Starting phenix.real_space_refine on Wed Mar 12 11:33:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dsp_27657/03_2025/8dsp_27657.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dsp_27657/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dsp_27657/03_2025/8dsp_27657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dsp_27657/03_2025/8dsp_27657.map" model { file = "/net/cci-nas-00/data/ceres_data/8dsp_27657/03_2025/8dsp_27657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dsp_27657/03_2025/8dsp_27657.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.08, per 1000 atoms: 0.66 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: 1.99 Conformation dependent library (CDL) restraints added in 683.0 milliseconds 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: 0.65 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: 2.42 Time building geometry restraints manager: 2.42 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: 3.470 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: 0.130 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.140 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- 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= 0.366 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (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 TRP 0.011 0.001 TRP C 162 HIS 0.001 0.000 HIS E 128 PHE 0.018 0.001 PHE E 24 TYR 0.018 0.001 TYR C 50 ARG 0.004 0.000 ARG C 165 *********************** 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 : 0.674 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: 0.3899 time to fit residues: 65.5117 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 : 0.606 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS F 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.085672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.076993 restraints weight = 37590.856| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.80 r_work: 0.3361 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3954 Z= 0.322 Angle : 0.739 7.024 5376 Z= 0.397 Chirality : 0.048 0.201 638 Planarity : 0.006 0.065 700 Dihedral : 5.053 28.918 548 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.50 % Favored : 89.88 % Rotamer: Outliers : 1.65 % Allowed : 14.86 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.35), residues: 484 helix: 0.47 (0.42), residues: 135 sheet: -2.05 (0.66), residues: 49 loop : -2.29 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 64 HIS 0.006 0.002 HIS E 128 PHE 0.025 0.002 PHE E 24 TYR 0.015 0.002 TYR E 26 ARG 0.007 0.001 ARG C 18 *********************** 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 89 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6761 (tm-30) REVERT: F 22 ILE cc_start: 0.7027 (mm) cc_final: 0.6800 (mt) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.4037 time to fit residues: 42.9704 Evaluate side-chains 70 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 38 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: ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.080036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070920 restraints weight = 39318.186| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.90 r_work: 0.3212 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.8878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 3954 Z= 0.410 Angle : 0.685 7.075 5376 Z= 0.383 Chirality : 0.046 0.214 638 Planarity : 0.005 0.039 700 Dihedral : 4.876 21.792 547 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.47 % Favored : 90.70 % Rotamer: Outliers : 1.89 % Allowed : 16.27 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.34), residues: 484 helix: 0.24 (0.40), residues: 132 sheet: -2.26 (0.54), residues: 71 loop : -2.25 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 162 HIS 0.004 0.001 HIS C 108 PHE 0.011 0.002 PHE C 52 TYR 0.013 0.002 TYR F 26 ARG 0.006 0.001 ARG E 77 *********************** 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 66 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7410 (tm-30) REVERT: E 163 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8790 (tm-30) REVERT: F 11 TYR cc_start: 0.8804 (m-80) cc_final: 0.8585 (m-80) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.3822 time to fit residues: 32.1388 Evaluate side-chains 52 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 0.0040 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.080263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.070954 restraints weight = 38642.079| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.92 r_work: 0.3219 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.9593 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= 0.246 Angle : 0.554 4.551 5376 Z= 0.308 Chirality : 0.042 0.140 638 Planarity : 0.004 0.042 700 Dihedral : 4.635 21.397 547 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.85 % Favored : 91.53 % Rotamer: Outliers : 0.94 % Allowed : 17.92 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.36), residues: 484 helix: 1.20 (0.43), residues: 123 sheet: -2.20 (0.64), residues: 49 loop : -1.99 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 64 HIS 0.005 0.001 HIS C 108 PHE 0.008 0.001 PHE C 52 TYR 0.008 0.001 TYR C 11 ARG 0.003 0.000 ARG C 135 *********************** 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 58 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.688 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: 