Starting phenix.real_space_refine on Fri Aug 22 12:58:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8owj_17238/08_2025/8owj_17238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8owj_17238/08_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_17238/08_2025/8owj_17238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8owj_17238/08_2025/8owj_17238.map" model { file = "/net/cci-nas-00/data/ceres_data/8owj_17238/08_2025/8owj_17238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8owj_17238/08_2025/8owj_17238.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.70, per 1000 atoms: 0.26 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: 0.23 Conformation dependent library (CDL) restraints added in 102.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.12 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: 0.42 Time building geometry restraints manager: 0.31 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: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.780 Find NCS groups from input model: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.070 ------------------------------------------------------------------------------- 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= 0.786 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 : 8.75 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG F 5 TYR 0.004 0.001 TYR E 10 PHE 0.041 0.014 PHE B 20 HIS 0.019 0.010 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.01211 ( 2770) covalent geometry : angle 2.25552 ( 3710) hydrogen bonds : bond 0.19778 ( 79) hydrogen bonds : angle 9.77856 ( 234) *********************** 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 : 0.068 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: 0.0426 time to fit residues: 5.8254 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 : 0.068 ------------------------------------------------------------------------------- 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 27 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 HIS E 27 ASN A 6 HIS C 27 ASN D 14 HIS H 27 ASN I 14 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.103612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.092920 restraints weight = 8413.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.094276 restraints weight = 4834.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.095047 restraints weight = 3457.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.095559 restraints weight = 2794.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.095927 restraints weight = 2438.839| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2770 Z= 0.173 Angle : 0.726 6.970 3710 Z= 0.402 Chirality : 0.048 0.133 400 Planarity : 0.003 0.011 480 Dihedral : 6.644 17.375 376 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 17.14 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.36), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.28), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 5 TYR 0.009 0.002 TYR D 10 PHE 0.008 0.001 PHE A 19 HIS 0.007 0.002 HIS H 6 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2770) covalent geometry : angle 0.72587 ( 3710) hydrogen bonds : bond 0.02737 ( 79) hydrogen bonds : angle 5.74096 ( 234) *********************** 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 46 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.121 Fit side-chains REVERT: E 11 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6614 (tm-30) REVERT: E 22 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 35 MET cc_start: 0.8052 (ptp) cc_final: 0.7555 (ptt) REVERT: B 22 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7433 (tm-30) REVERT: C 11 GLU cc_start: 0.7001 (tm-30) cc_final: 0.5991 (tm-30) REVERT: D 11 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6887 (tm-30) REVERT: F 11 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6769 (tm-30) REVERT: G 19 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6425 (m-80) REVERT: G 22 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7487 (tm-30) REVERT: I 35 MET cc_start: 0.7861 (ptp) cc_final: 0.7479 (ptt) REVERT: J 11 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6928 (tm-30) REVERT: J 22 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7866 (tm-30) outliers start: 3 outliers final: 0 residues processed: 46 average time/residue: 0.0429 time to fit residues: 2.6486 Evaluate side-chains 33 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 0 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.097412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.088224 restraints weight = 9435.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.089255 restraints weight = 5478.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.090041 restraints weight = 3940.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.090494 restraints weight = 3170.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.090756 restraints weight = 2736.363| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.6188 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= 0.276 Angle : 0.749 7.313 3710 Z= 0.424 Chirality : 0.048 0.130 400 Planarity : 0.004 0.014 480 Dihedral : 6.928 19.325 370 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.71 % Allowed : 23.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.37), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.28), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 5 TYR 0.014 0.003 TYR A 10 PHE 0.020 0.003 PHE G 20 HIS 0.007 0.003 HIS E 6 Details of bonding type rmsd covalent geometry : bond 0.00592 ( 2770) covalent geometry : angle 0.74859 ( 3710) hydrogen bonds : bond 0.02409 ( 79) hydrogen bonds : angle 5.13597 ( 234) *********************** 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 : 0.080 Fit side-chains REVERT: E 11 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6773 (tm-30) REVERT: E 22 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7946 (tm-30) REVERT: A 11 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6671 (pm20) REVERT: B 19 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: C 11 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6934 (tm-30) REVERT: D 15 GLN cc_start: 0.8030 (mt0) cc_final: 0.7492 (mp10) REVERT: G 19 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.6888 (m-80) REVERT: H 11 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7039 (tm-30) REVERT: H 35 MET cc_start: 0.7719 (ptp) cc_final: 0.7479 (ptp) REVERT: I 15 GLN cc_start: 0.8019 (mt0) cc_final: 0.7407 (mp10) REVERT: I 35 MET cc_start: 0.7751 (ptp) cc_final: 0.7230 (ptt) REVERT: J 11 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6613 (tm-30) outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 0.0401 time to fit residues: 2.0542 Evaluate side-chains 27 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 16 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.095551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.086295 restraints weight = 9325.