Starting phenix.real_space_refine on Thu Oct 22 19:06:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wfq_21652/10_2026/6wfq_21652.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wfq_21652/10_2026/6wfq_21652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wfq_21652/10_2026/6wfq_21652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wfq_21652/10_2026/6wfq_21652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wfq_21652/10_2026/6wfq_21652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wfq_21652/10_2026/6wfq_21652.map" } resolution = 3.9 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= 0.002 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 P 30 5.49 5 S 10 5.16 5 C 2508 2.51 5 N 769 2.21 5 O 847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4164 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1812 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "D" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1737 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain: "A" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 313 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 302 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Time building chain proxies: 1.20, per 1000 atoms: 0.29 Number of scatterers: 4164 At special positions: 0 Unit cell: (80.24, 99.96, 82.96, 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 10 16.00 P 30 15.00 O 847 8.00 N 769 7.00 C 2508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 83.9 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 854 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 75.2% alpha, 0.0% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'C' and resid 31 through 46 removed outlier: 4.013A pdb=" N MET C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 68 through 83 removed outlier: 3.714A pdb=" N VAL C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.585A pdb=" N ILE C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.691A pdb=" N PHE C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 142 Processing helix chain 'C' and resid 146 through 158 removed outlier: 4.130A pdb=" N LEU C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 181 removed outlier: 4.326A pdb=" N ILE C 169 " --> pdb=" O ASN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 210 through 232 Processing helix chain 'C' and resid 233 through 248 removed outlier: 3.782A pdb=" N ALA C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.956A pdb=" N MET D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 3.671A pdb=" N VAL D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.795A pdb=" N ILE D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.785A pdb=" N HIS D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.984A pdb=" N HIS D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 161 removed outlier: 3.996A pdb=" N LEU D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'D' and resid 185 through 203 Processing helix chain 'D' and resid 208 through 231 removed outlier: 3.621A pdb=" N GLU D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.803A pdb=" N ALA D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 248 " --> pdb=" O HIS D 244 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 0.73 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1063 1.33 - 1.45: 878 1.45 - 1.57: 2281 1.57 - 1.69: 58 1.69 - 1.80: 20 Bond restraints: 4300 Sorted by residual: bond pdb=" C2' DT A 3 " pdb=" C1' DT A 3 " ideal model delta sigma weight residual 1.518 1.537 -0.019 1.00e-02 1.00e+04 3.70e+00 bond pdb=" C1' DC A 8 " pdb=" N1 DC A 8 " ideal model delta sigma weight residual 1.468 1.494 -0.026 1.40e-02 5.10e+03 3.57e+00 bond pdb=" C3' DT B 3 " pdb=" C2' DT B 3 " ideal model delta sigma weight residual 1.516 1.531 -0.015 8.00e-03 1.56e+04 3.54e+00 bond pdb=" C1' DT A 3 " pdb=" N1 DT A 3 " ideal model delta sigma weight residual 1.468 1.494 -0.026 1.40e-02 5.10e+03 3.49e+00 bond pdb=" C2' DT B 3 " pdb=" C1' DT B 3 " ideal model delta sigma weight residual 1.518 1.536 -0.018 1.00e-02 1.00e+04 3.33e+00 ... (remaining 