Starting phenix.real_space_refine on Wed Sep 17 06:52:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgi_44513/09_2025/9bgi_44513.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgi_44513/09_2025/9bgi_44513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgi_44513/09_2025/9bgi_44513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgi_44513/09_2025/9bgi_44513.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgi_44513/09_2025/9bgi_44513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgi_44513/09_2025/9bgi_44513.cif" } resolution = 3.05 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= 0.012 sd= 0.067 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 4 5.21 5 S 18 5.16 5 C 3844 2.51 5 N 1140 2.21 5 O 1457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6511 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "B" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "F" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 1.99, per 1000 atoms: 0.31 Number of scatterers: 6511 At special positions: 0 Unit cell: (84.66, 86.32, 101.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 48 15.00 Mg 4 11.99 O 1457 8.00 N 1140 7.00 C 3844 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: 0.55 Conformation dependent library (CDL) restraints added in 287.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 47.6% alpha, 7.7% beta 22 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.694A pdb=" N GLU A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 123 removed outlier: 3.521A pdb=" N GLY A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 178 removed outlier: 4.264A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.621A pdb=" N GLN A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.998A pdb=" N TRP A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.618A pdb=" N GLN A 227 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 250 through 266 removed outlier: 3.935A pdb=" N LEU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'B' and resid 6 through 12 Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 90 through 122 Processing helix chain 'B' and resid 140 through 143 Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.962A pdb=" N VAL B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 250 through 266 removed outlier: 3.891A pdb=" N LEU B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.536A pdb=" N THR B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 149 removed outlier: 7.133A pdb=" N VAL A 193 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 235 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N GLU A 276 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 238 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS A 278 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA A 240 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N TYR A 314 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 277 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 148 removed outlier: 7.185A pdb=" N VAL B 193 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 235 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 274 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 280 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER B 244 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TYR B 314 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1564 1.33 - 1.45: 1459 1.45 - 1.57: 3417 1.57 - 1.69: 92 1.69 - 1.80: 32 Bond restraints: 6564 Sorted by residual: bond pdb=" N ASP B 63 " pdb=" CA ASP B 63 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.05e+00 bond pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.27e-02 6.20e+03 3.21e+00 bond pdb=" C GLN A 129 " pdb=" N PRO A 130 " ideal model delta sigma weight residual 1.333 1.349 -0.016 1.20e-02 6.94e+03 1.69e+00 bond pdb=" C ASP B 63 " pdb=" N TYR B 64 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.38e-02 5.25e+03 1.34e+00 bond pdb=" C4' DT F 16 " pdb=" O4' DT F 16 " ideal model delta sigma weight residual 1.450 1.429 0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 6559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8907 1.47 - 2.94: 167 2.94 - 4.42: 26 4.42 - 5.89: 7 5.89 - 7.36: 1 Bond angle restraints: 9108 Sorted by residual: angle pdb=" N ILE A 59 " pdb=" CA ILE A 59 " pdb=" C ILE A 59 " ideal model delta sigma weight residual 112.96 108.92 4.04 1.00e+00 1.00e+00 1.63e+01 angle pdb=" N VAL B 122 " pdb=" CA VAL B 122 " pdb=" C VAL B 122 " ideal model delta sigma weight residual 112.29 108.76 3.53 9.40e-01 1.13e+00 1.41e+01 angle pdb=" CA TRP B 156 " pdb=" CB TRP B 156 " pdb=" CG TRP B 156 " ideal model delta sigma weight residual 113.60 118.45 -4.85 1.90e+00 