Starting phenix.real_space_refine on Fri Aug 22 20:42:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dsp_27657/08_2025/8dsp_27657.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dsp_27657/08_2025/8dsp_27657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dsp_27657/08_2025/8dsp_27657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dsp_27657/08_2025/8dsp_27657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dsp_27657/08_2025/8dsp_27657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dsp_27657/08_2025/8dsp_27657.map" } resolution = 3.3 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= 0.000 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2425 2.51 5 N 709 2.21 5 O 757 1.98 5 H 3848 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 7745 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2554 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain: "E" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2596 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 3, 'TRANS': 160} Chain: "F" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2595 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 3, 'TRANS': 160} Time building chain proxies: 1.57, per 1000 atoms: 0.20 Number of scatterers: 7745 At special positions: 0 Unit cell: (80.1, 80.1, 87.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 757 8.00 N 709 7.00 C 2425 6.00 H 3848 1.00 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: 0.68 Conformation dependent library (CDL) restraints added in 290.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 926 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 11 sheets defined 30.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 95 through 120 removed outlier: 3.646A pdb=" N LEU C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.735A pdb=" N LEU C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 165 removed outlier: 3.563A pdb=" N SER C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 65 through 68 Processing helix chain 'E' and resid 95 through 120 removed outlier: 3.645A pdb=" N THR E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 166 removed outlier: 3.719A pdb=" N LEU E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 161 " --> pdb=" O MET E 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 95 through 118 removed outlier: 3.817A pdb=" N LEU F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR F 118 " --> pdb=" O ARG F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 167 Processing sheet with id=AA1, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.610A pdb=" N THR C 35 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'C' and resid 122 through 123 removed outlier: 4.024A pdb=" N GLY C 122 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.943A pdb=" N GLY F 122 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 8 through 9 Processing sheet with id=AA6, first strand: chain 'E' and resid 8 through 9 Processing sheet with id=AA7, first strand: chain 'E' and resid 19 through 21 removed outlier: 7.294A pdb=" N THR E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.750A pdb=" N GLY E 122 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.936A pdb=" N THR F 54 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER F 59 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE F 52 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 43 removed outlier: 6.705A pdb=" N ILE F 37 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 42 through 43 135 hydrogen bonds defined for protein. 366 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: 1.20 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3365 1.03 - 1.23: 488 1.23 - 1.42: 1647 1.42 - 1.62: 2290 1.62 - 1.81: 12 Bond restraints: 7802 Sorted by residual: bond pdb=" N ASP F 115 " pdb=" H ASP F 115 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N LEU E 85 " pdb=" H LEU E 85 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N PHE C 52 " pdb=" H PHE C 52 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N THR F 120 " pdb=" H THR F 120 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N ILE F 121 " pdb=" H ILE F 121 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 7797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 13376 1.44 - 2.89: 545 2.89 - 4.33: 87 4.33 - 5.77: 8 5.77 - 7.22: 3 Bond angle restraints: 14019 Sorted by residual: angle pdb=" CA VAL E 137 " pdb=" C VAL E 137 " pdb=" O VAL E 137 " ideal model delta sigma weight residual 120.80 116.27 4.53 8.90e-01 1.26e+00 2.59e+01 angle pdb=" CA VAL E 137 " pdb=" C VAL E 137 " pdb=" N ASN E 138 " ideal model delta sigma weight residual 117.15 121.08 -3.93 7.80e-01 1.64e+00 2.54e+01 angle pdb=" N VAL E 137 " pdb=" CA VAL E 137 " pdb=" C VAL E 137 " ideal model delta sigma weight residual 111.62 115.46 -3.84 7.90e-01 1.60e+00 2.36e+01 angle pdb=" N ASP C 49 " pdb=" CA ASP C 49 " pdb=" C ASP C 49 " ideal model delta sigma weight residual 113.41 107.49 5.92 1.22e+00 6.72e-01 2.36e+01 angle pdb=" N THR F 118 " pdb=" CA THR F 118 " pdb=" C THR F 118 " ideal model delta sigma weight residual 113.18 107.59 