Starting phenix.real_space_refine on Tue Aug 4 12:04:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9r_65786/08_2026/9w9r_65786.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9r_65786/08_2026/9w9r_65786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9r_65786/08_2026/9w9r_65786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9r_65786/08_2026/9w9r_65786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9r_65786/08_2026/9w9r_65786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9r_65786/08_2026/9w9r_65786.map" } resolution = 2.33 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= 0.000 sd= 0.003 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 3 5.16 5 C 1389 2.51 5 N 351 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2145 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 0.71, per 1000 atoms: 0.33 Number of scatterers: 2145 At special positions: 0 Unit cell: (66.03, 85.56, 31.62, 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 3 16.00 O 402 8.00 N 351 7.00 C 1389 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: 0.16 Conformation dependent library (CDL) restraints added in 84.1 milliseconds 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 522 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 49.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 16 removed outlier: 6.271A pdb=" N LEU A 12 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LYS B 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 6.573A pdb=" N VAL A 20 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 34 removed outlier: 6.379A pdb=" N ALA A 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL C 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN A 27 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL C 30 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA A 29 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL C 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ARG C 34 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE A 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.326A pdb=" N THR A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 9.272A pdb=" N VAL A 65 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE B 68 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A 67 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A 66 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY C 67 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 73 removed outlier: 6.296A pdb=" N GLU A 72 " --> pdb=" O ILE B 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 80 removed outlier: 9.292A pdb=" N LYS A 76 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N TRP B 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR A 78 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER A 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR C 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 99 removed outlier: 6.361A pdb=" N GLU A 92 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE B 95 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 94 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER B 97 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 96 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ASP B 99 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN A 98 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 110 removed outlier: 9.070A pdb=" N TYR A 105 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N ALA B 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE A 107 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LEU B 110 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 109 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR C 105 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 106 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE C 107 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA A 108 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.904A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 118 through 122 removed outlier: 5.655A pdb=" N THR A 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL C 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 111 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: 0.17 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 666 1.34 - 1.46: 464 1.46 - 1.57: 1060 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 2196 Sorted by residual: bond pdb=" CG1 ILE A 107 " pdb=" CD1 ILE A 107 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.48e-01 bond pdb=" CG1 ILE B 107 " pdb=" CD1 ILE B 107 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.41e-01 bond pdb=" CG1 ILE C 107 " pdb=" CD1 ILE C 107 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.38e-01 bond pdb=" CD ARG B 34 " pdb=" NE ARG B 34 " ideal model delta sigma weight residual 1.458 1.468 -0.010 1.40e-02 5.10e+03 4.67e-01 bond pdb=" CD ARG A 34 " pdb=" NE ARG A 34 " ideal model delta sigma weight residual 1.458 1.467 -0.009 1.40e-02 5.10e+03 4.33e-01 ... (remaining 2191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 2838 1.18 - 2.36: 121 2.36 - 3.54: 17 3.54 - 4.72: 9 4.72 - 5.90: 3 Bond