Starting phenix.real_space_refine on Fri Oct 23 02:20:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hby_52034/10_2026/9hby_52034.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hby_52034/10_2026/9hby_52034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hby_52034/10_2026/9hby_52034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hby_52034/10_2026/9hby_52034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hby_52034/10_2026/9hby_52034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hby_52034/10_2026/9hby_52034.map" } resolution = 3.1 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= 0.009 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 35 5.49 5 S 52 5.16 5 C 4911 2.51 5 N 1434 2.21 5 O 1544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 7976 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2286 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2418 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 148 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'RNA': 12} Modifications used: {'rna2p': 2, 'rna3p': 10} Link IDs: {'rna2p': 2, 'rna3p': 9} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "N" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'RNA': 12} Modifications used: {'rna2p': 2, 'rna3p': 10} Link IDs: {'rna2p': 2, 'rna3p': 9} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "O" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 222 Classifications: {'RNA': 11} Modifications used: {'rna2p': 1, 'rna3p': 10} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 1.60, per 1000 atoms: 0.20 Number of scatterers: 7976 At special positions: 0 Unit cell: (116.724, 100.284, 77.268, 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 52 16.00 P 35 15.00 O 1544 8.00 N 1434 7.00 C 4911 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: 0.60 Conformation dependent library (CDL) restraints added in 470.7 milliseconds 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 51.2% alpha, 5.3% beta 0 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.575A pdb=" N PHE A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 143 through 173 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 249 through 258 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.658A pdb=" N LEU A 266 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'C' and resid 36 through 51 removed outlier: 3.530A pdb=" N PHE C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 58 through 74 Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 119 through 128 Processing helix chain 'C' and resid 134 through 142 Processing helix chain 'C' and resid 143 through 173 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 205 through 214 removed outlier: 3.794A pdb=" N ALA C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.797A pdb=" N LEU C 266 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 3.652A pdb=" N GLU C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 307 through 312' Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 58 through 74 Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.666A pdb=" N VAL D 128 " --> pdb=" O CYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 142 Processing helix chain 'D' and resid 143 through 173 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 193 through 200 Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.817A pdb=" N LEU D 266 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 312 removed outlier: 4.085A pdb=" N GLY D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 320 removed outlier: 3.742A pdb=" N GLU D 320 " --> pdb=" O ASN D 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 320' Processing helix chain 'D' and resid 340 through 349 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA3, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AA4, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.518A pdb=" N LEU C 285 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA6, first strand: chain 'D' and resid 247 through 248 removed outlier: 7.600A pdb=" N ILE D 279 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER D 273 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 284 through 286 329 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2530 