5.59 1.21e+00 6.83e-01 2.13e+01 ... (remaining 14014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 3257 16.02 - 32.04: 283 32.04 - 48.07: 63 48.07 - 64.09: 26 64.09 - 80.11: 2 Dihedral angle restraints: 3631 sinusoidal: 1999 harmonic: 1632 Sorted by residual: dihedral pdb=" CA TYR F 50 " pdb=" C TYR F 50 " pdb=" N ARG F 51 " pdb=" CA ARG F 51 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA GLN C 163 " pdb=" CB GLN C 163 " pdb=" CG GLN C 163 " pdb=" CD GLN C 163 " ideal model delta sinusoidal sigma weight residual 60.00 117.29 -57.29 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N SER E 92 " pdb=" CA SER E 92 " pdb=" CB SER E 92 " pdb=" OG SER E 92 " ideal model delta sinusoidal sigma weight residual -180.00 -123.29 -56.71 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 475 0.044 - 0.087: 86 0.087 - 0.131: 63 0.131 - 0.174: 13 0.174 - 0.218: 1 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA ILE E 136 " pdb=" N ILE E 136 " pdb=" C ILE E 136 " pdb=" CB ILE E 136 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE E 5 " pdb=" N ILE E 5 " pdb=" C ILE E 5 " pdb=" CB ILE E 5 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 635 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 141 " -0.225 2.00e-02 2.50e+03 2.21e-01 7.35e+02 pdb=" CG ASN E 141 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN E 141 " 0.214 2.00e-02 2.50e+03 pdb=" ND2 ASN E 141 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN E 141 " 0.310 2.00e-02 2.50e+03 pdb="HD22 ASN E 141 " -0.318 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 163 " -0.187 2.00e-02 2.50e+03 1.81e-01 4.93e+02 pdb=" CD GLN C 163 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN C 163 " 0.175 2.00e-02 2.50e+03 pdb=" NE2 GLN C 163 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 163 " 0.252 2.00e-02 2.50e+03 pdb="HE22 GLN C 163 " -0.260 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 166 " 0.069 2.00e-02 2.50e+03 6.66e-02 6.66e+01 pdb=" CG ASN C 166 " -0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN C 166 " -0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN C 166 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 166 " -0.091 2.00e-02 2.50e+03 pdb="HD22 ASN C 166 " 0.095 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 701 2.21 - 2.81: 16662 2.81 - 3.40: 21289 3.40 - 4.00: 28031 4.00 - 4.60: 42205 Nonbonded interactions: 108888 Sorted by model distance: nonbonded pdb=" H ASN F 124 " pdb=" O HIS F 128 " model vdw 1.610 2.450 nonbonded pdb=" H LEU E 13 " pdb=" O THR E 71 " model vdw 1.623 2.450 nonbonded pdb=" OD1 ASN C 124 " pdb=" H ASN C 125 " model vdw 1.627 2.450 nonbonded pdb=" O ALA F 131 " pdb=" HE ARG F 134 " model vdw 1.663 2.450 nonbonded pdb=" O ARG E 165 " pdb="HH11 ARG E 165 " model vdw 1.676 2.450 ... (remaining 108883 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 'C' and (resid 6 through 78 or (resid 79 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB or \ name HG21 or name HG22 or name HG23)) or resid 80 through 162 or (resid 163 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HE21 or name HE22)) or resid 164 through 167)) selection = (chain 'E' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ \ 1 or name HZ2 or name HZ3)) or (resid 7 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG \ 21 or name HG22 or name HG23)) or resid 8 through 156 or (resid 157 and (name N \ or name CA or name C or name O or name CB or name CG or name SD or name CE or na \ me H or name HA )) or resid 158 through 162 or (resid 163 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE \ 22)) or resid 164 through 167)) selection = (chain 'F' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ \ 1 or name HZ2 or name HZ3)) or resid 7 through 78 or (resid 79 and (name N or na \ me CA or name C or name O or name CB or name OG1 or name CG2 or name H or name H \ A or name HB or name HG21 or name HG22 or name HG23)) or resid 80 through 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB or name CG or \ name SD or name CE or name H or name HA )) or resid 158 through 167)) } 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: 5.280 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: 0.030 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.980 Find NCS groups from input model: 0.130 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 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 : 0.005 0.038 3954 Z= 0.372 Angle : 0.794 7.218 5376 Z= 0.556 Chirality : 0.051 0.218 638 Planarity : 0.003 0.047 700 Dihedral : 12.778 80.110 1444 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.88 % Favored : 90.50 % Rotamer: Outliers : 0.47 % Allowed : 2.59 % Favored : 96.93 % 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: -1.65 (0.37), residues: 484 helix: 1.18 (0.45), residues: 126 sheet: -1.75 (0.69), residues: 61 loop : -2.09 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 165 TYR 0.018 0.001 TYR C 50 PHE 0.018 0.001 PHE E 24 TRP 0.011 0.001 TRP C 162 HIS 0.001 0.000 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 3954) covalent geometry : angle 0.79356 ( 5376) hydrogen