angle restraints: 2988 Sorted by residual: angle pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " pdb=" NE ARG A 34 " ideal model delta sigma weight residual 112.00 117.90 -5.90 2.20e+00 2.07e-01 7.19e+00 angle pdb=" CG ARG B 34 " pdb=" CD ARG B 34 " pdb=" NE ARG B 34 " ideal model delta sigma weight residual 112.00 117.89 -5.89 2.20e+00 2.07e-01 7.17e+00 angle pdb=" CG ARG C 34 " pdb=" CD ARG C 34 " pdb=" NE ARG C 34 " ideal model delta sigma weight residual 112.00 117.88 -5.88 2.20e+00 2.07e-01 7.15e+00 angle pdb=" CD ARG C 34 " pdb=" NE ARG C 34 " pdb=" CZ ARG C 34 " ideal model delta sigma weight residual 124.40 128.06 -3.66 1.40e+00 5.10e-01 6.82e+00 angle pdb=" CD ARG A 34 " pdb=" NE ARG A 34 " pdb=" CZ ARG A 34 " ideal model delta sigma weight residual 124.40 128.04 -3.64 1.40e+00 5.10e-01 6.75e+00 ... (remaining 2983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.76: 1056 11.76 - 23.52: 156 23.52 - 35.29: 48 35.29 - 47.05: 21 47.05 - 58.81: 18 Dihedral angle restraints: 1299 sinusoidal: 495 harmonic: 804 Sorted by residual: dihedral pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " pdb=" NE ARG A 34 " pdb=" CZ ARG A 34 " ideal model delta sinusoidal sigma weight residual -90.00 -40.13 -49.87 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CG ARG B 34 " pdb=" CD ARG B 34 " pdb=" NE ARG B 34 " pdb=" CZ ARG B 34 " ideal model delta sinusoidal sigma weight residual -90.00 -40.14 -49.86 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CG ARG C 34 " pdb=" CD ARG C 34 " pdb=" NE ARG C 34 " pdb=" CZ ARG C 34 " ideal model delta sinusoidal sigma weight residual -90.00 -40.19 -49.81 2 1.50e+01 4.44e-03 1.24e+01 ... (remaining 1296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 178 0.025 - 0.051: 90 0.051 - 0.076: 35 0.076 - 0.102: 12 0.102 - 0.127: 39 Chirality restraints: 354 Sorted by residual: chirality pdb=" CA ILE C 107 " pdb=" N ILE C 107 " pdb=" C ILE C 107 " pdb=" CB ILE C 107 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE A 107 " pdb=" N ILE A 107 " pdb=" C ILE A 107 " pdb=" CB ILE A 107 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 351 not shown) Planarity restraints: 366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 34 " 0.142 9.50e-02 1.11e+02 6.42e-02 3.28e+00 pdb=" NE ARG B 34 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 34 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 34 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 34 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 34 " 0.142 9.50e-02 1.11e+02 6.42e-02 3.27e+00 pdb=" NE ARG A 34 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 34 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 34 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 34 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 34 " 0.142 9.50e-02 1.11e+02 6.42e-02 3.24e+00 pdb=" NE ARG C 34 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 34 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 34 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 34 " 0.000 2.00e-02 2.50e+03 ... (remaining 363 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 696 2.87 - 3.38: 1658 3.38 - 3.88: 3738 3.88 - 4.39: 3839 4.39 - 4.90: 7624 Nonbonded interactions: 17555 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" OH TYR C 105 " model vdw 2.360 3.040 nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR C 114 " model vdw 2.361 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" OG1 THR B 119 " model vdw 2.362 3.040 nonbonded pdb=" OH TYR A 105 " pdb=" OD2 ASP B 74 " model vdw 2.369 3.040 nonbonded pdb=" NZ LYS A 76 " pdb=" OD1 ASP C 74 " model vdw 2.373 3.120 ... (remaining 17550 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.660 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.003 0.029 2196 Z= 0.120 Angle : 0.607 5.899 2988 Z= 0.339 Chirality : 0.049 0.127 354 Planarity : 0.007 0.064 366 Dihedral : 15.547 58.810 777 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 18.99 % Favored : 81.01 % 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 are not related in a simple way. whole: -2.34 (0.43), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG B 34 TYR 0.020 0.002 TYR A 114 PHE 0.012 0.002 PHE C 64 TRP 0.002 0.001 TRP A 79 HIS 0.001 0.000 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 2196) covalent geometry : angle 0.60686 / 0.34 ( 2988) hydrogen bonds : bond 0.14011 / 9.81 ( 37) hydrogen bonds : angle 10.08925 / 6.93 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.082 Fit side-chains REVERT: A 21 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7911 (ttt90) REVERT: B 104 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7950 (mtt-85) REVERT: C 35 LYS cc_start: 0.8169 (tttt) cc_final: 0.7863 (tppp) REVERT: C 104 ARG cc_start: 0.8198 (mtt90) cc_final: 0.7814 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.6424 time to fit residues: 34.4891 Evaluate side-chains 53 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.118056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099438 restraints weight = 2261.363| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.54 r_work: 