0.8183 (tm-30) cc_final: 0.7560 (tm-30) REVERT: E 163 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8739 (tm-30) REVERT: F 11 TYR cc_start: 0.9049 (m-80) cc_final: 0.8666 (m-80) outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.3196 time to fit residues: 22.7115 Evaluate side-chains 48 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 41 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 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 = 0.3483 r_free = 0.3483 target = 0.078688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069416 restraints weight = 38770.099| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.95 r_work: 0.3187 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 1.0297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3954 Z= 0.269 Angle : 0.539 4.767 5376 Z= 0.301 Chirality : 0.042 0.136 638 Planarity : 0.004 0.034 700 Dihedral : 4.543 20.134 547 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.09 % Favored : 90.29 % Rotamer: Outliers : 1.42 % Allowed : 17.45 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.37), residues: 484 helix: 1.43 (0.44), residues: 123 sheet: -2.25 (0.59), residues: 57 loop : -1.95 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 64 HIS 0.001 0.001 HIS F 108 PHE 0.009 0.001 PHE C 52 TYR 0.011 0.001 TYR C 70 ARG 0.003 0.000 ARG E 41 *********************** 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 54 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.733 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: 0.8303 (tm-30) cc_final: 0.7713 (tm-30) REVERT: E 163 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8800 (tm-30) REVERT: F 11 TYR cc_start: 0.9056 (m-80) cc_final: 0.8731 (m-80) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.4954 time to fit residues: 31.4218 Evaluate side-chains 50 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 E residue 137 VAL Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 31 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 12 GLN C 163 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 = 0.3459 r_free = 0.3459 target = 0.077476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068281 restraints weight = 39312.551| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.94 r_work: 0.3165 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 1.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3954 Z= 0.300 Angle : 0.546 4.696 5376 Z= 0.305 Chirality : 0.042 0.137 638 Planarity : 0.004 0.037 700 Dihedral : 4.681 22.303 547 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.92 % Favored : 89.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.37), residues: 484 helix: 1.34 (0.45), residues: 123 sheet: -2.14 (0.60), residues: 57 loop : -1.93 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 64 HIS 0.001 0.001 HIS C 128 PHE 0.011 0.001 PHE C 52 TYR 0.011 0.001 TYR C 70 ARG 0.002 0.000 ARG C 18 *********************** 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: 7 poor density : 46 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8475 (mpp80) REVERT: E 163 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8808 (tm-30) REVERT: F 74 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8603 (tm-30) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.3004 time to fit residues: 19.9966 Evaluate side-chains 48 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 79 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 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 = 0.3438 r_free = 0.3438 target = 0.076409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067319 restraints weight = 40185.113| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.88 r_work: 0.3143 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 1.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3954 Z= 0.322 Angle : 0.570 5.453 5376 Z= 0.318 Chirality : 0.042 0.132 638 Planarity : 0.004 0.034 700 Dihedral : 4.715 21.941 547 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.74 % Favored : 88.84 % Rotamer: Outliers : 1.42 % Allowed : 19.34 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.37), residues: 484 helix: 1.56 (0.45), residues: 117 sheet: -1.80 (0.60), residues: 71 loop : -2.19 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 64 HIS 0.001 0.000 HIS C 128 PHE 0.009 0.001 PHE C 52 TYR 0.012 0.002 TYR C 70 ARG 0.003 0.000 ARG F 77 *********************** 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 49 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 163 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8821 (tm-30) REVERT: F 11 TYR cc_start: 0.9106 (m-80) cc_final: 0.8756 (m-80) REVERT: F 74 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8673 (tm-30) outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.2781 time to fit residues: 17.5614 Evaluate side-chains 46 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 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 = 0.3474 r_free = 0.3474 target = 0.078154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069067 restraints weight = 39153.611| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.83 r_work: 0.3182 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 1.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3954 Z= 0.192 Angle : 0.538 6.966 5376 Z= 0.294 Chirality : 0.041 0.126 638 Planarity : 0.003 0.030 700 Dihedral : 4.508 21.124 547 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.30 % Favored : 90.29 % Rotamer: Outliers : 1.42 % Allowed : 19.