bonds : bond 0.17611 ( 129) hydrogen bonds : angle 6.90020 ( 366) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 THR cc_start: 0.7345 (m) cc_final: 0.6732 (m) REVERT: E 30 LYS cc_start: 0.8304 (ptmt) cc_final: 0.8056 (ptpp) REVERT: E 138 ASN cc_start: 0.6115 (p0) cc_final: 0.5701 (p0) REVERT: F 160 ASN cc_start: 0.7816 (t0) cc_final: 0.7513 (t0) outliers start: 2 outliers final: 1 residues processed: 139 average time/residue: 0.1578 time to fit residues: 26.2349 Evaluate side-chains 84 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.0670 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 HIS F 103 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.086817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.078312 restraints weight = 37276.566| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.71 r_work: 0.3381 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3954 Z= 0.159 Angle : 0.615 5.726 5376 Z= 0.333 Chirality : 0.044 0.149 638 Planarity : 0.005 0.050 700 Dihedral : 4.622 29.641 548 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.47 % Favored : 90.70 % Rotamer: Outliers : 2.36 % Allowed : 12.26 % Favored : 85.38 % 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: -1.79 (0.35), residues: 484 helix: 0.90 (0.42), residues: 135 sheet: -2.06 (0.65), residues: 49 loop : -2.16 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 18 TYR 0.008 0.001 TYR F 11 PHE 0.017 0.002 PHE E 24 TRP 0.003 0.001 TRP F 162 HIS 0.004 0.001 HIS E 108 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3954) covalent geometry : angle 0.61478 ( 5376) hydrogen bonds : bond 0.05226 ( 129) hydrogen bonds : angle 5.06983 ( 366) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6681 (tm-30) REVERT: F 22 ILE cc_start: 0.6117 (mm) cc_final: 0.5713 (mp) outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 0.1443 time to fit residues: 17.9029 Evaluate side-chains 87 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 PHE Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 123 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN C 158 ASN C 163 GLN E 141 ASN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.084251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075335 restraints weight = 37577.998| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.80 r_work: 0.3316 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.7829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 3954 Z= 0.229 Angle : 0.724 12.563 5376 Z= 0.393 Chirality : 0.046 0.160 638 Planarity : 0.007 0.097 700 Dihedral : 4.777 19.324 547 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.92 % Favored : 89.46 % Rotamer: Outliers : 1.89 % Allowed : 15.57 % Favored : 82.55 % 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: -1.84 (0.36), residues: 484 helix: 0.72 (0.41), residues: 131 sheet: -2.21 (0.62), residues: 49 loop : -2.05 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 55 TYR 0.014 0.002 TYR E 26 PHE 0.025 0.003 PHE E 52 TRP 0.007 0.002 TRP C 162 HIS 0.005 0.002 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 3954) covalent geometry : angle 0.72429 ( 5376) hydrogen bonds : bond 0.05756 ( 129) hydrogen bonds : angle 4.84404 ( 366) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.7814 (tm-30) cc_final: 0.6998 (tm-30) REVERT: E 136 ILE cc_start: 0.6755 (pt) cc_final: 0.6331 (mp) REVERT: E 163 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8724 (tm-30) REVERT: F 11 TYR cc_start: 0.8801 (m-80) cc_final: 0.8412 (m-80) REVERT: F 22 ILE cc_start: 0.7879 (mm) cc_final: 0.7672 (mt) outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.1329 time to fit residues: 12.1872 Evaluate side-chains 60 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 99 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.080160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070826 restraints weight = 39343.743| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.92 r_work: 0.3214 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.9401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3954 Z= 0.219 Angle : 0.602 7.697 5376 Z= 0.336 Chirality : 0.044 0.146 638 Planarity : 0.005 0.050 700 Dihedral : 4.640 22.426 547 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.30 % Favored : 90.08 % Rotamer: Outliers : 1.42 % Allowed : 18.40 % Favored : 80.19 % 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: -1.99 (0.35), residues: 484 helix: 0.69 (0.43), residues: 130 sheet: -2.04 (0.63), residues: 49 loop : -2.24 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 135 TYR 0.011 0.001 TYR C 70 PHE 0.010 0.002 PHE C 52 TRP 0.005 0.001 TRP C 64 HIS 0.004 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 3954) covalent geometry : angle 0.60195 ( 5376) hydrogen bonds : bond 0.05394 ( 129) hydrogen bonds : angle 5.00940 ( 366) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 ILE cc_start: 0.8498 (mm) cc_final: 0.8257 (mm) REVERT: E 74 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7489 (tm-30) REVERT: E 163 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8706 (tm-30) REVERT: F 11 TYR cc_start: 0.8949 (m-80) cc_final: 0.8575 (m-80) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.1218 time to fit residues: 9.5029 Evaluate side-chains 53 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 99 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 45 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.079234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.069891 restraints weight = 39410.968| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.90 r_work: 0.3194 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 1.0231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3954 Z= 0.183 Angle : 0.558 7.714 5376 Z= 0.309 Chirality : 0.042 0.140 638 Planarity : 0.004 0.037 700 Dihedral : 4.501 21.489 547 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.30 % Favored : 90.08 % Rotamer: Outliers : 1.65 % Allowed : 18.16 % Favored : 80.19 % 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: -1.56 (0.36), residues: 484 helix: 1.11 (0.43), residues: 123 sheet: -2.03 (0.64), residues: 49 loop : -1.87 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 77 TYR 0.007 0.001 TYR C 50 PHE 0.009 0.002 PHE C 24 TRP 0.004 0.001 TRP E 162 HIS 0.001 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3954) covalent geometry : angle 0.55778 ( 5376) hydrogen bonds : bond 0.05177 ( 129) hydrogen bonds : angle 4.69764 ( 366) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7707 (tm-30) REVERT: E 163 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8793 (tm-30) REVERT: F 11 TYR cc_start: 0.9060 (m-80) cc_final: 0.8670 (m-80) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 0.1391 time to fit residues: 9.7653 Evaluate side-chains 51 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.079513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070138 restraints weight = 38907.001| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.87 r_work: 0.3201 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 1.0444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3954 Z= 0.145 Angle : 0.536 7.711 5376 Z= 0.295 Chirality : 0.041 0.133 638 Planarity : 0.004 0.032 700 Dihedral : 4.420 19.682 547 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.68 % Favored : 90.70 % Rotamer: Outliers : 1.18 % Allowed : 19.10 % Favored : 79.72 % 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: -1.46 (0.36), residues: 484 helix: 1.19 (0.43), residues: 123 sheet: -1.93 (0.64), residues: 49 loop : -1.82 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.007 0.001 TYR C 50 PHE 0.006 0.001 PHE C 52 TRP 0.003 0.001 TRP E 162 HIS 0.002 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3954) covalent geometry : angle 0.53583 ( 5376) hydrogen bonds : bond 0.04989 ( 129) hydrogen bonds : angle 4.57197 ( 366) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7707 (tm-30) REVERT: E 163 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8761 (tm-30) REVERT: F 11 TYR cc_start: 0.9070 (m-80) cc_final: 0.8668 (m-80) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1492 time to fit residues: 9.2591 Evaluate side-chains 50 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.078259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.069683 restraints weight = 38842.903| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.64 r_work: 0.3186 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 1.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3954 Z= 0.222 Angle : 0.584 6.786 5376 Z= 0.326 Chirality : 0.043 0.143 638 Planarity : 0.004 0.038 700 Dihedral : 4.682 20.952 547 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.16 % Favored : 88.43 % Rotamer: Outliers : 2.12 % Allowed : 19.10 % Favored : 78.77 % 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: -1.66 (0.37), residues: 484 helix: 1.12 (0.44), residues: 123 sheet: -1.89 (0.62), residues: 57 loop : -2.01 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 146 TYR 0.010 0.002 TYR C 50 PHE 0.013 0.001 PHE C 52 TRP 0.004 0.001 TRP C 64 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 3954) covalent geometry : angle 0.58418 ( 5376) hydrogen bonds : bond 0.05676 ( 129) hydrogen bonds : angle 4.73101 ( 366) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.8659 (tm-30) cc_final: 0.7975 (tm-30) REVERT: E 84 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8511 (mpp80) REVERT: E 163 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8839 (tm-30) REVERT: F 11 TYR cc_start: 0.9254 (m-80) cc_final: 0.8718 (m-80) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.1203 time to fit residues: 7.6657 Evaluate side-chains 48 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 41 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.080785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071782 restraints weight = 38436.750| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.78 r_work: 0.3242 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 1.