0.3281 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2196 Z= 0.250 Angle : 0.641 3.880 2988 Z= 0.359 Chirality : 0.052 0.154 354 Planarity : 0.005 0.029 366 Dihedral : 5.766 21.423 294 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.27 % Allowed : 18.57 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.47), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG C 34 TYR 0.018 0.002 TYR A 114 PHE 0.014 0.003 PHE A 64 TRP 0.003 0.001 TRP C 79 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 ( 2196) covalent geometry : angle 0.64119 / 0.36 ( 2988) hydrogen bonds : bond 0.03379 / 2.54 ( 37) hydrogen bonds : angle 6.62570 / 4.68 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.050 Fit side-chains REVERT: B 104 ARG cc_start: 0.8421 (mtt90) cc_final: 0.8180 (mtt-85) REVERT: C 35 LYS cc_start: 0.8141 (tttt) cc_final: 0.7832 (tppp) REVERT: C 62 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7867 (mp0) REVERT: C 104 ARG cc_start: 0.8443 (mtt90) cc_final: 0.7978 (mtt-85) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.8006 time to fit residues: 41.3404 Evaluate side-chains 51 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.119272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100702 restraints weight = 2288.780| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.55 r_work: 0.3311 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2196 Z= 0.182 Angle : 0.572 3.861 2988 Z= 0.321 Chirality : 0.050 0.147 354 Planarity : 0.005 0.032 366 Dihedral : 5.616 20.762 294 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.69 % Allowed : 18.14 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.47), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG A 34 TYR 0.018 0.002 TYR A 114 PHE 0.012 0.002 PHE A 64 TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 2196) covalent geometry : angle 0.57182 / 0.32 ( 2988) hydrogen bonds : bond 0.02752 / 2.05 ( 37) hydrogen bonds : angle 6.11455 / 4.32 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.059 Fit side-chains REVERT: A 21 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8140 (ttt90) REVERT: A 66 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: B 13 MET cc_start: 0.8127 (ttt) cc_final: 0.7834 (ttt) REVERT: B 104 ARG cc_start: 0.8445 (mtt90) cc_final: 0.8218 (mtt-85) REVERT: C 35 LYS cc_start: 0.8182 (tttt) cc_final: 0.7878 (tppp) REVERT: C 62 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7725 (mp0) REVERT: C 104 ARG cc_start: 0.8429 (mtt90) cc_final: 0.7970 (mtt-85) outliers start: 4 outliers final: 0 residues processed: 51 average time/residue: 0.6965 time to fit residues: 35.9680 Evaluate side-chains 52 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 66 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.103434 restraints weight = 2254.813| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.55 r_work: 0.3353 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2196 Z= 0.121 Angle : 0.523 4.578 2988 Z= 0.289 Chirality : 0.049 0.139 354 Planarity : 0.004 0.036 366 Dihedral : 5.314 19.847 294 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.69 % Allowed : 18.57 % Favored : 79.75 % 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 are not related in a simple way. whole: -2.13 (0.47), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 104 TYR 0.016 0.001 TYR A 114 PHE 0.010 0.002 PHE A 64 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.000 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 2196) covalent geometry : angle 0.52282 / 0.29 ( 2988) hydrogen bonds : bond 0.02251 / 1.69 ( 37) hydrogen bonds : angle 5.70699 / 4.04 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.087 Fit side-chains REVERT: A 35 LYS cc_start: 0.8156 (tttt) cc_final: 0.7769 (tppp) REVERT: A 66 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: B 13 MET cc_start: 0.8109 (ttt) cc_final: 0.7834 (ttt) REVERT: B 66 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: B 104 ARG cc_start: 0.8422 (mtt90) cc_final: 0.8214 (mtt-85) REVERT: C 13 MET cc_start: 0.8148 (ttt) cc_final: 0.7899 (ttt) REVERT: C 35 LYS cc_start: 0.8200 (tttt) cc_final: 0.7851 (tppp) REVERT: C 62 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7758 (mp0) REVERT: C 104 ARG cc_start: 0.8424 (mtt90) cc_final: 0.8075 (mtt-85) outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.8680 time to fit residues: 46.5838 Evaluate side-chains 52 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain C residue 61 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098358 restraints weight = 2299.509| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.55 r_work: 0.3264 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 2196 Z= 0.321 Angle : 0.691 4.973 2988 Z= 0.384 Chirality : 0.054 0.159 354 Planarity : 0.005 0.029 366 Dihedral : 6.005 20.957 294 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.11 % Allowed : 18.14 % Favored : 79.75 % 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 are not related in a simple way. whole: -2.10 (0.46), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG A 104 TYR 0.016 0.002 TYR B 114 PHE 0.016 0.003 PHE A 64 TRP 0.004 