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7397 (tm-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1035 time to fit residues: 7.5429 Evaluate side-chains 52 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.094717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.087163 restraints weight = 9772.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.088262 restraints weight = 5204.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.089013 restraints weight = 3510.946| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.8393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2770 Z= 0.325 Angle : 0.784 7.599 3710 Z= 0.418 Chirality : 0.049 0.133 400 Planarity : 0.003 0.016 480 Dihedral : 5.923 19.028 370 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 36.07 % Favored : 63.93 % 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: -3.29 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 6 PHE 0.019 0.003 PHE C 20 TYR 0.011 0.003 TYR H 10 ARG 0.001 0.000 ARG I 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 964.27 seconds wall clock time: 18 minutes 7.13 seconds (1087.13 seconds total)