Starting phenix.real_space_refine on Wed Mar 5 16:27:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8owj_17238/03_2025/8owj_17238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8owj_17238/03_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_17238/03_2025/8owj_17238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8owj_17238/03_2025/8owj_17238.map" model { file = "/net/cci-nas-00/data/ceres_data/8owj_17238/03_2025/8owj_17238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8owj_17238/03_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-5624/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: 2.24, 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: 0.60 Conformation dependent library (CDL) restraints added in 341.9 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: 0.34 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: 0.73 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: 0.03 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: 0.010 Normalize map: mean=0, sd=1: 0.600 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- 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 : 0.324 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: 0.1176 time to fit residues: 15.7614 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 : 0.284 ------------------------------------------------------------------------------- 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 = 0.092709 restraints weight = 5038.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.093422 restraints weight = 3571.383| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.290 Fit side-chains REVERT: E 11 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6077 (tm-30) REVERT: E 22 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7575 (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: 0.7225 (m-80) REVERT: C 11 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6528 (tm-30) REVERT: F 11 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7091 (tm-30) REVERT: G 19 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.6450 (m-80) REVERT: G 22 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7465 (tm-30) REVERT: I 35 MET cc_start: 0.7919 (ptp) cc_final: 0.7475 (ptt) REVERT: J 11 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6737 (tm-30) REVERT: J 22 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7856 (tm-30) REVERT: J 35 MET cc_start: 0.7592 (ptp) cc_final: 0.7349 (ptt) outliers start: 4 outliers final: 0 residues processed: 49 average time/residue: 0.1080 time to fit residues: 6.8253 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 : 0.317 ------------------------------------------------------------------------------- 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: 9.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 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: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.097213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.088118 restraints weight = 9356.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.089166 restraints weight = 5385.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.089941 restraints weight = 3861.256| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2770 Z= 0.377 Angle : 0.761 7.300 3710 Z= 0.429 Chirality : 0.049 0.128 400 Planarity : 0.003 0.015 480 Dihedral : 6.771 18.436 370 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.71 % Allowed : 24.64 % Favored : 74.64 % 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: -2.49 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 6 PHE 0.021 0.003 PHE G 20 TYR 0.016 0.003 TYR D 10 ARG 0.002 0.001 ARG I 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: 2 poor density : 37 time to evaluate : 0.325 Fit side-chains REVERT: E 11 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6600 (tm-30) REVERT: E 22 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7973 (tm-30) REVERT: B 19 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: C 11 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6890 (tm-30) REVERT: G 19 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.6796 (m-80) REVERT: H 11 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7080 (tm-30) REVERT: I 35 MET cc_start: 0.7665 (ptp) cc_final: 0.7117 (ptt) REVERT: J 11 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6604 (tm-30) REVERT: J 35 MET cc_start: 0.7506 (ptp) cc_final: 0.7149 (ptt) outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 0.1162 time to fit residues: 5.9015 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 : 0.327 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 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 = 0.3906 r_free = 0.3906 target = 0.094889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.086077 restraints weight = 9613.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.087171 restraints weight = 5546.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.087880 restraints weight = 3924.677| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2770 Z= 0.419 Angle : 0.772 5.670 3710 Z= 0.440 Chirality : 0.050 0.134 400 Planarity : 0.003 0.014 480 Dihedral : 6.842 19.015 370 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.86 % Allowed : 23.93 % 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: -2.57 (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 0.021 0.003 PHE G 20 TYR 0.015 0.004 TYR C 10 ARG 0.002 0.001 ARG I 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 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.317 Fit side-chains REVERT: E 11 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6769 (tm-30) REVERT: E 22 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 28 LYS cc_start: 0.8169 (ptpt) cc_final: 0.7060 (tptp) REVERT: B 19 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: C 11 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6564 (tm-30) REVERT: C 19 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.6890 (m-10) REVERT: D 22 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7620 (tm-30) REVERT: D 35 MET cc_start: 0.7525 (ptp) cc_final: 0.7281 (ttm) REVERT: F 11 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6960 (tm-30) REVERT: G 19 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: H 11 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6704 (tm-30) REVERT: H 19 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7024 (m-10) REVERT: I 22 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7976 (tm-30) REVERT: I 35 MET cc_start: 0.8034 (ptp) cc_final: 0.7472 (ptt) REVERT: J 11 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6631 (tm-30) REVERT: J 35 MET cc_start: 0.7437 (ptp) cc_final: 0.6965 (ptt) outliers start: 8 outliers final: 1 residues processed: 47 average time/residue: 0.1185 time to fit residues: 7.0959 Evaluate side-chains 36 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 D 27 ASN I 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.095157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.087527 restraints weight = 10111.