1.34 - 1.46: 1928 1.46 - 1.58: 3597 1.58 - 1.69: 66 1.69 - 1.81: 70 Bond restraints: 8191 Sorted by residual: bond pdb=" N3 Y5P N 2 " pdb=" C4 Y5P N 2 " ideal model delta sigma weight residual 1.458 1.333 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" N3 Y5P M 2 " pdb=" C4 Y5P M 2 " ideal model delta sigma weight residual 1.458 1.334 0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C2 Y5P N 8 " pdb=" N3 Y5P N 8 " ideal model delta sigma weight residual 1.268 1.373 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C2 Y5P M 12 " pdb=" N3 Y5P M 12 " ideal model delta sigma weight residual 1.268 1.373 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C2 Y5P N 12 " pdb=" N3 Y5P N 12 " ideal model delta sigma weight residual 1.268 1.372 -0.104 2.00e-02 2.50e+03 2.72e+01 ... (remaining 8186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 10943 2.37 - 4.75: 155 4.75 - 7.12: 45 7.12 - 9.49: 16 9.49 - 11.87: 9 Bond angle restraints: 11168 Sorted by residual: angle pdb=" N1 Y5P M 8 " pdb=" C2 Y5P M 8 " pdb=" N3 Y5P M 8 " ideal model delta sigma weight residual 126.68 114.81 11.87 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N1 Y5P M 12 " pdb=" C2 Y5P M 12 " pdb=" N3 Y5P M 12 " ideal model delta sigma weight residual 126.68 114.83 11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N1 Y5P O 9 " pdb=" C2 Y5P O 9 " pdb=" N3 Y5P O 9 " ideal model delta sigma weight residual 126.68 114.84 11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N1 Y5P N 8 " pdb=" C2 Y5P N 8 " pdb=" N3 Y5P N 8 " ideal model delta sigma weight residual 126.68 114.86 11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N1 Y5P O 8 " pdb=" C2 Y5P O 8 " pdb=" N3 Y5P O 8 " ideal model delta sigma weight residual 126.68 114.88 11.80 3.00e+00 1.11e-01 1.55e+01 ... (remaining 11163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.28: 4821 20.28 - 40.55: 431 40.55 - 60.83: 131 60.83 - 81.11: 94 81.11 - 101.39: 36 Dihedral angle restraints: 5513 sinusoidal: 2808 harmonic: 2705 Sorted by residual: dihedral pdb=" P Y5P M 12 " pdb=" O5' Y5P M 12 " pdb=" C5' Y5P M 12 " pdb=" C4' Y5P M 12 " ideal model delta sinusoidal sigma weight residual 248.90 147.51 101.39 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" P Y5P M 8 " pdb=" O5' Y5P M 8 " pdb=" C5' Y5P M 8 " pdb=" C4' Y5P M 8 " ideal model delta sinusoidal sigma weight residual 248.90 149.61 99.29 1 3.00e+01 1.11e-03 1.24e+01 dihedral pdb=" CG ARG A 241 " pdb=" CD ARG A 241 " pdb=" NE ARG A 241 " pdb=" CZ ARG A 241 " ideal model delta sinusoidal sigma weight residual -180.00 -136.49 -43.51 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 5510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 869 0.028 - 0.055: 268 0.055 - 0.083: 55 0.083 - 0.111: 39 0.111 - 0.138: 21 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA ILE D 230 " pdb=" N ILE D 230 " pdb=" C ILE D 230 " pdb=" CB ILE D 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE C 230 " pdb=" N ILE C 230 " pdb=" C ILE C 230 " pdb=" CB ILE C 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE A 230 " pdb=" N ILE A 230 " pdb=" C ILE A 230 " pdb=" CB ILE A 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1249 not shown) Planarity restraints: 1314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 231 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.15e+00 pdb=" N PRO C 232 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 232 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 232 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 35 " -0.015 5.00e-02 4.00e+02 2.30e-02 8.48e-01 pdb=" N PRO D 36 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 285 " -0.015 5.00e-02 4.00e+02 2.27e-02 8.22e-01 pdb=" N PRO A 286 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.013 5.00e-02 4.00e+02 ... (remaining 1311 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 75 2.61 - 3.18: 6850 3.18 - 3.76: 12105 3.76 - 4.33: 16719 4.33 - 4.90: 27883 Nonbonded interactions: 63632 Sorted by model distance: nonbonded pdb=" OD1 ASN D 225 " pdb=" OG1 THR D 290 " model vdw 2.040 3.040 nonbonded pdb=" OG SER D 340 " pdb=" O LEU E 295 " model vdw 2.111 3.040 nonbonded pdb=" OE2 GLU D 321 " pdb=" OG