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.087296 restraints weight = 5431.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.088056 restraints weight = 3940.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.088522 restraints weight = 3179.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.088795 restraints weight = 2752.938| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2770 Z= 0.232 Angle : 0.716 5.904 3710 Z= 0.406 Chirality : 0.049 0.134 400 Planarity : 0.003 0.015 480 Dihedral : 6.491 18.891 370 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.71 % Allowed : 24.29 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 5 TYR 0.013 0.003 TYR D 10 PHE 0.019 0.002 PHE G 20 HIS 0.006 0.002 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 2770) covalent geometry : angle 0.71562 ( 3710) hydrogen bonds : bond 0.02155 ( 79) hydrogen bonds : angle 4.99058 ( 234) *********************** 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 42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.113 Fit side-chains REVERT: E 11 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6749 (tm-30) REVERT: B 19 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: B 22 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 11 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6422 (tm-30) REVERT: C 35 MET cc_start: 0.8259 (ptp) cc_final: 0.7835 (ttp) REVERT: D 22 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7429 (tm-30) REVERT: D 35 MET cc_start: 0.7687 (ptp) cc_final: 0.7464 (ttm) REVERT: F 11 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6871 (tm-30) REVERT: G 19 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: H 11 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6597 (tm-30) REVERT: I 22 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7970 (tm-30) REVERT: I 35 MET cc_start: 0.7961 (ptp) cc_final: 0.7462 (ptt) REVERT: J 11 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6718 (tm-30) outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 0.0402 time to fit residues: 2.2700 Evaluate side-chains 31 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain G residue 19 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.093924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.085135 restraints weight = 9684.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.086269 restraints weight = 5596.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.086932 restraints weight = 3985.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.087365 restraints weight = 3206.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.087666 restraints weight = 2781.258| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 2770 Z= 0.316 Angle : 0.766 6.048 3710 Z= 0.442 Chirality : 0.050 0.129 400 Planarity : 0.004 0.011 480 Dihedral : 6.959 19.236 370 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.86 % Allowed : 22.14 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 5 TYR 0.017 0.004 TYR I 10 PHE 0.021 0.003 PHE G 20 HIS 0.007 0.003 HIS E 6 Details of bonding type rmsd covalent geometry : bond 0.00673 ( 2770) covalent geometry : angle 0.76636 ( 3710) hydrogen bonds : bond 0.02260 ( 79) hydrogen bonds : angle 5.07554 ( 234) *********************** 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: 8 poor density : 39 time to evaluate : 0.091 Fit side-chains REVERT: E 11 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7101 (tm-30) REVERT: A 28 LYS cc_start: 0.8304 (ptpt) cc_final: 0.7137 (tptp) REVERT: B 19 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: C 11 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6550 (tm-30) REVERT: C 19 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.6908 (m-10) REVERT: D 11 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7223 (tm-30) REVERT: D 22 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8032 (tm-30) REVERT: D 35 MET cc_start: 0.7689 (ptp) cc_final: 0.7354 (ttm) REVERT: F 11 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7062 (tm-30) REVERT: G 11 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7075 (tm-30) REVERT: G 19 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.6836 (m-80) REVERT: G 20 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7655 (t80) REVERT: H 11 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6719 (tm-30) REVERT: H 19 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7131 (m-10) REVERT: I 22 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7647 (tm-30) REVERT: J 11 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6762 (tm-30) outliers start: 8 outliers final: 1 residues processed: 46 average time/residue: 0.0452 time to fit residues: 2.6964 Evaluate side-chains 37 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 G residue 20 PHE Chi-restraints excluded: chain H residue 19 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 19 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 = 0.3917 r_free = 0.3917 target = 0.094122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.086661 restraints weight = 10262.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.087661 restraints weight = 5660.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.088377 restraints weight = 3884.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.088739 restraints weight = 2996.