4295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 5670 1.27 - 2.54: 226 2.54 - 3.81: 29 3.81 - 5.08: 7 5.08 - 6.35: 3 Bond angle restraints: 5935 Sorted by residual: angle pdb=" N3 DT A 5 " pdb=" C4 DT A 5 " pdb=" O4 DT A 5 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT B 3 " pdb=" C4 DT B 3 " pdb=" O4 DT B 3 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT A 14 " pdb=" C4 DT A 14 " pdb=" O4 DT A 14 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT B 1 " pdb=" C4 DT B 1 " pdb=" O4 DT B 1 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT A 3 " pdb=" C4 DT A 3 " pdb=" O4 DT A 3 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.65e+01 ... (remaining 5930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 2176 16.59 - 33.17: 233 33.17 - 49.76: 106 49.76 - 66.34: 37 66.34 - 82.93: 2 Dihedral angle restraints: 2554 sinusoidal: 1251 harmonic: 1303 Sorted by residual: dihedral pdb=" N LEU C 79 " pdb=" CA LEU C 79 " pdb=" CB LEU C 79 " pdb=" CG LEU C 79 " ideal model delta sinusoidal sigma weight residual -60.00 -119.66 59.66 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS C 82 " pdb=" CB LYS C 82 " pdb=" CG LYS C 82 " pdb=" CD LYS C 82 " ideal model delta sinusoidal sigma weight residual 180.00 121.92 58.08 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB LYS C 82 " pdb=" CG LYS C 82 " pdb=" CD LYS C 82 " pdb=" CE LYS C 82 " ideal model delta sinusoidal sigma weight residual -60.00 -2.32 -57.68 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 335 0.023 - 0.045: 198 0.045 - 0.068: 72 0.068 - 0.090: 42 0.090 - 0.113: 12 Chirality restraints: 659 Sorted by residual: chirality pdb=" CA ILE D 87 " pdb=" N ILE D 87 " pdb=" C ILE D 87 " pdb=" CB ILE D 87 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 chirality pdb=" CA ILE C 87 " pdb=" N ILE C 87 " pdb=" C ILE C 87 " pdb=" CB ILE C 87 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.87e-01 chirality pdb=" CA PRO C 118 " pdb=" N PRO C 118 " pdb=" C PRO C 118 " pdb=" CB PRO C 118 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.76e-01 ... (remaining 656 not shown) Planarity restraints: 686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 244 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C HIS C 244 " 0.079 2.00e-02 2.50e+03 pdb=" O HIS C 244 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU C 245 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 244 " -0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C HIS D 244 " 0.065 2.00e-02 2.50e+03 pdb=" O HIS D 244 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU D 245 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 69 " -0.014 5.00e-02 4.00e+02 2.08e-02 6.92e-01 pdb=" N PRO C 70 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO C 70 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 70 " -0.012 5.00e-02 4.00e+02 ... (remaining 683 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 941 2.79 - 3.32: 4114 3.32 - 3.85: 7107 3.85 - 4.37: 7847 4.37 - 4.90: 12239 Nonbonded interactions: 32248 Sorted by model distance: nonbonded pdb=" O PHE D 131 " pdb=" OG SER D 134 " model vdw 2.265 3.040 nonbonded pdb=" O LEU D 211 " pdb=" ND2 ASN D 215 " model vdw 2.360 3.120 nonbonded pdb=" O SER C 99 " pdb=" OG1 THR C 102 " model vdw 2.390 3.040 nonbonded pdb=" O ASN D 158 " pdb=" OG SER D 161 " model vdw 2.399 3.040 nonbonded pdb=" O GLU C 156 " pdb=" OG SER C 159 " model vdw 2.399 3.040 ... (remaining 32243 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 30 through 248) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.860 Find NCS groups from input model: 0.060 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4300 Z= 0.270 Angle : 0.564 6.347 5935 Z= 0.442 Chirality : 0.036 0.113 659 Planarity : 0.003 0.045 686 Dihedral : 16.898 82.929 1700 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.80 % Allowed : 5.32 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.35), residues: 443 helix: -0.75 (0.26), residues: 316 sheet: None (None), residues: 0 loop : -3.85 (0.44), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 46 TYR 0.014 0.001 TYR D 219 