2.77e-01 6.53e+00 angle pdb=" C ASP B 155 " pdb=" N TRP B 156 " pdb=" CA TRP B 156 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.45e+00 angle pdb=" CA ASP A 63 " pdb=" C ASP A 63 " pdb=" O ASP A 63 " ideal model delta sigma weight residual 121.15 118.56 2.59 1.10e+00 8.26e-01 5.53e+00 ... (remaining 9103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3076 17.70 - 35.41: 432 35.41 - 53.11: 244 53.11 - 70.82: 52 70.82 - 88.52: 6 Dihedral angle restraints: 3810 sinusoidal: 1852 harmonic: 1958 Sorted by residual: dihedral pdb=" CA GLN B 129 " pdb=" C GLN B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLN A 129 " pdb=" C GLN A 129 " pdb=" N PRO A 130 " pdb=" CA PRO A 130 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CB GLU B 292 " pdb=" CG GLU B 292 " pdb=" CD GLU B 292 " pdb=" OE1 GLU B 292 " ideal model delta sinusoidal sigma weight residual 0.00 -88.52 88.52 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 527 0.024 - 0.048: 271 0.048 - 0.072: 119 0.072 - 0.096: 38 0.096 - 0.120: 47 Chirality restraints: 1002 Sorted by residual: chirality pdb=" CA ILE B 51 " pdb=" N ILE B 51 " pdb=" C ILE B 51 " pdb=" CB ILE B 51 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA VAL A 28 " pdb=" N VAL A 28 " pdb=" C VAL A 28 " pdb=" CB VAL A 28 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 999 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 186 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO B 187 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 187 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 187 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 129 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO A 130 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 130 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 130 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 129 " 0.023 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO B 130 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.019 5.00e-02 4.00e+02 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 117 2.50 - 3.10: 4258 3.10 - 3.70: 9785 3.70 - 4.30: 15291 4.30 - 4.90: 24863 Nonbonded interactions: 54314 Sorted by model distance: nonbonded pdb="MG MG A 401 " pdb=" O HOH C 105 " model vdw 1.899 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 515 " model vdw 1.918 2.170 nonbonded pdb=" OP2 DC F 12 " pdb="MG MG B 402 " model vdw 1.919 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH E 102 " model vdw 1.922 2.170 nonbonded pdb=" OP2 DC D 12 " pdb="MG MG A 402 " model vdw 1.926 2.170 ... (remaining 54309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 2.460 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: 0.020 Process input model: 8.750 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 : 0.004 0.039 6564 Z= 0.162 Angle : 0.523 7.362 9108 Z= 0.295 Chirality : 0.040 0.120 1002 Planarity : 0.004 0.048 1032 Dihedral : 20.545 88.520 2546 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.77 % Allowed : 16.84 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.34), residues: 672 helix: 1.39 (0.32), residues: 284 sheet: -0.94 (0.69), residues: 54 loop : -0.32 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.010 0.001 TYR B 5 PHE 0.009 0.001 PHE B 3 TRP 0.015 0.002 TRP B 117 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6564) covalent geometry : angle 0.52307 ( 9108) hydrogen bonds : bond 0.14871 ( 281) hydrogen bonds : angle 5.56149 ( 759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.252 Fit side-chains REVERT: A 64 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.7685 (t80) REVERT: A 200 ASN cc_start: 0.8969 (m-40) cc_final: 0.8748 (m-40) REVERT: A 243 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7806 (ttt-90) REVERT: A 333 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7636 (tpt90) REVERT: B 200 ASN cc_start: 0.8832 (m-40) cc_final: 0.8562 (t0) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.1184 time to fit residues: 7.7367 Evaluate side-chains 49 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.139718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105941 restraints weight = 7416.942| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.55 r_work: 0.3260 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6564 Z= 0.149 Angle : 0.500 5.725 9108 Z= 0.270 Chirality : 0.040 0.124 1002 Planarity : 0.004 0.043 1032 Dihedral : 21.361 85.857 1285 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.30 % Allowed : 17.20 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.35), residues: 672 helix: 1.70 (0.32), residues: 288 sheet: -0.59 (0.72), residues: 48 loop : -0.10 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.008 