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.088930 restraints weight = 2522.142| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.7445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 2770 Z= 0.288 Angle : 0.740 5.491 3710 Z= 0.429 Chirality : 0.049 0.133 400 Planarity : 0.003 0.010 480 Dihedral : 6.769 18.720 370 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.50 % Allowed : 23.57 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 5 TYR 0.015 0.004 TYR F 10 PHE 0.020 0.003 PHE G 20 HIS 0.006 0.003 HIS E 6 Details of bonding type rmsd covalent geometry : bond 0.00613 ( 2770) covalent geometry : angle 0.73978 ( 3710) hydrogen bonds : bond 0.02235 ( 79) hydrogen bonds : angle 4.95933 ( 234) *********************** 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 53 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.109 Fit side-chains REVERT: E 11 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7068 (tm-30) REVERT: A 28 LYS cc_start: 0.8324 (ptpt) cc_final: 0.7099 (mmtm) REVERT: B 19 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: C 11 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6527 (tm-30) REVERT: C 19 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.6892 (m-10) REVERT: C 35 MET cc_start: 0.8326 (ttp) cc_final: 0.8122 (ttp) REVERT: D 11 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6990 (tm-30) REVERT: D 22 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7984 (tm-30) REVERT: D 35 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7605 (ttm) REVERT: F 11 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6512 (tm-30) REVERT: G 11 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6723 (tm-30) REVERT: G 19 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: G 22 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8004 (tm-30) REVERT: H 11 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6856 (tm-30) REVERT: H 19 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: I 22 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7749 (tm-30) REVERT: J 11 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6819 (tm-30) outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 0.0444 time to fit residues: 3.0198 Evaluate side-chains 42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 19 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 overall best weight: 7.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN H 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.092857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.085591 restraints weight = 10409.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.086600 restraints weight = 5704.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.087279 restraints weight = 3882.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.087659 restraints weight = 2999.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.087922 restraints weight = 2513.441| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.7790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 2770 Z= 0.337 Angle : 0.804 6.702 3710 Z= 0.464 Chirality : 0.050 0.131 400 Planarity : 0.004 0.010 480 Dihedral : 6.856 18.770 370 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 27.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.57 % Allowed : 26.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 5 TYR 0.018 0.004 TYR C 10 PHE 0.019 0.003 PHE G 20 HIS 0.008 0.003 HIS E 6 Details of bonding type rmsd covalent geometry : bond 0.00714 ( 2770) covalent geometry : angle 0.80390 ( 3710) hydrogen bonds : bond 0.02313 ( 79) hydrogen bonds : angle 5.09716 ( 234) *********************** 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 53 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.119 Fit side-chains REVERT: E 11 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6965 (tm-30) REVERT: A 28 LYS cc_start: 0.8461 (ptpt) cc_final: 0.7375 (mmtm) REVERT: B 19 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: C 11 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6425 (tm-30) REVERT: C 19 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7062 (m-10) REVERT: D 22 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7925 (tm-30) REVERT: D 35 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7605 (ttm) REVERT: F 11 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6540 (tm-30) REVERT: G 11 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7186 (tm-30) REVERT: G 19 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: H 11 GLU cc_start: 0.7496 (tm-30) cc_final: 0.6737 (tm-30) REVERT: H 19 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.6663 (m-10) REVERT: I 22 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7642 (tm-30) REVERT: J 11 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6951 (tm-30) outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 0.0296 time to fit residues: 2.0479 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 : 0.117 ------------------------------------------------------------------------------- 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 D 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.094812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.087084 restraints weight = 10225.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.088199 restraints weight = 5473.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.088908 restraints weight = 3650.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.089375 restraints weight = 2783.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.089658 restraints weight = 2328.543| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.7830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2770 Z= 0.181 Angle : 0.686 7.948 3710 Z= 0.389 Chirality : 0.050 0.135 400 Planarity : 0.002 0.012 480 Dihedral : 5.946 17.281 370 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.26 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 5 TYR 0.009 0.002 TYR C 10 PHE 0.019 0.002 PHE J 20 HIS 0.004 0.002 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 2770) covalent geometry : angle 0.68613 ( 3710) hydrogen bonds : bond 0.02008 ( 79) hydrogen bonds : angle 4.70336 ( 234) *********************** 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 : 0.068 Fit side-chains REVERT: E 11 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 28 LYS cc_start: 0.8380 (ptpt) cc_final: 0.7333 (mmtm) REVERT: C 11 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6577 (tm-30) REVERT: D 11 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6822 (tm-30) REVERT: D 22 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7948 (tm-30) REVERT: D 35 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7553 (ttm) REVERT: F 11 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6590 (tm-30) REVERT: G 11 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6749 (tm-30) REVERT: G 22 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7950 (tm-30) REVERT: H 11 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6724 (tm-30) REVERT: H 35 MET cc_start: 0.8107 (ttp) cc_final: 0.7789 (ttm) REVERT: I 22 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7545 (tm-30) REVERT: J 11 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6681 (tm-30) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.0392 time to fit residues: 2.6352 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 : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.094783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.086972 restraints weight = 10297.