PHE 0.003 0.000 PHE C 131 TRP 0.001 0.000 TRP D 198 HIS 0.004 0.000 HIS C 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.27 ( 4300) covalent geometry : angle 0.56400 / 0.44 ( 5935) hydrogen bonds : bond 0.15908 / 10.90 ( 259) hydrogen bonds : angle 5.18924 / 3.66 ( 747) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 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: C 126 GLN cc_start: 0.9374 (tt0) cc_final: 0.8509 (tp40) REVERT: C 130 PHE cc_start: 0.9371 (m-10) cc_final: 0.8486 (m-80) REVERT: C 138 TYR cc_start: 0.8711 (t80) cc_final: 0.8335 (t80) REVERT: C 153 LYS cc_start: 0.9737 (pptt) cc_final: 0.9444 (tppt) REVERT: C 157 ILE cc_start: 0.9453 (tp) cc_final: 0.9055 (tp) REVERT: C 196 LEU cc_start: 0.9633 (mm) cc_final: 0.9379 (pp) REVERT: C 212 HIS cc_start: 0.9478 (p-80) cc_final: 0.9228 (m-70) REVERT: D 89 ASN cc_start: 0.8707 (t0) cc_final: 0.8426 (m-40) REVERT: D 135 LEU cc_start: 0.8854 (mt) cc_final: 0.8618 (mt) REVERT: D 147 GLN cc_start: 0.9042 (mp10) cc_final: 0.8619 (mp10) outliers start: 3 outliers final: 0 residues processed: 122 average time/residue: 0.0706 time to fit residues: 10.7376 Evaluate side-chains 74 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN D 192 HIS D 214 HIS D 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.069262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.048031 restraints weight = 21306.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.049789 restraints weight = 14555.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.051054 restraints weight = 11213.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.051901 restraints weight = 9342.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.052540 restraints weight = 8237.174| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4300 Z= 0.165 Angle : 0.720 10.494 5935 Z= 0.379 Chirality : 0.042 0.245 659 Planarity : 0.004 0.025 686 Dihedral : 18.596 58.227 822 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.60 % Allowed : 15.69 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.38), residues: 443 helix: 0.23 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -3.71 (0.44), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 46 TYR 0.024 0.003 TYR C 219 PHE 0.007 0.001 PHE D 124 TRP 0.004 0.001 TRP D 198 HIS 0.004 0.001 HIS C 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 ( 4300) covalent geometry : angle 0.72022 / 0.38 ( 5935) hydrogen bonds : bond 0.04837 / 3.28 ( 259) hydrogen bonds : angle 4.11921 / 2.96 ( 747) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.152 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 42 GLN cc_start: 0.8761 (pt0) cc_final: 0.8341 (pt0) REVERT: C 101 ASP cc_start: 0.9593 (t0) cc_final: 0.9370 (p0) REVERT: C 126 GLN cc_start: 0.9472 (tt0) cc_final: 0.8596 (tp40) REVERT: C 130 PHE cc_start: 0.9395 (m-10) cc_final: 0.8587 (m-80) REVERT: C 138 TYR cc_start: 0.8774 (t80) cc_final: 0.8366 (t80) REVERT: C 212 HIS cc_start: 0.9391 (p-80) cc_final: 0.9170 (m-70) REVERT: D 35 MET cc_start: 0.9572 (tmm) cc_final: 0.9205 (ppp) REVERT: D 89 ASN cc_start: 0.8814 (t0) cc_final: 0.8582 (m-40) REVERT: D 147 GLN cc_start: 0.8998 (mp10) cc_final: 0.8592 (mp10) outliers start: 6 outliers final: 3 residues processed: 81 average time/residue: 0.0735 time to fit residues: 7.4968 Evaluate side-chains 74 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 170 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [14, 29, 40, 19, 35, 13, 24, 4, 27, 2, 5] chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.067140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.046989 restraints weight = 21727.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.048533 restraints weight = 14767.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.049624 restraints weight = 11505.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.050444 restraints weight = 9617.