SER E 303 " model vdw 2.161 3.040 nonbonded pdb=" O ASP C 185 " pdb=" OH TYR C 191 " model vdw 2.172 3.040 nonbonded pdb=" O SER A 113 " pdb=" OG SER A 113 " model vdw 2.212 3.040 ... (remaining 63627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 34 through 349) selection = (chain 'C' and (resid 34 through 295 or resid 316 through 349)) selection = (chain 'D' and (resid 34 through 295 or resid 316 through 349)) } ncs_group { reference = (chain 'M' and resid 3 through 12) selection = (chain 'N' and resid 3 through 12) selection = (chain 'O' and resid 3 through 12) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.560 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.008 0.125 8191 Z= 0.415 Angle : 0.837 11.866 11168 Z= 0.328 Chirality : 0.035 0.138 1252 Planarity : 0.003 0.027 1314 Dihedral : 20.548 101.386 3775 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.04 % Allowed : 17.27 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.29), residues: 941 helix: 1.79 (0.26), residues: 446 sheet: -0.36 (0.78), residues: 40 loop : 0.07 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.008 0.001 TYR C 170 PHE 0.005 0.001 PHE A 189 TRP 0.008 0.001 TRP C 259 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00836 / 0.41 ( 8191) covalent geometry : angle 0.83722 / 0.33 (11168) hydrogen bonds : bond 0.12955 / 9.19 ( 329) hydrogen bonds : angle 5.18522 / 3.66 ( 957) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.6666 (tt0) cc_final: 0.6135 (mm-30) REVERT: A 187 GLN cc_start: 0.7833 (tt0) cc_final: 0.7558 (pt0) REVERT: A 323 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7443 (tt) REVERT: C 40 GLU cc_start: 0.7844 (tt0) cc_final: 0.7556 (tt0) REVERT: C 60 SER cc_start: 0.8192 (t) cc_final: 0.7695 (t) REVERT: C 64 ASP cc_start: 0.7471 (m-30) cc_final: 0.7240 (m-30) REVERT: C 94 ARG cc_start: 0.7492 (ttp-170) cc_final: 0.7056 (ttm110) REVERT: C 119 ARG cc_start: 0.8453 (mtm180) cc_final: 0.8161 (ttp-110) REVERT: C 134 LYS cc_start: 0.7988 (mttt) cc_final: 0.7581 (mttp) REVERT: C 151 LYS cc_start: 0.8253 (mttt) cc_final: 0.7984 (mttm) REVERT: C 178 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8119 (mm-30) REVERT: C 195 ASP cc_start: 0.8262 (m-30) cc_final: 0.8053 (m-30) REVERT: D 49 VAL cc_start: 0.8220 (t) cc_final: 0.7769 (m) REVERT: D 119 ARG cc_start: 0.6808 (mtm110) cc_final: 0.6532 (mmm-85) REVERT: D 122 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7352 (mt-10) REVERT: D 127 CYS cc_start: 0.8732 (m) cc_final: 0.8433 (t) REVERT: D 225 ASN cc_start: 0.8472 (m-40) cc_final: 0.8192 (m-40) REVERT: D 271 SER cc_start: 0.8140 (t) cc_final: 0.7660 (p) outliers start: 8 outliers final: 5 residues processed: 203 average time/residue: 0.1222 time to fit residues: 31.2297 Evaluate side-chains 130 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN C 154 ASN C 240 HIS C 247 GLN C 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.224928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.164901 restraints weight = 8409.024| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.87 r_work: 0.3639 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8191 Z= 0.134 Angle : 0.563 4.961 11168 Z= 0.276 Chirality : 0.038 0.134 1252 Planarity : 0.003 0.039 1314 Dihedral : 21.586 105.031 2058 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.56 % Allowed : 18.57 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.13 (0.29), residues: 941 helix: 1.59 (0.25), residues: 462 sheet: -0.25 (0.79), residues: 38 loop : 0.03 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 56 TYR 0.012 0.002 TYR A 197 PHE 0.012 0.001 PHE A 50 TRP 0.010 0.001 TRP D 259 HIS 0.004 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 8191) covalent geometry : angle 0.56338 / 0.28 (11168) hydrogen bonds : bond 0.03744 / 2.52 ( 329) hydrogen bonds : angle 4.26676 / 3.09 ( 957) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.6634 (tt0) cc_final: 0.6086 (mm-30) REVERT: A 114 LEU cc_start: 0.7504 (mt) cc_final: 0.7164 (mt) REVERT: A 187 GLN cc_start: 0.7855 (tt0) cc_final: 0.7544 (pt0) REVERT: C 60 SER cc_start: 0.8274 (t) cc_final: 0.7780 (t) REVERT: C 64 ASP cc_start: 0.7578 (m-30) cc_final: 0.7328 (m-30) REVERT: C 119 ARG cc_start: 