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3954 Z= 0.111 Angle : 0.519 7.078 5376 Z= 0.284 Chirality : 0.041 0.128 638 Planarity : 0.003 0.031 700 Dihedral : 4.393 21.012 547 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.47 % Favored : 90.91 % Rotamer: Outliers : 0.94 % Allowed : 21.23 % Favored : 77.83 % 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: -1.27 (0.37), residues: 484 helix: 1.62 (0.44), residues: 117 sheet: -1.27 (0.71), residues: 56 loop : -1.87 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 77 TYR 0.007 0.001 TYR C 70 PHE 0.005 0.001 PHE C 151 TRP 0.004 0.001 TRP E 162 HIS 0.001 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3954) covalent geometry : angle 0.51930 ( 5376) hydrogen bonds : bond 0.04907 ( 129) hydrogen bonds : angle 4.42782 ( 366) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.8590 (tm-30) cc_final: 0.7920 (tm-30) REVERT: E 163 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8791 (tm-30) REVERT: F 11 TYR cc_start: 0.9230 (m-80) cc_final: 0.8704 (m-80) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.1447 time to fit residues: 8.7804 Evaluate side-chains 47 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.078127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069522 restraints weight = 38871.177| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.62 r_work: 0.3186 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 1.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3954 Z= 0.237 Angle : 0.578 5.965 5376 Z= 0.323 Chirality : 0.043 0.150 638 Planarity : 0.004 0.033 700 Dihedral : 4.616 21.393 547 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.95 % Favored : 88.43 % Rotamer: Outliers : 0.94 % Allowed : 20.99 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.55 (0.37), residues: 484 helix: 1.31 (0.44), residues: 117 sheet: -1.38 (0.71), residues: 56 loop : -2.03 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 84 TYR 0.009 0.002 TYR C 50 PHE 0.011 0.001 PHE C 52 TRP 0.004 0.001 TRP E 162 HIS 0.002 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 3954) covalent geometry : angle 0.57809 ( 5376) hydrogen bonds : bond 0.05558 ( 129) hydrogen bonds : angle 4.63512 ( 366) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8031 (tm-30) REVERT: E 163 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8859 (tm-30) REVERT: F 11 TYR cc_start: 0.9270 (m-80) cc_final: 0.8796 (m-80) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.1270 time to fit residues: 6.8886 Evaluate side-chains 44 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.0170 chunk 41 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 39 optimal weight: 0.3980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.080064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.071256 restraints weight = 38068.010| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.66 r_work: 0.3228 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 1.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3954 Z= 0.127 Angle : 0.534 6.864 5376 Z= 0.293 Chirality : 0.041 0.126 638 Planarity : 0.003 0.028 700 Dihedral : 4.438 21.546 547 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.26 % Favored : 91.32 % Rotamer: Outliers : 0.94 % Allowed : 21.70 % Favored : 77.36 % 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: -1.36 (0.37), residues: 484 helix: 1.39 (0.44), residues: 117 sheet: -1.25 (0.72), residues: 56 loop : -1.87 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.008 0.001 TYR C 50 PHE 0.007 0.001 PHE C 24 TRP 0.004 0.001 TRP E 162 HIS 0.002 0.000 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3954) covalent geometry : angle 0.53395 ( 5376) hydrogen bonds : bond 0.05092 ( 129) hydrogen bonds : angle 4.41823 ( 366) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8388 (tm-30) REVERT: E 163 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8821 (tm-30) REVERT: F 11 TYR cc_start: 0.9254 (m-80) cc_final: 0.8763 (m-80) outliers start: 4 outliers final: 4 residues processed: 46 average time/residue: 0.0926 time to fit residues: 5.6865 Evaluate side-chains 42 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.078832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.070238 restraints weight = 38999.085| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.59 r_work: 0.3208 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 1.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3954 Z= 0.187 Angle : 0.568 7.942 5376 Z= 0.311 Chirality : 0.042 0.136 638 Planarity : 0.004 0.038 700 Dihedral : 4.466 20.863 547 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.71 % Favored : 89.67 % Rotamer: Outliers : 0.94 % Allowed : 22.41 % Favored : 76.65 % 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: -1.44 (0.37), residues: 484 helix: 1.36 (0.44), residues: 117 sheet: -1.29 (0.71), residues: 56 loop : -1.94 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 77 TYR 0.009 0.001 TYR C 50 PHE 0.008 0.001 PHE C 52 TRP 0.003 0.001 TRP E 162 HIS 0.002 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 3954) covalent geometry : angle 0.56787 ( 5376) hydrogen bonds : bond 0.05269 ( 129) hydrogen bonds : angle 4.46195 ( 366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1966.01 seconds wall clock time: 33 minutes 56.98 seconds (2036.98 seconds total)