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.051043 restraints weight = 8438.327| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4300 Z= 0.196 Angle : 0.708 8.407 5935 Z= 0.382 Chirality : 0.041 0.168 659 Planarity : 0.004 0.038 686 Dihedral : 18.596 59.116 822 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.86 % Allowed : 18.62 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.39), residues: 443 helix: 0.23 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -3.57 (0.46), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 94 TYR 0.020 0.003 TYR D 219 PHE 0.014 0.002 PHE D 114 TRP 0.004 0.001 TRP D 198 HIS 0.016 0.002 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.20 ( 4300) covalent geometry : angle 0.70769 / 0.38 ( 5935) hydrogen bonds : bond 0.04860 / 3.21 ( 259) hydrogen bonds : angle 4.28129 / 3.02 ( 747) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.145 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: C 42 GLN cc_start: 0.8851 (pt0) cc_final: 0.8633 (pt0) REVERT: C 43 MET cc_start: 0.9369 (mmm) cc_final: 0.9125 (mmm) REVERT: C 62 MET cc_start: 0.8371 (ttp) cc_final: 0.7948 (mtm) REVERT: C 101 ASP cc_start: 0.9590 (t0) cc_final: 0.9364 (p0) REVERT: C 126 GLN cc_start: 0.9501 (tt0) cc_final: 0.8580 (tp-100) REVERT: C 130 PHE cc_start: 0.9465 (m-10) cc_final: 0.8726 (m-80) REVERT: C 153 LYS cc_start: 0.9761 (pptt) cc_final: 0.9490 (tptp) REVERT: C 212 HIS cc_start: 0.9401 (p-80) cc_final: 0.9148 (m-70) REVERT: D 42 GLN cc_start: 0.9557 (tp-100) cc_final: 0.9327 (tm-30) REVERT: D 43 MET cc_start: 0.9639 (mmm) cc_final: 0.9355 (mmm) REVERT: D 89 ASN cc_start: 0.8802 (t0) cc_final: 0.8595 (m-40) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.0672 time to fit residues: 5.9347 Evaluate side-chains 67 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 170 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [25, 30, 31, 13, 28, 34, 24, 44, 19, 14, 7] chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 126 GLN ** D 192 HIS ** 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 = 0.3769 r_free = 0.3769 target = 0.066882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.046768 restraints weight = 20765.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.048299 restraints weight = 14289.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.049452 restraints weight = 11042.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.050239 restraints weight = 9180.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.050821 restraints weight = 8051.521| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 4300 Z= 0.170 Angle : 0.693 8.791 5935 Z= 0.371 Chirality : 0.042 0.203 659 Planarity : 0.004 0.033 686 Dihedral : 18.613 58.610 822 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.13 % Allowed : 17.82 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.39), residues: 443 helix: 0.50 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -3.40 (0.49), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 94 TYR 0.020 0.003 TYR D 219 PHE 0.015 0.001 PHE D 114 TRP 0.005 0.001 TRP C 198 HIS 0.013 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 ( 4300) covalent geometry : angle 0.69293 / 0.37 ( 5935) hydrogen bonds : bond 0.04120 / 2.75 ( 259) hydrogen bonds : angle 4.05561 / 2.87 ( 747) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 GLN cc_start: 0.8827 (pt0) cc_final: 0.8542 (pt0) REVERT: C 43 MET cc_start: 0.9344 (mmm) cc_final: 0.9073 (mmm) REVERT: C 62 MET cc_start: 0.8466 (ttp) cc_final: 0.8192 (mtm) REVERT: C 101 ASP cc_start: 0.9594 (t0) cc_final: 0.9390 (p0) REVERT: C 126 GLN cc_start: 0.9483 (tt0) cc_final: 0.8560 (tp-100) REVERT: C 130 PHE cc_start: 0.9474 (m-10) cc_final: 0.8743 (m-80) REVERT: C 153 LYS cc_start: 0.9756 (pptt) cc_final: 0.9482 (tptp) REVERT: C 181 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8857 (mt-10) REVERT: C 212 HIS cc_start: 0.9388 (p-80) cc_final: 0.9132 (m-70) REVERT: D 35 MET cc_start: 0.9563 (tmm) cc_final: 0.9213 (ppp) REVERT: D 42 GLN cc_start: 0.9556 (tp-100) cc_final: 0.9341 (tm-30) REVERT: D 43 MET cc_start: 0.9640 (mmm) cc_final: 0.9366 (mmm) REVERT: D 62 MET cc_start: 0.1590 (ttt) cc_final: 0.1043 (tpp) REVERT: D 97 ARG cc_start: 0.8999 (mmp80) cc_final: 0.8264 (mmp80) REVERT: D 110 MET cc_start: 0.8086 (tpt) cc_final: 0.7158 (tpt) REVERT: D 112 LYS cc_start: 0.9072 (mmtm) cc_final: 0.8823 (mttt) REVERT: D 147 GLN cc_start: 0.9014 (mp10) cc_final: 0.8636 (mp10) REVERT: D 188 PHE cc_start: 0.9477 (m-80) cc_final: 0.9199 (m-80) outliers start: 8 outliers final: 3 residues processed: 80 average time/residue: 0.0712 time to fit residues: 7.1615 Evaluate side-chains 74 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [44, 24, 1, 26, 17, 16, 20, 32, 34, 35, 5] chunk 44 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.066282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.045962 restraints weight = 21177.