0.002 TRP C 79 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.32 ( 2196) covalent geometry : angle 0.69114 / 0.38 ( 2988) hydrogen bonds : bond 0.03100 / 2.31 ( 37) hydrogen bonds : angle 6.25624 / 4.39 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.086 Fit side-chains REVERT: A 21 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8176 (ttt90) REVERT: A 66 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: B 13 MET cc_start: 0.8154 (ttt) cc_final: 0.7873 (ttt) REVERT: C 35 LYS cc_start: 0.8285 (tttt) cc_final: 0.7941 (tppp) REVERT: C 62 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7726 (mp0) REVERT: C 104 ARG cc_start: 0.8418 (mtt90) cc_final: 0.7980 (mtt-85) outliers start: 5 outliers final: 1 residues processed: 55 average time/residue: 0.8486 time to fit residues: 47.2691 Evaluate side-chains 55 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 66 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.119700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.100802 restraints weight = 2228.187| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.55 r_work: 0.3305 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2196 Z= 0.177 Angle : 0.567 4.205 2988 Z= 0.317 Chirality : 0.050 0.145 354 Planarity : 0.004 0.036 366 Dihedral : 5.669 20.494 294 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.53 % Allowed : 18.99 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.47), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 104 TYR 0.018 0.002 TYR A 114 PHE 0.013 0.002 PHE A 64 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 2196) covalent geometry : angle 0.56655 / 0.32 ( 2988) hydrogen bonds : bond 0.02614 / 1.95 ( 37) hydrogen bonds : angle 5.93510 / 4.18 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.052 Fit side-chains REVERT: A 21 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8127 (ttt90) REVERT: A 35 LYS cc_start: 0.8176 (tttt) cc_final: 0.7750 (tppp) REVERT: A 66 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: B 13 MET cc_start: 0.8150 (ttt) cc_final: 0.7864 (ttt) REVERT: C 35 LYS cc_start: 0.8239 (tttt) cc_final: 0.7867 (tppp) REVERT: C 62 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7710 (mp0) REVERT: C 66 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: C 104 ARG cc_start: 0.8421 (mtt90) cc_final: 0.7979 (mtt-85) outliers start: 6 outliers final: 2 residues processed: 51 average time/residue: 0.8566 time to fit residues: 44.2620 Evaluate side-chains 54 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 66 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.103047 restraints weight = 2254.721| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.53 r_work: 0.3358 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2196 Z= 0.123 Angle : 0.536 5.669 2988 Z= 0.293 Chirality : 0.049 0.140 354 Planarity : 0.004 0.039 366 Dihedral : 5.376 19.790 294 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.53 % Allowed : 18.99 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.47), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 104 TYR 0.016 0.001 TYR A 114 PHE 0.010 0.002 PHE A 64 TRP 0.001 0.001 TRP C 79 HIS 0.002 0.000 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 2196) covalent geometry : angle 0.53574 / 0.29 ( 2988) hydrogen bonds : bond 0.02266 / 1.71 ( 37) hydrogen bonds : angle 5.61027 / 3.97 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.087 Fit side-chains REVERT: A 21 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8099 (ttt90) REVERT: A 35 LYS cc_start: 0.8189 (tttt) cc_final: 0.7762 (tppp) REVERT: A 66 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: B 13 MET cc_start: 0.8133 (ttt) cc_final: 0.7843 (ttt) REVERT: B 66 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: C 13 MET cc_start: 0.8195 (ttt) cc_final: 0.7984 (ttt) REVERT: C 35 LYS cc_start: 0.8244 (tttt) cc_final: 0.7874 (tppp) REVERT: C 62 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7713 (mp0) REVERT: C 66 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: C 104 ARG cc_start: 0.8410 (mtt90) cc_final: 0.7995 (mtt-85) REVERT: C 107 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8202 (mm) outliers start: 6 outliers final: 0 residues processed: 53 average time/residue: 0.8833 time to fit residues: 47.4117 Evaluate side-chains 55 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.118588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099498 restraints weight = 2248.581| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.55 r_work: 0.3283 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 2196 Z= 0.255 Angle : 0.645 5.897 2988 Z= 0.356 Chirality : 0.052 0.153 354 Planarity : 0.005 0.034 366 Dihedral : 5.855 20.832 294 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.38 % Allowed : 18.14 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.47), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG A 104 TYR 0.017 0.002 TYR A 114 PHE 0.014 0.003 PHE A 64 TRP 0.003 0.001 TRP C 79 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 ( 2196) covalent geometry : angle 0.64489 / 0.36 ( 2988) hydrogen bonds : bond 0.02842 / 