0.001 TYR A 5 PHE 0.008 0.001 PHE B 3 TRP 0.012 0.001 TRP B 117 HIS 0.001 0.000 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6564) covalent geometry : angle 0.50040 ( 9108) hydrogen bonds : bond 0.04434 ( 281) hydrogen bonds : angle 4.00414 ( 759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.241 Fit side-chains REVERT: A 64 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.8290 (t80) REVERT: A 333 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7620 (tpt90) REVERT: B 169 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 176 ARG cc_start: 0.8342 (mmm160) cc_final: 0.7905 (tpt90) REVERT: B 200 ASN cc_start: 0.8840 (m-40) cc_final: 0.8586 (t0) outliers start: 13 outliers final: 8 residues processed: 53 average time/residue: 0.1010 time to fit residues: 7.0879 Evaluate side-chains 49 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.147372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.114662 restraints weight = 7308.590| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.54 r_work: 0.3405 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6564 Z= 0.099 Angle : 0.454 5.161 9108 Z= 0.244 Chirality : 0.038 0.128 1002 Planarity : 0.003 0.038 1032 Dihedral : 21.225 86.234 1275 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.42 % Allowed : 17.73 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.35), residues: 672 helix: 2.02 (0.32), residues: 288 sheet: -0.17 (0.74), residues: 58 loop : 0.06 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.009 0.001 TYR B 5 PHE 0.004 0.001 PHE A 83 TRP 0.013 0.001 TRP B 156 HIS 0.000 0.000 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 6564) covalent geometry : angle 0.45450 ( 9108) hydrogen bonds : bond 0.03226 ( 281) hydrogen bonds : angle 3.49997 ( 759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.247 Fit side-chains REVERT: A 64 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8546 (t80) REVERT: A 260 MET cc_start: 0.8944 (ttm) cc_final: 0.8743 (ttt) REVERT: A 333 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7539 (tpt90) REVERT: B 169 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 176 ARG cc_start: 0.8307 (mmm160) cc_final: 0.7889 (tpt90) REVERT: B 200 ASN cc_start: 0.8882 (m-40) cc_final: 0.8606 (t0) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.1075 time to fit residues: 7.7605 Evaluate side-chains 49 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107499 restraints weight = 7309.606| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.49 r_work: 0.3296 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6564 Z= 0.153 Angle : 0.491 6.265 9108 Z= 0.263 Chirality : 0.040 0.128 1002 Planarity : 0.004 0.035 1032 Dihedral : 21.247 84.320 1269 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.48 % Allowed : 16.84 % Favored : 80.67 % 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 aren not related in a simple way. whole: 1.24 (0.35), residues: 672 helix: 1.99 (0.32), residues: 288 sheet: -0.66 (0.72), residues: 48 loop : 0.10 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.014 0.001 TYR B 5 PHE 0.007 0.001 PHE B 329 TRP 0.011 0.001 TRP B 156 HIS 0.001 0.000 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6564) covalent geometry : angle 0.49130 ( 9108) hydrogen bonds : bond 0.04116 ( 281) hydrogen bonds : angle 3.58500 ( 759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.231 Fit side-chains REVERT: A 64 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8427 (t80) REVERT: A 333 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7629 (tpt90) REVERT: B 169 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7931 (mm-30) REVERT: B 176 ARG cc_start: 0.8372 (mmm160) cc_final: 0.7905 (tpt90) REVERT: B 200 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8566 (t0) outliers start: 14 outliers final: 9 residues processed: 51 average time/residue: 0.1036 time to fit residues: 6.8942 Evaluate side-chains 52 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.0060 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.147824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114181 restraints weight = 7462.434| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.57 r_work: 0.3381 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6564 Z= 0.099 Angle : 0.458 5.446 9108 Z= 0.245 Chirality : 0.038 0.129 1002 Planarity : 0.003 0.033 1032 Dihedral : 21.156 84.671 1269 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.30 % Allowed : 16.49 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.35), residues: 672 helix: 2.09 (0.32), residues: 290 sheet: -0.20 (0.74), residues: 58 loop : 0.22 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.007 