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.047532 restraints weight = 14389.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.048658 restraints weight = 11097.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.049493 restraints weight = 9208.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.050119 restraints weight = 8030.337| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4300 Z= 0.166 Angle : 0.710 10.863 5935 Z= 0.373 Chirality : 0.043 0.342 659 Planarity : 0.004 0.033 686 Dihedral : 18.671 58.044 822 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.66 % Allowed : 19.15 % Favored : 78.19 % 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 are not related in a simple way. whole: -0.65 (0.39), residues: 443 helix: 0.61 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -3.37 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.019 0.003 TYR D 219 PHE 0.020 0.001 PHE D 175 TRP 0.003 0.001 TRP D 198 HIS 0.010 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 ( 4300) covalent geometry : angle 0.71037 / 0.37 ( 5935) hydrogen bonds : bond 0.04083 / 2.72 ( 259) hydrogen bonds : angle 4.02600 / 2.86 ( 747) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 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: C 42 GLN cc_start: 0.8867 (pt0) cc_final: 0.8544 (pt0) REVERT: C 43 MET cc_start: 0.9372 (mmm) cc_final: 0.9090 (mmm) REVERT: C 126 GLN cc_start: 0.9463 (tt0) cc_final: 0.8658 (tp40) REVERT: C 130 PHE cc_start: 0.9466 (m-10) cc_final: 0.8865 (m-80) REVERT: C 153 LYS cc_start: 0.9758 (pptt) cc_final: 0.9493 (tptp) REVERT: C 181 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8876 (mt-10) REVERT: C 212 HIS cc_start: 0.9435 (p-80) cc_final: 0.9109 (m-70) REVERT: D 35 MET cc_start: 0.9560 (tmm) cc_final: 0.9255 (ppp) REVERT: D 42 GLN cc_start: 0.9562 (tp-100) cc_final: 0.9341 (tm-30) REVERT: D 43 MET cc_start: 0.9658 (mmm) cc_final: 0.9392 (mmm) REVERT: D 89 ASN cc_start: 0.8357 (t0) cc_final: 0.8153 (m-40) REVERT: D 97 ARG cc_start: 0.9034 (mmp80) cc_final: 0.8324 (mmp80) REVERT: D 110 MET cc_start: 0.8060 (tpt) cc_final: 0.7674 (tpt) REVERT: D 147 GLN cc_start: 0.9034 (mp10) cc_final: 0.8655 (mp10) REVERT: D 181 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8903 (mt-10) REVERT: D 188 PHE cc_start: 0.9470 (m-80) cc_final: 0.9233 (m-80) REVERT: D 221 GLN cc_start: 0.9076 (mt0) cc_final: 0.8683 (mt0) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.0696 time to fit residues: 6.9513 Evaluate side-chains 80 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [10, 43, 34, 32, 9, 27, 26, 0, 18, 21, 20] chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 18 optimal weight: 0.0770 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 215 ASN D 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.066259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.046120 restraints weight = 21570.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047678 restraints weight = 14480.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.048780 restraints weight = 11161.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.049619 restraints weight = 9302.