0.8481 (mtm180) cc_final: 0.8073 (ttp-110) REVERT: C 151 LYS cc_start: 0.8320 (mttt) cc_final: 0.8043 (mttm) REVERT: D 127 CYS cc_start: 0.8744 (m) cc_final: 0.8426 (t) REVERT: D 177 ASP cc_start: 0.7764 (t0) cc_final: 0.7537 (t0) REVERT: D 268 GLU cc_start: 0.7185 (tp30) cc_final: 0.6901 (tp30) REVERT: D 271 SER cc_start: 0.8101 (t) cc_final: 0.7468 (p) outliers start: 12 outliers final: 5 residues processed: 138 average time/residue: 0.1006 time to fit residues: 18.3020 Evaluate side-chains 119 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 340 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [62, 93, 51, 37, 78, 3, 30, 45, 44, 41, 21] chunk 62 optimal weight: 0.0000 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN D 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.222294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.160440 restraints weight = 8319.801| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.85 r_work: 0.3471 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8191 Z= 0.108 Angle : 0.531 4.689 11168 Z= 0.257 Chirality : 0.037 0.132 1252 Planarity : 0.003 0.039 1314 Dihedral : 21.386 109.107 2052 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.82 % Allowed : 19.22 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.11 (0.29), residues: 941 helix: 1.64 (0.25), residues: 462 sheet: -0.33 (0.79), residues: 38 loop : -0.06 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 56 TYR 0.009 0.001 TYR C 123 PHE 0.012 0.001 PHE A 50 TRP 0.009 0.001 TRP D 259 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8191) covalent geometry : angle 0.53063 / 0.26 (11168) hydrogen bonds : bond 0.03320 / 2.21 ( 329) hydrogen bonds : angle 4.06824 / 2.96 ( 957) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.6638 (tt0) cc_final: 0.6012 (mm-30) REVERT: A 114 LEU cc_start: 0.7511 (mt) cc_final: 0.7188 (mt) REVERT: A 187 GLN cc_start: 0.7802 (tt0) cc_final: 0.7434 (pt0) REVERT: C 60 SER cc_start: 0.8337 (t) cc_final: 0.7778 (t) REVERT: C 64 ASP cc_start: 0.7564 (m-30) cc_final: 0.7274 (m-30) REVERT: C 83 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6346 (mttt) REVERT: C 119 ARG cc_start: 0.8536 (mtm180) cc_final: 0.8067 (ttp-110) REVERT: C 151 LYS cc_start: 0.8265 (mttt) cc_final: 0.7958 (mttm) REVERT: C 220 ASN cc_start: 0.7981 (p0) cc_final: 0.7711 (p0) REVERT: C 247 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7402 (mm-40) REVERT: D 127 CYS cc_start: 0.8639 (m) cc_final: 0.8377 (t) REVERT: D 177 ASP cc_start: 0.7642 (t0) cc_final: 0.7320 (t0) REVERT: D 268 GLU cc_start: 0.7133 (tp30) cc_final: 0.6807 (tp30) REVERT: D 271 SER cc_start: 0.8101 (t) cc_final: 0.7458 (p) REVERT: D 326 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6766 (tm-30) REVERT: D 347 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6023 (pt0) outliers start: 14 outliers final: 4 residues processed: 131 average time/residue: 0.1047 time to fit residues: 18.0679 Evaluate side-chains 117 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 344 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [38, 56, 73, 82, 89, 41, 68, 67, 95, 13, 11] chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN C 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.224554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.165893 restraints weight = 8499.737| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.00 r_work: 0.3637 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8191 Z= 0.110 Angle : 0.530 4.590 11168 Z= 0.258 Chirality : 0.037 0.130 1252 Planarity : 0.003 0.044 1314 Dihedral : 21.227 110.922 2050 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.21 % Allowed : 18.96 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.05 (0.29), residues: 941 helix: 1.63 (0.25), residues: 464 sheet: -0.54 (0.80), residues: 38 loop : -0.14 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 198 TYR 0.009 0.001 TYR C 170 PHE 0.011 0.001 PHE A 50 TRP 0.010 0.001 TRP C 259 HIS 0.004 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 8191) covalent geometry : angle 0.53032 / 0.26 (11168) hydrogen bonds : bond 0.03209 / 2.14 ( 329) hydrogen bonds : angle 4.02570 / 2.94 ( 957) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7644 (mpt180) cc_final: 0.7151 (mmt90) REVERT: A 114 LEU cc_start: 0.7597 (mt) cc_final: 0.7303 (mt) REVERT: A 187 GLN cc_start: 0.7838 (tt0) cc_final: 0.7479 (pt0) REVERT: C 83 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6742 (mttt) REVERT: C 119 ARG cc_start: 0.8469 (mtm180) cc_final: 0.8077 (ttp-110) REVERT: C 151 LYS cc_start: 0.8347 (mttt) cc_final: 0.8047 (mttm) REVERT: C 220 ASN cc_start: 0.7962 (p0) cc_final: 0.7659 (p0) REVERT: C 247 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7534 (mm-40) REVERT: D 127 CYS cc_start: 0.8662 (m) cc_final: 0.8443 (t) REVERT: D 177 ASP cc_start: 0.7647 (t0) cc_final: 0.7333 (t0) REVERT: D 268 GLU cc_start: 0.7000 (tp30) cc_final: 0.6732 (tp30) REVERT: D 271 SER cc_start: 0.8092 (t) cc_final: 0.7457 (p) REVERT: D 347 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6119 (pt0) outliers start: 17 outliers final: 11 residues processed: 135 average time/residue: 0.1065 time to fit residues: 18.7651 Evaluate side-chains 129 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [81, 42, 95, 51, 87, 59, 24, 69, 14, 0, 94] chunk 81 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 87 optimal weight: 0.2980 chunk 59 optimal weight: 0.0770 chunk 24 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.222144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.160294 restraints weight = 8475.017| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.89 r_work: 0.3479 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8191 Z= 0.107 Angle : 0.523 4.463 11168 Z= 0.254 Chirality : 0.037 0.130 1252 Planarity : 0.003 0.050 1314 Dihedral : 21.093 113.693 2050 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.99 % Allowed : 17.92 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.06 (0.29), residues: 941 helix: 1.67 (0.25), residues: 460 sheet: -0.51 (0.82), residues: 38 loop : -0.16 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 198 TYR 0.009 0.001 TYR C 170 PHE 0.013 0.001 PHE A 50 TRP 0.010 0.001 TRP D 259 HIS 0.003 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8191) covalent geometry : angle 0.52342 / 0.25 (11168) hydrogen bonds : bond 0.03122 / 2.08 ( 329) hydrogen bonds : angle 3.99081 / 2.93 ( 957) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7649 (mpt180) cc_final: 0.7168 (mmt90) REVERT: A 114 LEU cc_start: 0.7639 (mt) cc_final: 0.7337 (mt) REVERT: A 187 GLN cc_start: 0.7837 (tt0) cc_final: 0.7404 (pt0) REVERT: C 83 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6701 (mttt) REVERT: C 119 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8071 (ttp-110) REVERT: C 151 LYS cc_start: 0.8369 (mttt) cc_final: 0.8069 (mttm) REVERT: C 220 ASN cc_start: 0.7952 (p0) cc_final: 0.7652 (p0) REVERT: C 247 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7924 (mm-40) REVERT: C 299 SER cc_start: 0.8064 (p) cc_final: 0.7797 (m) REVERT: D 127 CYS cc_start: 0.8625 (m) cc_final: 0.8417 (t) REVERT: D 177 ASP cc_start: 0.7722 (t0) cc_final: 0.7369 (t0) REVERT: D 268 GLU cc_start: 0.7056 (tp30) cc_final: 0.6750 (tp30) REVERT: D 271 SER cc_start: 0.8114 (t) cc_final: 0.7499 (p) REVERT: D 347 GLU cc_start: 0.6913 (tm-30) cc_final: 0.6148 (pt0) outliers start: 23 outliers final: 16 residues processed: 135 average time/residue: 0.0960 time to fit residues: 17.2989 Evaluate side-chains 129 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 340 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [23, 32, 3, 31, 42, 82, 76, 18, 13, 19, 36] chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.217824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.157832 restraints weight = 8366.486| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.94 r_work: 0.3477 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8191 Z= 0.127 Angle : 0.534 4.363 11168 Z= 0.259 Chirality : 0.037 0.134 1252 Planarity : 0.003 0.054 1314 Dihedral : 21.023 115.523 2050 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.73 % Allowed : 19.09 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.01 (0.29), residues: 941 helix: 1.62 (0.25), residues: 460 sheet: -0.44 (0.83), residues: 38 loop : -0.18 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 56 TYR 0.010 0.001 TYR C 170 PHE 0.012 