0.001 TYR A 5 PHE 0.004 0.001 PHE B 3 TRP 0.013 0.001 TRP B 156 HIS 0.000 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 6564) covalent geometry : angle 0.45775 ( 9108) hydrogen bonds : bond 0.03153 ( 281) hydrogen bonds : angle 3.37399 ( 759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.258 Fit side-chains REVERT: A 64 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8473 (t80) REVERT: A 333 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7598 (tpt90) REVERT: B 169 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7951 (mm-30) REVERT: B 176 ARG cc_start: 0.8356 (mmm160) cc_final: 0.7922 (tpt90) REVERT: B 200 ASN cc_start: 0.8874 (m-40) cc_final: 0.8597 (t0) outliers start: 13 outliers final: 8 residues processed: 56 average time/residue: 0.1130 time to fit residues: 8.0575 Evaluate side-chains 53 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.140810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.106835 restraints weight = 7444.220| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.56 r_work: 0.3275 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6564 Z= 0.138 Angle : 0.479 5.349 9108 Z= 0.256 Chirality : 0.039 0.129 1002 Planarity : 0.003 0.031 1032 Dihedral : 21.185 83.088 1269 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.95 % Allowed : 17.20 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.35), residues: 672 helix: 2.10 (0.32), residues: 288 sheet: -0.72 (0.72), residues: 48 loop : 0.19 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.015 0.001 TYR A 5 PHE 0.007 0.001 PHE B 3 TRP 0.011 0.001 TRP B 156 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6564) covalent geometry : angle 0.47938 ( 9108) hydrogen bonds : bond 0.03877 ( 281) hydrogen bonds : angle 3.47066 ( 759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.236 Fit side-chains REVERT: A 64 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8514 (t80) REVERT: A 200 ASN cc_start: 0.8891 (m-40) cc_final: 0.8645 (m-40) REVERT: A 333 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7663 (tpt90) REVERT: B 121 MET cc_start: 0.7651 (mtp) cc_final: 0.7385 (mtp) REVERT: B 169 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7926 (mm-30) REVERT: B 176 ARG cc_start: 0.8364 (mmm160) cc_final: 0.7900 (tpt90) REVERT: B 200 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8573 (t0) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.0971 time to fit residues: 6.5837 Evaluate side-chains 51 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101861 restraints weight = 7395.506| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.51 r_work: 0.3201 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6564 Z= 0.243 Angle : 0.559 5.611 9108 Z= 0.300 Chirality : 0.044 0.131 1002 Planarity : 0.004 0.032 1032 Dihedral : 21.465 81.196 1269 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.84 % Allowed : 16.49 % Favored : 80.67 % 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 aren not related in a simple way. whole: 0.96 (0.34), residues: 672 helix: 1.72 (0.32), residues: 288 sheet: -1.02 (0.66), residues: 52 loop : 0.03 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 29 TYR 0.026 0.002 TYR A 5 PHE 0.012 0.002 PHE B 3 TRP 0.011 0.002 TRP A 111 HIS 0.002 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 6564) covalent geometry : angle 0.55915 ( 9108) hydrogen bonds : bond 0.05252 ( 281) hydrogen bonds : angle 3.78921 ( 759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.243 Fit side-chains REVERT: A 64 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8324 (t80) REVERT: A 231 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8167 (mm-40) REVERT: A 333 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.7742 (tpt90) REVERT: B 121 MET cc_start: 0.7710 (mtp) cc_final: 0.7399 (mmm) REVERT: B 200 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8529 (t0) outliers start: 16 outliers final: 11 residues processed: 51 average time/residue: 0.0986 time to fit residues: 6.6282 Evaluate side-chains 51 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.135187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101610 restraints weight = 7422.990| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.51 r_work: 0.3194 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6564 Z= 0.241 Angle : 0.558 5.644 9108 Z= 0.301 Chirality : 0.044 0.130 1002 Planarity : 0.004 0.034 1032 Dihedral : 21.477 79.575 1269 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.84 % Allowed : 16.67 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.34), residues: 672 helix: 1.55 (0.31), residues: 288 sheet: -1.05 (0.66), residues: 52 loop : -0.03 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 