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.050205 restraints weight = 8151.362| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4300 Z= 0.161 Angle : 0.705 9.968 5935 Z= 0.370 Chirality : 0.041 0.219 659 Planarity : 0.004 0.035 686 Dihedral : 18.748 58.342 822 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.13 % Allowed : 20.48 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.39), residues: 443 helix: 0.65 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -3.22 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 94 TYR 0.019 0.003 TYR D 219 PHE 0.020 0.001 PHE D 175 TRP 0.004 0.001 TRP C 198 HIS 0.012 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 4300) covalent geometry : angle 0.70506 / 0.37 ( 5935) hydrogen bonds : bond 0.03928 / 2.63 ( 259) hydrogen bonds : angle 4.02112 / 2.84 ( 747) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.143 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: C 42 GLN cc_start: 0.8854 (pt0) cc_final: 0.8508 (pt0) REVERT: C 43 MET cc_start: 0.9384 (mmm) cc_final: 0.9075 (mmm) REVERT: C 62 MET cc_start: 0.8199 (mtm) cc_final: 0.7778 (mtt) REVERT: C 126 GLN cc_start: 0.9467 (tt0) cc_final: 0.8685 (tp40) REVERT: C 130 PHE cc_start: 0.9479 (m-10) cc_final: 0.8809 (m-80) REVERT: C 153 LYS cc_start: 0.9744 (pptt) cc_final: 0.9470 (tptp) REVERT: C 181 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8853 (mt-10) REVERT: D 42 GLN cc_start: 0.9567 (tp-100) cc_final: 0.9336 (tm-30) REVERT: D 43 MET cc_start: 0.9642 (mmm) cc_final: 0.9366 (mmm) REVERT: D 62 MET cc_start: 0.1349 (ttt) cc_final: 0.0911 (tpt) REVERT: D 89 ASN cc_start: 0.8347 (t0) cc_final: 0.8132 (m-40) REVERT: D 110 MET cc_start: 0.7885 (tpt) cc_final: 0.7528 (tpt) REVERT: D 147 GLN cc_start: 0.9011 (mp10) cc_final: 0.8633 (mp10) REVERT: D 221 GLN cc_start: 0.9052 (mt0) cc_final: 0.8657 (mt0) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.0642 time to fit residues: 6.5919 Evaluate side-chains 75 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 117 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [6, 41, 44, 17, 21, 8, 25, 11, 2, 29, 15] chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 192 HIS ** 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 = 0.3755 r_free = 0.3755 target = 0.066400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.046401 restraints weight = 21295.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.047860 restraints weight = 14341.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.048980 restraints weight = 11242.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.049816 restraints weight = 9344.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.050389 restraints weight = 8145.668| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4300 Z= 0.149 Angle : 0.721 10.144 5935 Z= 0.379 Chirality : 0.043 0.270 659 Planarity : 0.004 0.035 686 Dihedral : 18.791 58.018 822 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.60 % Allowed : 22.87 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.40), residues: 443 helix: 0.82 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -3.09 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 94 TYR 0.019 0.003 TYR D 219 PHE 0.022 0.001 PHE D 175 TRP 0.002 0.001 TRP C 198 HIS 0.008 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 4300) covalent geometry : angle 0.72080 / 0.38 ( 5935) hydrogen bonds : bond 0.03915 / 2.58 ( 259) hydrogen bonds : angle 3.99232 / 2.84 ( 747) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.141 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: C 37 GLU cc_start: 0.9514 (pp20) cc_final: 0.9276 (pp20) REVERT: C 43 MET cc_start: 0.9417 (mmm) cc_final: 0.9119 (tpp) REVERT: C 62 MET cc_start: 0.8290 (mtm) cc_final: 0.7867 (mtt) REVERT: C 126 GLN cc_start: 0.9451 (tt0) cc_final: 0.8687 (tp40) REVERT: C 130 PHE cc_start: 0.9470 (m-10) cc_final: 0.8808 (m-80) REVERT: C 153 LYS cc_start: 0.9739 (pptt) cc_final: 0.9462 (tptp) REVERT: C 181 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8714 (mt-10) REVERT: D 42 GLN cc_start: 0.9563 (tp-100) cc_final: 0.9330 (tm-30) REVERT: D 43 MET cc_start: 0.9642 (mmm) cc_final: 0.9367 (mmm) REVERT: D 62 MET cc_start: 0.1504 (ttt) cc_final: 0.0981 (tpp) REVERT: D 89 ASN cc_start: 0.8349 (t0) cc_final: 0.8133 (m-40) REVERT: D 110 MET cc_start: 0.7882 (tpt) cc_final: 0.7528 (tpt) REVERT: D 147 GLN cc_start: 0.8987 (mp10) cc_final: 0.8611 (mp10) REVERT: D 221 GLN cc_start: 0.9032 (mt0) cc_final: 0.8644 (mt0) outliers start: 6 outliers final: 6 residues processed: 79 average time/residue: 0.0682 time to fit residues: 6.7698 Evaluate side-chains 76 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [1, 20, 35, 29, 19, 30, 4, 7, 31, 3, 12] chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.064478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.044697 restraints weight = 21456.