0.001 PHE A 50 TRP 0.011 0.001 TRP C 259 HIS 0.003 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8191) covalent geometry : angle 0.53368 / 0.26 (11168) hydrogen bonds : bond 0.03216 / 2.14 ( 329) hydrogen bonds : angle 4.03281 / 2.96 ( 957) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7671 (mpt180) cc_final: 0.7205 (mmt90) REVERT: A 114 LEU cc_start: 0.7630 (mt) cc_final: 0.7357 (mt) REVERT: A 187 GLN cc_start: 0.7804 (tt0) cc_final: 0.7330 (pt0) REVERT: A 197 TYR cc_start: 0.8106 (t80) cc_final: 0.7829 (t80) REVERT: A 288 GLN cc_start: 0.7895 (tt0) cc_final: 0.7679 (tt0) REVERT: C 83 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6453 (mttt) REVERT: C 119 ARG cc_start: 0.8462 (mtm180) cc_final: 0.8004 (ttp-110) REVERT: C 151 LYS cc_start: 0.8296 (mttt) cc_final: 0.7991 (mttm) REVERT: C 220 ASN cc_start: 0.7984 (p0) cc_final: 0.7726 (p0) REVERT: C 317 ASN cc_start: 0.8487 (p0) cc_final: 0.7862 (p0) REVERT: D 109 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.6960 (ttm-80) REVERT: D 127 CYS cc_start: 0.8626 (m) cc_final: 0.8358 (t) REVERT: D 177 ASP cc_start: 0.7720 (t0) cc_final: 0.7337 (t0) REVERT: D 268 GLU cc_start: 0.7060 (tp30) cc_final: 0.6733 (tp30) REVERT: D 271 SER cc_start: 0.8098 (t) cc_final: 0.7465 (p) REVERT: D 347 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6093 (pt0) outliers start: 21 outliers final: 17 residues processed: 130 average time/residue: 0.0960 time to fit residues: 16.4363 Evaluate side-chains 124 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 340 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [22, 72, 0, 2, 76, 35, 87, 12, 28, 31, 39] chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 87 optimal weight: 0.0060 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 39 optimal weight: 3.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.219938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160526 restraints weight = 8418.022| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.95 r_work: 0.3514 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8191 Z= 0.088 Angle : 0.508 4.708 11168 Z= 0.245 Chirality : 0.036 0.129 1252 Planarity : 0.003 0.052 1314 Dihedral : 20.908 117.582 2050 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.21 % Allowed : 19.48 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.15 (0.29), residues: 941 helix: 1.75 (0.25), residues: 460 sheet: -0.25 (0.86), residues: 38 loop : -0.15 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 56 TYR 0.019 0.001 TYR A 123 PHE 0.010 0.001 PHE A 50 TRP 0.009 0.001 TRP D 259 HIS 0.003 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 8191) covalent geometry : angle 0.50825 / 0.24 (11168) hydrogen bonds : bond 0.02933 / 1.95 ( 329) hydrogen bonds : angle 3.94144 / 2.90 ( 957) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7631 (mpt180) cc_final: 0.7177 (mmt90) REVERT: A 114 LEU cc_start: 0.7624 (mt) cc_final: 0.7394 (mt) REVERT: A 197 TYR cc_start: 0.8080 (t80) cc_final: 0.7796 (t80) REVERT: A 288 GLN cc_start: 0.7878 (tt0) cc_final: 0.7654 (tt0) REVERT: C 83 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.6449 (mttp) REVERT: C 119 ARG cc_start: 0.8441 (mtm180) cc_final: 0.7975 (ttp-110) REVERT: C 151 LYS cc_start: 0.8297 (mttt) cc_final: 0.7976 (mttm) REVERT: C 220 ASN cc_start: 0.7986 (p0) cc_final: 0.7735 (p0) REVERT: C 247 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7985 (mm-40) REVERT: C 317 ASN cc_start: 0.8451 (p0) cc_final: 0.7891 (p0) REVERT: D 109 ARG cc_start: 0.7359 (ttm-80) cc_final: 0.6854 (ttm-80) REVERT: D 127 CYS cc_start: 0.8613 (m) cc_final: 0.8372 (t) REVERT: D 177 ASP cc_start: 0.7677 (t0) cc_final: 0.7300 (t0) REVERT: D 268 GLU cc_start: 0.7072 (tp30) cc_final: 0.6767 (tp30) REVERT: D 271 SER cc_start: 0.8130 (t) cc_final: 0.7474 (p) REVERT: D 347 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6125 (pt0) outliers start: 17 outliers final: 14 residues processed: 129 average time/residue: 0.0960 time to fit residues: 16.3748 Evaluate side-chains 124 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 340 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [65, 76, 38, 87, 77, 29, 93, 2, 63, 7, 21] chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.220529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.163081 restraints weight = 8305.037| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.79 r_work: 0.3584 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8191 Z= 0.164 Angle : 0.554 4.352 11168 Z= 0.269 Chirality : 0.038 0.141 1252 Planarity : 0.003 0.058 1314 Dihedral : 20.885 116.173 2050 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.12 % Allowed : 18.70 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.99 (0.29), residues: 941 helix: 1.60 (0.25), residues: 458 sheet: -0.25 (0.86), residues: 38 loop : -0.20 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 56 TYR 0.012 0.002 TYR A 123 PHE 0.010 0.002 PHE A 50 TRP 0.012 0.002 TRP C 259 HIS 0.003 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.16 ( 8191) covalent geometry : angle 0.55385 / 0.27 (11168) hydrogen bonds : bond 0.03346 / 2.24 ( 329) hydrogen bonds : angle 4.05206 / 2.97 ( 957) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7558 (mpt180) cc_final: 0.7107 (mmt90) REVERT: A 114 LEU cc_start: 0.7620 (mt) cc_final: 0.7344 (mt) REVERT: A 187 GLN cc_start: 0.7834 (tt0) cc_final: 0.7343 (pt0) REVERT: A 197 TYR cc_start: 0.8067 (t80) cc_final: 0.7806 (t80) REVERT: A 288 GLN cc_start: 0.8000 (tt0) cc_final: 0.7750 (tt0) REVERT: C 119 ARG cc_start: 0.8482 (mtm180) cc_final: 0.8009 (ttp-110) REVERT: C 151 LYS cc_start: 0.8276 (mttt) cc_final: 0.7962 (mttm) REVERT: C 220 ASN cc_start: 0.8010 (p0) cc_final: 0.7792 (p0) REVERT: C 247 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7983 (mm-40) REVERT: C 317 ASN cc_start: 0.8432 (p0) cc_final: 0.7875 (p0) REVERT: D 95 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8238 (mm-30) REVERT: D 109 ARG cc_start: 0.7402 (ttm-80) cc_final: 0.6925 (ttm-80) REVERT: D 127 CYS cc_start: 0.8629 (m) cc_final: 0.8366 (t) REVERT: D 177 ASP cc_start: 0.7748 (t0) cc_final: 0.7372 (t0) REVERT: D 268 GLU cc_start: 0.7013 (tp30) cc_final: 0.6669 (tp30) REVERT: D 271 SER cc_start: 0.8142 (t) cc_final: 0.7423 (p) REVERT: D 347 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6094 (pt0) outliers start: 24 outliers final: 17 residues processed: 129 average time/residue: 0.0966 time to fit residues: 16.7560 Evaluate side-chains 125 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 340 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [41, 9, 65, 89, 48, 68, 13, 14, 77, 30, 11] chunk 41 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.223628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.163232 restraints weight = 8515.292| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.89 r_work: 0.3652 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8191 Z= 0.118 Angle : 0.539 4.956 11168 Z= 0.261 Chirality : 0.037 0.133 1252 Planarity : 0.003 0.061 1314 Dihedral : 20.851 119.624 2050 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.21 % Allowed : 19.74 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.00 (0.29), residues: 941 helix: 1.62 (0.25), residues: 460 sheet: -0.25 (0.87), residues: 38 loop : -0.21 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 56 TYR 0.019 0.002 TYR A 123 PHE 0.010 0.001 PHE A 50 TRP 0.010 0.001 TRP D 259 HIS 0.003 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 8191) covalent geometry : angle 0.53928 / 0.26 (11168) hydrogen bonds : bond 0.03139 / 2.08 ( 329) hydrogen bonds : angle 4.01714 / 2.95 ( 957) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7545 (mpt180) cc_final: 0.7110 (mmt90) REVERT: A 114 LEU cc_start: 0.7749 (mt) cc_final: 0.7447 (mt) REVERT: A 197 TYR cc_start: 0.8119 (t80) cc_final: 0.7894 (t80) REVERT: A 288 GLN cc_start: 0.7992 (tt0) cc_final: 0.7790 (tt0) REVERT: C 119 ARG cc_start: 0.8461 (mtm180) cc_final: 0.8054 (ttp-110) REVERT: C 151 LYS cc_start: 0.8377 (mttt) cc_final: 0.8067 (mttm) REVERT: C 220 ASN cc_start: 0.8069 (p0) cc_final: 0.7855 (p0) REVERT: C 247 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8033 (mm-40) REVERT: C 317 ASN cc_start: 0.8470 (p0) cc_final: 0.7905 (p0) REVERT: D 95 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8281 (mm-30) REVERT: D 109 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.6945 (ttm-80) REVERT: D 127 CYS