29 TYR 0.025 0.002 TYR A 5 PHE 0.012 0.001 PHE B 102 TRP 0.010 0.002 TRP A 111 HIS 0.002 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 6564) covalent geometry : angle 0.55800 ( 9108) hydrogen bonds : bond 0.05126 ( 281) hydrogen bonds : angle 3.80866 ( 759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.155 Fit side-chains REVERT: A 64 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.8389 (t80) REVERT: A 231 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8148 (mm-40) REVERT: A 333 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7803 (tpt90) REVERT: B 200 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8504 (t0) REVERT: B 229 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8249 (mmt-90) outliers start: 16 outliers final: 11 residues processed: 54 average time/residue: 0.1115 time to fit residues: 7.6453 Evaluate side-chains 53 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105092 restraints weight = 7490.979| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.55 r_work: 0.3250 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6564 Z= 0.143 Angle : 0.496 5.378 9108 Z= 0.266 Chirality : 0.040 0.123 1002 Planarity : 0.004 0.031 1032 Dihedral : 21.269 81.256 1269 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.30 % Allowed : 17.20 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.34), residues: 672 helix: 1.84 (0.32), residues: 288 sheet: -1.00 (0.67), residues: 52 loop : 0.07 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.014 0.001 TYR A 5 PHE 0.008 0.001 PHE B 3 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6564) covalent geometry : angle 0.49630 ( 9108) hydrogen bonds : bond 0.04031 ( 281) hydrogen bonds : angle 3.56252 ( 759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.242 Fit side-chains REVERT: A 64 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8448 (t80) REVERT: A 231 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8164 (mm-40) REVERT: A 333 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7749 (tpt90) REVERT: B 200 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8534 (t0) REVERT: B 229 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8142 (mmt-90) outliers start: 13 outliers final: 10 residues processed: 54 average time/residue: 0.0995 time to fit residues: 7.0312 Evaluate side-chains 56 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.142113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108792 restraints weight = 7441.849| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.56 r_work: 0.3311 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6564 Z= 0.110 Angle : 0.472 5.197 9108 Z= 0.252 Chirality : 0.038 0.127 1002 Planarity : 0.003 0.032 1032 Dihedral : 21.156 80.906 1269 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.77 % Allowed : 17.91 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.35), residues: 672 helix: 2.05 (0.32), residues: 290 sheet: -0.28 (0.73), residues: 58 loop : 0.27 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.008 0.001 TYR A 5 PHE 0.004 0.001 PHE A 35 TRP 0.014 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6564) covalent geometry : angle 0.47169 ( 9108) hydrogen bonds : bond 0.03390 ( 281) hydrogen bonds : angle 3.41015 ( 759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.189 Fit side-chains REVERT: A 64 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8508 (t80) REVERT: A 333 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7722 (tpt90) REVERT: B 200 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8528 (t0) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.1002 time to fit residues: 6.3300 Evaluate side-chains 52 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106140 restraints weight = 7421.091| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.54 r_work: 0.3267 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6564 Z= 0.139 Angle : 0.489 5.259 9108 Z= 0.261 Chirality : 0.040 0.128 1002 Planarity : 0.003 0.031 1032 Dihedral : 21.150 79.872 1269 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.13 % Allowed : 17.55 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.35), residues: 672 helix: 2.02 (0.32), residues: 290 sheet: -0.28 (0.72), residues: 58 loop : 0.29 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.015 0.001 TYR A 5 PHE 0.007 0.001 PHE B 3 TRP 0.020 0.002 TRP B 117 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6564) covalent geometry : angle 0.48912 ( 9108) hydrogen bonds : bond 0.03890 ( 281) hydrogen bonds : angle 3.45879 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1757.39 seconds wall clock time: 30 minutes 44.83 seconds (1844.83 seconds total)