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.046208 restraints weight = 14583.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.047302 restraints weight = 11261.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.048050 restraints weight = 9407.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.048641 restraints weight = 8291.409| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4300 Z= 0.202 Angle : 0.784 12.291 5935 Z= 0.412 Chirality : 0.043 0.322 659 Planarity : 0.004 0.033 686 Dihedral : 18.906 58.406 822 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.66 % Allowed : 23.14 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.39), residues: 443 helix: 0.69 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.99 (0.53), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 94 TYR 0.019 0.003 TYR D 219 PHE 0.025 0.002 PHE D 175 TRP 0.004 0.001 TRP C 198 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 ( 4300) covalent geometry : angle 0.78402 / 0.41 ( 5935) hydrogen bonds : bond 0.04529 / 2.95 ( 259) hydrogen bonds : angle 4.26628 / 3.04 ( 747) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 MET cc_start: 0.9532 (tmm) cc_final: 0.9164 (ppp) REVERT: C 43 MET cc_start: 0.9437 (mmm) cc_final: 0.9097 (tpp) REVERT: C 62 MET cc_start: 0.8410 (mtm) cc_final: 0.8027 (mtt) REVERT: C 126 GLN cc_start: 0.9464 (tt0) cc_final: 0.8753 (tp40) REVERT: C 130 PHE cc_start: 0.9496 (m-10) cc_final: 0.8966 (m-80) REVERT: C 138 TYR cc_start: 0.8996 (t80) cc_final: 0.8613 (t80) REVERT: C 181 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8822 (mt-10) REVERT: D 89 ASN cc_start: 0.8333 (t0) cc_final: 0.8130 (m-40) REVERT: D 110 MET cc_start: 0.7915 (tpt) cc_final: 0.7530 (tpt) REVERT: D 221 GLN cc_start: 0.9049 (mt0) cc_final: 0.8673 (mt0) outliers start: 10 outliers final: 6 residues processed: 77 average time/residue: 0.0600 time to fit residues: 5.9905 Evaluate side-chains 68 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [43, 18, 1, 25, 15, 41, 8, 11, 6, 32, 40] chunk 43 optimal weight: 40.0000 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.065775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.045674 restraints weight = 21154.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.047261 restraints weight = 14065.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.048420 restraints weight = 10744.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.049080 restraints weight = 8902.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.049813 restraints weight = 7879.857| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4300 Z= 0.163 Angle : 0.891 14.250 5935 Z= 0.449 Chirality : 0.046 0.317 659 Planarity : 0.004 0.034 686 Dihedral : 18.964 58.268 822 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.13 % Allowed : 24.20 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.39), residues: 443 helix: 0.57 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -2.92 (0.53), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 94 TYR 0.018 0.003 TYR D 219 PHE 0.021 0.001 PHE D 175 TRP 0.004 0.001 TRP D 198 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 4300) covalent geometry : angle 0.89114 / 0.45 ( 5935) hydrogen bonds : bond 0.04050 / 2.68 ( 259) hydrogen bonds : angle 4.28978 / 2.99 ( 747) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.9591 (pp20) cc_final: 0.9372 (pp20) REVERT: C 43 MET cc_start: 0.9442 (mmm) cc_final: 0.9080 (tpp) REVERT: C 62 MET cc_start: 0.8450 (mtm) cc_final: 0.8054 (mtt) REVERT: C 126 GLN cc_start: 0.9426 (tt0) cc_final: 0.8720 (tp40) REVERT: C 130 PHE cc_start: 0.9494 (m-10) cc_final: 0.8931 (m-80) REVERT: C 138 