2.13 ( 37) hydrogen bonds : angle 5.99519 / 4.22 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.053 Fit side-chains REVERT: A 21 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8149 (ttt90) REVERT: A 66 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: B 13 MET cc_start: 0.8137 (ttt) cc_final: 0.7840 (ttt) REVERT: C 35 LYS cc_start: 0.8261 (tttt) cc_final: 0.7933 (tppp) REVERT: C 62 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7726 (mp0) REVERT: C 66 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: C 104 ARG cc_start: 0.8404 (mtt90) cc_final: 0.7973 (mtt-85) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.5871 time to fit residues: 32.0973 Evaluate side-chains 57 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 97 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.104659 restraints weight = 2216.737| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.53 r_work: 0.3380 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2196 Z= 0.102 Angle : 0.524 6.753 2988 Z= 0.283 Chirality : 0.048 0.136 354 Planarity : 0.004 0.040 366 Dihedral : 5.288 19.504 294 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.11 % Allowed : 18.99 % Favored : 78.90 % 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 are not related in a simple way. whole: -2.05 (0.47), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 104 TYR 0.015 0.001 TYR C 114 PHE 0.010 0.002 PHE A 64 TRP 0.002 0.000 TRP C 79 HIS 0.002 0.000 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 2196) covalent geometry : angle 0.52419 / 0.28 ( 2988) hydrogen bonds : bond 0.02106 / 1.59 ( 37) hydrogen bonds : angle 5.51741 / 3.90 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.085 Fit side-chains REVERT: A 21 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8062 (ttt90) REVERT: A 35 LYS cc_start: 0.8119 (tttt) cc_final: 0.7650 (tppp) REVERT: A 66 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: B 13 MET cc_start: 0.8120 (ttt) cc_final: 0.7854 (ttt) REVERT: C 21 ARG cc_start: 0.8308 (mtp85) cc_final: 0.8012 (mtp85) REVERT: C 35 LYS cc_start: 0.8259 (tttt) cc_final: 0.7890 (tppp) REVERT: C 62 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7706 (mp0) REVERT: C 66 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: C 104 ARG cc_start: 0.8388 (mtt90) cc_final: 0.8059 (mtt-85) outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 0.7253 time to fit residues: 38.2021 Evaluate side-chains 54 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.119015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.100326 restraints weight = 2315.236| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.54 r_work: 0.3302 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2196 Z= 0.195 Angle : 0.604 6.792 2988 Z= 0.332 Chirality : 0.050 0.149 354 Planarity : 0.005 0.038 366 Dihedral : 5.674 20.636 294 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.53 % Allowed : 18.57 % Favored : 78.90 % 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 are not related in a simple way. whole: -2.03 (0.47), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 104 TYR 0.019 0.002 TYR A 114 PHE 0.012 0.002 PHE A 64 TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 2196) covalent geometry : angle 0.60433 / 0.33 ( 2988) hydrogen bonds : bond 0.02581 / 1.94 ( 37) hydrogen bonds : angle 5.71507 / 4.04 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.083 Fit side-chains REVERT: A 21 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8135 (ttt90) REVERT: A 66 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: B 13 MET cc_start: 0.8156 (ttt) cc_final: 0.7864 (ttt) REVERT: C 35 LYS cc_start: 0.8243 (tttt) cc_final: 0.7905 (tppp) REVERT: C 62 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7731 (mp0) REVERT: C 66 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: C 104 ARG cc_start: 0.8431 (mtt90) cc_final: 0.7994 (mtt-85) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.8092 time to fit residues: 42.6793 Evaluate side-chains 55 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.0270 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.120279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101696 restraints weight = 2281.990| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.54 r_work: 0.3333 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2196 Z= 0.152 Angle : 0.575 7.365 2988 Z= 0.312 Chirality : 0.049 0.142 354 Planarity : 0.005 0.040 366 Dihedral : 5.535 20.128 294 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.53 % Allowed : 19.41 % Favored : 78.06 % 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 are not related in a simple way. whole: -2.04 (0.47), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 104 TYR 0.018 0.002 TYR A 114 PHE 0.011 0.002 PHE A 64 TRP 0.002 0.001 TRP C 79 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 2196) covalent geometry : angle 0.57469 / 0.31 ( 2988) hydrogen bonds : bond 0.02381 / 1.80 ( 37) hydrogen bonds : angle 5.60533 / 3.96 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1184.06 seconds wall clock time: 20 minutes 50.69 seconds (1250.69 seconds total)