cc_start: 0.8636 (m) cc_final: 0.8402 (t) REVERT: D 177 ASP cc_start: 0.7756 (t0) cc_final: 0.7409 (t0) REVERT: D 268 GLU cc_start: 0.7039 (tp30) cc_final: 0.6714 (tp30) REVERT: D 347 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6135 (pt0) outliers start: 17 outliers final: 14 residues processed: 128 average time/residue: 0.0941 time to fit residues: 16.1626 Evaluate side-chains 122 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 340 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [15, 6, 4, 79, 39, 16, 19, 10, 60, 38, 62] chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.0070 chunk 10 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 38 optimal weight: 0.0020 chunk 62 optimal weight: 1.9990 overall best weight: 0.9410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.216050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156802 restraints weight = 8433.861| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.02 r_work: 0.3451 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8191 Z= 0.142 Angle : 0.559 4.938 11168 Z= 0.272 Chirality : 0.038 0.138 1252 Planarity : 0.004 0.068 1314 Dihedral : 20.793 120.050 2050 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.60 % Allowed : 19.22 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.99 (0.28), residues: 941 helix: 1.65 (0.25), residues: 452 sheet: -0.31 (0.87), residues: 38 loop : -0.22 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 198 TYR 0.010 0.002 TYR C 123 PHE 0.009 0.002 PHE A 50 TRP 0.011 0.001 TRP D 259 HIS 0.004 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 8191) covalent geometry : angle 0.55863 / 0.27 (11168) hydrogen bonds : bond 0.03346 / 2.24 ( 329) hydrogen bonds : angle 4.07097 / 2.99 ( 957) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7496 (mpt180) cc_final: 0.7067 (mmt90) REVERT: A 197 TYR cc_start: 0.8111 (t80) cc_final: 0.7852 (t80) REVERT: A 288 GLN cc_start: 0.7985 (tt0) cc_final: 0.7753 (tt0) REVERT: C 119 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8006 (ttp-110) REVERT: C 151 LYS cc_start: 0.8356 (mttt) cc_final: 0.8014 (mttm) REVERT: C 247 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8028 (mm-40) REVERT: C 317 ASN cc_start: 0.8418 (p0) cc_final: 0.7825 (p0) REVERT: D 95 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8270 (mm-30) REVERT: D 109 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.6923 (ttm-80) REVERT: D 177 ASP cc_start: 0.7762 (t0) cc_final: 0.7379 (t0) REVERT: D 268 GLU cc_start: 0.7084 (tp30) cc_final: 0.6753 (tp30) REVERT: D 326 GLN cc_start: 0.6908 (tm-30) cc_final: 0.6623 (tp40) REVERT: D 347 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6113 (pt0) outliers start: 20 outliers final: 17 residues processed: 126 average time/residue: 0.0951 time to fit residues: 16.1810 Evaluate side-chains 126 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 340 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [12, 80, 95, 71, 10, 31, 19, 66, 33, 69, 83] chunk 12 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.0370 chunk 19 optimal weight: 0.0070 chunk 66 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.217657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158676 restraints weight = 8394.056| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.05 r_work: 0.3455 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8191 Z= 0.106 Angle : 0.544 9.414 11168 Z= 0.264 Chirality : 0.040 0.548 1252 Planarity : 0.003 0.061 1314 Dihedral : 20.706 121.072 2050 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.34 % Allowed : 19.61 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.07 (0.29), residues: 941 helix: 1.73 (0.25), residues: 458 sheet: -0.23 (0.89), residues: 38 loop : -0.23 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 56 TYR 0.009 0.001 TYR C 170 PHE 0.033 0.001 PHE A 50 TRP 0.010 0.001 TRP D 259 HIS 0.003 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8191) covalent geometry : angle 0.54450 / 0.26 (11168) hydrogen bonds : bond 0.03118 / 2.04 ( 329) hydrogen bonds : angle 4.00832 / 2.94 ( 957) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2137.51 seconds wall clock time: 37 minutes 29.69 seconds (2249.69 seconds total)