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.088128 restraints weight = 5446.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.088863 restraints weight = 3611.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.089348 restraints weight = 2736.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.089504 restraints weight = 2269.342| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.7934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2770 Z= 0.178 Angle : 0.699 8.147 3710 Z= 0.388 Chirality : 0.049 0.135 400 Planarity : 0.002 0.009 480 Dihedral : 5.709 16.002 370 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.36 % Allowed : 31.07 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.33 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 5 TYR 0.009 0.002 TYR I 10 PHE 0.019 0.002 PHE J 20 HIS 0.004 0.002 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 2770) covalent geometry : angle 0.69873 ( 3710) hydrogen bonds : bond 0.01866 ( 79) hydrogen bonds : angle 4.47764 ( 234) *********************** 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 : 0.115 Fit side-chains REVERT: E 11 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6771 (tm-30) REVERT: A 28 LYS cc_start: 0.8381 (ptpt) cc_final: 0.7318 (mmtm) REVERT: C 11 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6489 (tm-30) REVERT: D 11 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6794 (tm-30) REVERT: D 22 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7825 (tm-30) REVERT: F 11 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6531 (tm-30) REVERT: G 11 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6711 (tm-30) REVERT: G 22 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7938 (tm-30) REVERT: H 11 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6615 (tm-30) REVERT: H 35 MET cc_start: 0.8083 (ttp) cc_final: 0.7837 (ttm) REVERT: I 22 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7432 (tm-30) REVERT: J 11 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6663 (tm-30) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.0410 time to fit residues: 2.7610 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.092950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.085723 restraints weight = 10497.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.086791 restraints weight = 5540.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.087472 restraints weight = 3671.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.087916 restraints weight = 2832.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.088140 restraints weight = 2364.318| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.8123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2770 Z= 0.273 Angle : 0.777 7.598 3710 Z= 0.437 Chirality : 0.049 0.133 400 Planarity : 0.003 0.012 480 Dihedral : 6.284 17.750 370 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 0.36 % Allowed : 30.71 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 5 TYR 0.016 0.004 TYR I 10 PHE 0.018 0.003 PHE G 20 HIS 0.006 0.002 HIS E 6 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 2770) covalent geometry : angle 0.77725 ( 3710) hydrogen bonds : bond 0.02018 ( 79) hydrogen bonds : angle 4.73819 ( 234) ********************** 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 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.117 Fit side-chains REVERT: E 11 GLU cc_start: 0.7281 (tm-30) cc_final: 0.7052 (tm-30) REVERT: A 28 LYS cc_start: 0.8515 (ptpt) cc_final: 0.7381 (mmtm) REVERT: C 11 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6400 (tm-30) REVERT: D 11 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6861 (tm-30) REVERT: D 22 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8013 (tm-30) REVERT: F 11 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6603 (tm-30) REVERT: F 19 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: G 22 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7982 (tm-30) REVERT: H 11 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6815 (tm-30) REVERT: H 35 MET cc_start: 0.8155 (ttp) cc_final: 0.7794 (ttm) REVERT: I 22 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7567 (tm-30) REVERT: J 11 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6901 (tm-30) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.0432 time to fit residues: 2.8227 Evaluate side-chains 48 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 5 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.094116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.086378 restraints weight = 10055.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.087436 restraints weight = 5359.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.088109 restraints weight = 3652.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.088601 restraints weight = 2839.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.088863 restraints weight = 2357.784| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.8169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2770 Z= 0.201 Angle : 0.753 8.257 3710 Z= 0.415 Chirality : 0.050 0.136 400 Planarity : 0.003 0.024 480 Dihedral : 5.922 16.611 370 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 20.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 5 TYR 0.010 0.003 TYR H 10 PHE 0.019 0.002 PHE J 20 HIS 0.005 0.002 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 2770) covalent geometry : angle 0.75285 ( 3710) hydrogen bonds : bond 0.01899 ( 79) hydrogen bonds : angle 4.60783 ( 234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 535.54 seconds wall clock time: 10 minutes 0.76 seconds (600.76 seconds total)