TYR cc_start: 0.8955 (t80) cc_final: 0.8557 (t80) REVERT: C 181 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8771 (mt-10) REVERT: D 110 MET cc_start: 0.7847 (tpt) cc_final: 0.7437 (tpt) REVERT: D 147 GLN cc_start: 0.9002 (mp10) cc_final: 0.8633 (mp10) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.0586 time to fit residues: 5.5380 Evaluate side-chains 75 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [22, 2, 36, 17, 27, 10, 41, 44, 4, 15, 26] chunk 22 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 44 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.064655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.045092 restraints weight = 20955.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.046562 restraints weight = 14355.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047633 restraints weight = 11162.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.048386 restraints weight = 9345.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.048936 restraints weight = 8236.476| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4300 Z= 0.204 Angle : 0.893 13.636 5935 Z= 0.461 Chirality : 0.047 0.329 659 Planarity : 0.004 0.042 686 Dihedral : 19.027 59.899 822 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.60 % Allowed : 25.27 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.39), residues: 443 helix: 0.44 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -2.90 (0.52), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 94 TYR 0.020 0.003 TYR D 219 PHE 0.029 0.002 PHE D 175 TRP 0.008 0.002 TRP D 198 HIS 0.006 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 ( 4300) covalent geometry : angle 0.89321 / 0.46 ( 5935) hydrogen bonds : bond 0.04582 / 3.01 ( 259) hydrogen bonds : angle 4.48809 / 3.14 ( 747) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 MET cc_start: 0.9452 (mmm) cc_final: 0.9083 (tpp) REVERT: C 62 MET cc_start: 0.8448 (mtm) cc_final: 0.8083 (mtt) REVERT: C 126 GLN cc_start: 0.9456 (tt0) cc_final: 0.8773 (tp40) REVERT: C 130 PHE cc_start: 0.9504 (m-10) cc_final: 0.9018 (m-80) REVERT: C 138 TYR cc_start: 0.8987 (t80) cc_final: 0.8571 (t80) REVERT: C 181 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8819 (mt-10) REVERT: D 110 MET cc_start: 0.7839 (tpt) cc_final: 0.7449 (tpt) REVERT: D 147 GLN cc_start: 0.9036 (mp10) cc_final: 0.8670 (mp10) REVERT: D 189 MET cc_start: 0.9409 (tpt) cc_final: 0.9201 (mmm) REVERT: D 221 GLN cc_start: 0.9038 (mt0) cc_final: 0.8826 (mp10) outliers start: 6 outliers final: 6 residues processed: 73 average time/residue: 0.0632 time to fit residues: 6.0955 Evaluate side-chains 72 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [16, 17, 38, 40, 14, 28, 41, 23, 7, 9, 22] chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.065775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.045498 restraints weight = 20892.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.047104 restraints weight = 13911.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.048210 restraints weight = 10719.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.049020 restraints weight = 8954.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.049568 restraints weight = 7866.722| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4300 Z= 0.165 Angle : 0.902 14.007 5935 Z= 0.458 Chirality : 0.047 0.307 659 Planarity : 0.004 0.034 686 Dihedral : 19.058 58.392 822 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.86 % Allowed : 25.27 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.39), residues: 443 helix: 0.49 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.87 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 94 TYR 0.018 0.003 TYR D 219 PHE 0.027 0.001 PHE D 175 TRP 0.007 0.001 TRP D 198 HIS 0.016 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 4300) covalent geometry : angle 0.90180 / 0.46 ( 5935) hydrogen bonds : bond 0.04254 / 2.78 ( 259) hydrogen bonds : angle 4.44804 / 3.11 ( 747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 931.51 seconds wall clock time: 16 minutes 45.71 seconds (1005.71 seconds total)