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.37), residues: 484 helix: 1.73 (0.45), residues: 117 sheet: -1.54 (0.65), residues: 64 loop : -1.94 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 64 HIS 0.002 0.001 HIS F 128 PHE 0.005 0.001 PHE C 24 TYR 0.007 0.001 TYR C 50 ARG 0.002 0.000 ARG F 77 *********************** 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 52 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8433 (mpp80) REVERT: E 163 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8796 (tm-30) REVERT: F 11 TYR cc_start: 0.9105 (m-80) cc_final: 0.8751 (m-80) REVERT: F 74 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8557 (tm-30) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.3255 time to fit residues: 21.0000 Evaluate side-chains 49 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR 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 Chi-restraints excluded: chain F residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 45 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 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 = 0.3460 r_free = 0.3460 target = 0.077461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068317 restraints weight = 39671.281| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.89 r_work: 0.3163 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 1.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3954 Z= 0.251 Angle : 0.539 6.253 5376 Z= 0.297 Chirality : 0.042 0.132 638 Planarity : 0.004 0.030 700 Dihedral : 4.494 20.339 547 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.92 % Favored : 89.67 % Rotamer: Outliers : 1.42 % Allowed : 19.58 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.37), residues: 484 helix: 1.59 (0.45), residues: 117 sheet: -1.21 (0.76), residues: 51 loop : -1.97 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 64 HIS 0.001 0.000 HIS F 128 PHE 0.008 0.001 PHE C 52 TYR 0.012 0.001 TYR C 70 ARG 0.003 0.000 ARG F 77 *********************** 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 47 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8484 (mpp80) REVERT: E 163 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8818 (tm-30) REVERT: F 74 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8594 (tm-30) outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 0.3333 time to fit residues: 19.5727 Evaluate side-chains 46 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR 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 Chi-restraints excluded: chain F residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.0470 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 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 = 0.3504 r_free = 0.3504 target = 0.078929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.070421 restraints weight = 38893.349| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.67 r_work: 0.3213 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 1.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3954 Z= 0.233 Angle : 0.534 6.231 5376 Z= 0.293 Chirality : 0.041 0.127 638 Planarity : 0.003 0.026 700 Dihedral : 4.475 20.641 547 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.50 % Favored : 90.08 % Rotamer: Outliers : 1.65 % Allowed : 18.87 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.37), residues: 484 helix: 1.57 (0.44), residues: 117 sheet: -1.47 (0.68), residues: 61 loop : -1.94 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 64 HIS 0.001 0.001 HIS F 108 PHE 0.006 0.001 PHE E 151 TYR 0.010 0.001 TYR C 70 ARG 0.003 0.000 ARG F 77 ********************** 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: 7 poor density : 40 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8468 (mpp80) REVERT: E 163 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8846 (tm-30) REVERT: F 74 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8582 (tm-30) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.2948 time to fit residues: 17.7512 Evaluate side-chains 45 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 79 THR 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 Chi-restraints excluded: chain F residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.0070 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.0870 chunk 1 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.080532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072128 restraints weight = 38734.684| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.65 r_work: 0.3255 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 1.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3954 Z= 0.161 Angle : 0.515 5.550 5376 Z= 0.279 Chirality : 0.041 0.124 638 Planarity : 0.003 0.026 700 Dihedral : 4.240 18.540 547 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.88 % Favored : 90.70 % Rotamer: Outliers : 0.94 % Allowed : 20.05 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.37), residues: 484 helix: 1.66 (0.45), residues: 117 sheet: -1.35 (0.69), residues: 61 loop : -1.85 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 64 HIS 0.001 0.000 HIS F 108 PHE 0.007 0.001 PHE E 151 TYR 0.007 0.001 TYR C 70 ARG 0.002 0.000 ARG F 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4802.68 seconds wall clock time: 86 minutes 8.99 seconds (5168.99 seconds total)