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.088552 restraints weight = 5597.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.089250 restraints weight = 3859.445| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.7290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2770 Z= 0.421 Angle : 0.759 7.243 3710 Z= 0.432 Chirality : 0.050 0.130 400 Planarity : 0.003 0.014 480 Dihedral : 6.819 19.064 370 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.50 % Allowed : 25.00 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS E 6 PHE 0.021 0.003 PHE G 20 TYR 0.015 0.004 TYR C 10 ARG 0.003 0.001 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 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.323 Fit side-chains REVERT: E 11 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6961 (tm-30) REVERT: E 22 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 28 LYS cc_start: 0.8285 (ptpt) cc_final: 0.7084 (tptp) REVERT: B 19 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: B 22 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7382 (tm-30) REVERT: C 11 GLU cc_start: 0.7530 (tm-30) cc_final: 0.6551 (tm-30) REVERT: C 19 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.6878 (m-10) REVERT: D 11 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7176 (tm-30) REVERT: D 35 MET cc_start: 0.7629 (ptp) cc_final: 0.7331 (ttm) REVERT: F 11 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6934 (tm-30) REVERT: G 11 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6977 (tm-30) REVERT: G 19 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: G 39 VAL cc_start: 0.9091 (t) cc_final: 0.8732 (t) REVERT: H 11 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6579 (tm-30) REVERT: H 19 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: J 11 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6803 (tm-30) outliers start: 7 outliers final: 1 residues processed: 48 average time/residue: 0.1107 time to fit residues: 6.8422 Evaluate side-chains 40 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain J 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: 8.9990 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.095462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.087596 restraints weight = 10180.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.088696 restraints weight = 5585.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.089396 restraints weight = 3813.728| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.7488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2770 Z= 0.363 Angle : 0.739 7.368 3710 Z= 0.414 Chirality : 0.049 0.135 400 Planarity : 0.003 0.013 480 Dihedral : 6.431 18.539 370 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.43 % Allowed : 27.86 % Favored : 70.71 % 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: -2.97 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 6 PHE 0.019 0.002 PHE G 20 TYR 0.013 0.003 TYR C 10 ARG 0.002 0.000 ARG E 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 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.360 Fit side-chains REVERT: E 11 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6894 (tm-30) REVERT: A 28 LYS cc_start: 0.8254 (ptpt) cc_final: 0.7009 (mmtm) REVERT: B 19 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: B 22 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7393 (tm-30) REVERT: C 11 GLU cc_start: 0.7596 (tm-30) cc_final: 0.6573 (tm-30) REVERT: D 35 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7328 (ttm) REVERT: F 11 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6529 (tm-30) REVERT: G 11 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6537 (tm-30) REVERT: G 19 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: G 22 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7932 (tm-30) REVERT: H 11 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6731 (tm-30) REVERT: I 22 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7672 (tm-30) REVERT: J 11 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6788 (tm-30) outliers start: 4 outliers final: 0 residues processed: 48 average time/residue: 0.1135 time to fit residues: 7.0130 Evaluate side-chains 40 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain G 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: 3.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.095775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.087766 restraints weight = 10205.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.088973 restraints weight = 5482.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.089670 restraints weight = 3659.531| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.7693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2770 Z= 0.307 Angle : 0.712 7.287 3710 Z= 0.396 Chirality : 0.049 0.133 400 Planarity : 0.003 0.010 480 Dihedral : 6.074 17.663 370 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.43 % Allowed : 29.29 % Favored : 69.29 % 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: -3.04 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 6 PHE 0.017 0.003 PHE G 20 TYR 0.010 0.003 TYR C 10 ARG 0.001 0.000 ARG B 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 52 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.366 Fit side-chains REVERT: E 11 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6889 (tm-30) REVERT: A 28 LYS cc_start: 0.8285 (ptpt) cc_final: 0.7128 (mmtm) REVERT: C 11 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6627 (tm-30) REVERT: D 35 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7366 (ttm) REVERT: F 11 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6604 (tm-30) REVERT: F 19 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: G 11 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6638 (tm-30) REVERT: G 22 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7854 (tm-30) REVERT: H 11 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6648 (tm-30) REVERT: I 22 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7475 (tm-30) REVERT: J 11 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6691 (tm-30) outliers start: 4 outliers final: 1 residues processed: 49 average time/residue: 0.1060 time to fit residues: 6.7419 Evaluate side-chains 45 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain F 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: 10.0000 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.095297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.087406 restraints weight = 9882.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.088545 restraints weight = 5285.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.089230 restraints weight = 3593.390| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2770 Z= 0.310 Angle : 0.757 7.608 3710 Z= 0.410 Chirality : 0.049 0.133 400 Planarity : 0.002 0.009 480 Dihedral : 6.009 18.075 370 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.71 % Allowed : 32.50 % Favored : 66.79 % 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: -3.10 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 6 PHE 0.017 0.002 PHE G 20 TYR 0.010 0.003 TYR F 10 ARG 0.001 0.000 ARG I 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 54 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.297 Fit side-chains REVERT: E 11 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6868 (tm-30) REVERT: A 28 LYS cc_start: 0.8317 (ptpt) cc_final: 0.7225 (mmtm) REVERT: C 11 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6480 (tm-30) REVERT: F 11 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6460 (tm-30) REVERT: F 19 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: G 11 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6542 (tm-30) REVERT: G 22 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7788 (tm-30) REVERT: H 11 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6564 (tm-30) REVERT: I 22 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7362 (tm-30) REVERT: J 11 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6672 (tm-30) outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 0.1053 time to fit residues: 7.2606 Evaluate side-chains 45 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.095287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.087363 restraints weight = 9913.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.088572 restraints weight = 5313.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.089317 restraints weight = 3557.774| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.8073 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= 0.323 Angle : 0.775 7.649 3710 Z= 0.419 Chirality : 0.049 0.134 400 Planarity : 0.003 0.014 480 Dihedral : 5.998 18.203 370 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 0.36 % Allowed : 32.86 % Favored : 66.79 % 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: -3.21 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 6 PHE 0.017 0.002 PHE G 20 TYR 0.013 0.003 TYR I 10 ARG 0.001 0.000 ARG E 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: 1 poor density : 51 time to evaluate : 0.296 Fit side-chains REVERT: E 11 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6967 (tm-30) REVERT: A 28 LYS cc_start: 0.8363 (ptpt) cc_final: 0.7316 (mmtm) REVERT: A 35 MET cc_start: 0.7084 (ttt) cc_final: 0.6788 (ttt) REVERT: C 11 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6471 (tm-30) REVERT: F 11 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6505 (tm-30) REVERT: F 19 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7832 (m-10) REVERT: G 11 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6812 (tm-30) REVERT: G 22 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7852 (tm-30) REVERT: H 11 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6635 (tm-30) REVERT: I 22 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7396 (tm-30) REVERT: J 11 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6782 (tm-30) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.0960 time to fit residues: 6.5339 Evaluate side-chains 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F 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: 7.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.095275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.087265 restraints weight = 9929.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.088507 restraints weight = 5332.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.089244 restraints weight = 3565.142| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.8195 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= 0.323 Angle : 0.790 7.757 3710 Z= 0.422 Chirality : 0.049 0.133 400 Planarity : 0.002 0.014 480 Dihedral : 5.972 18.430 370 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.36 % Allowed : 33.57 % 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: -3.31 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 6 PHE 0.017 0.002 PHE G 20 TYR 0.011 0.003 TYR H 10 ARG 0.002 0.000 ARG I 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 55 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.314 Fit side-chains REVERT: E 11 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6858 (tm-30) REVERT: A 28 LYS cc_start: 0.8402 (ptpt) cc_final: 0.7303 (mmtm) REVERT: C 11 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6438 (tm-30) REVERT: F 11 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6382 (tm-30) REVERT: F 19 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: G 11 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6791 (tm-30) REVERT: G 22 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7852 (tm-30) REVERT: H 11 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6587 (tm-30) REVERT: I 22 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7306 (tm-30) REVERT: J 11 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6806 (tm-30) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.0969 time to fit residues: 6.9766 Evaluate side-chains 53 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 PHE 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: 10.0000 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.092902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.084302 restraints weight = 9558.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.085657 restraints weight = 5164.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.086380 restraints weight = 3478.086| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.8405 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= 0.448 Angle : 0.866 7.132 3710 Z= 0.465 Chirality : 0.050 0.130 400 Planarity : 0.003 0.011 480 Dihedral : 6.507 20.054 370 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 0.71 % Allowed : 35.00 % Favored : 64.29 % 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: -3.40 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 6 PHE 0.018 0.003 PHE G 20 TYR 0.017 0.004 TYR I 10 ARG 0.002 0.001 ARG I 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 993.03 seconds wall clock time: 18 minutes 30.34 seconds (1110.34 seconds total)