Starting phenix.real_space_refine on Wed Feb 4 01:31:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j22_61086/02_2026/9j22_61086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j22_61086/02_2026/9j22_61086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j22_61086/02_2026/9j22_61086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j22_61086/02_2026/9j22_61086.map" model { file = "/net/cci-nas-00/data/ceres_data/9j22_61086/02_2026/9j22_61086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j22_61086/02_2026/9j22_61086.cif" } resolution = 2.75 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= 0.002 sd= 0.051 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 5496 2.51 5 N 1254 2.21 5 O 1416 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8238 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2654 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 327} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2654 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 327} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2654 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 327} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 128 Unusual residues: {'PLM': 6, 'URE': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 74 Unusual residues: {'PLM': 3, 'URE': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 74 Unusual residues: {'PLM': 3, 'URE': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 2.16, per 1000 atoms: 0.26 Number of scatterers: 8238 At special positions: 0 Unit cell: (95.45, 92.13, 73.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1416 8.00 N 1254 7.00 C 5496 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: 0.68 Conformation dependent library (CDL) restraints added in 236.4 milliseconds 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 74 through 89 Processing helix chain 'A' and resid 89 through 110 Processing helix chain 'A' and resid 113 through 119 Processing helix chain 'A' and resid 123 through 136 removed outlier: 3.747A pdb=" N LEU A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 169 removed outlier: 3.507A pdb=" N CYS A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Proline residue: A 158 - end of helix removed outlier: 3.828A pdb=" N MET A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.960A pdb=" N ILE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 238 through 253 Processing helix chain 'A' and resid 253 through 274 Processing helix chain 'A' and resid 277 through 283 Processing helix chain 'A' and resid 289 through 298 Processing helix chain 'A' and resid 305 through 332 removed outlier: 3.761A pdb=" N GLU A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.854A pdb=" N VAL A 367 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 74 through 89 Processing helix chain 'B' and resid 89 through 110 Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 123 through 136 removed outlier: 3.756A pdb=" N LEU B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 169 removed outlier: 3.543A pdb=" N CYS B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Proline residue: B 158 - end of helix removed outlier: 3.715A pdb=" N MET B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.982A pdb=" N ILE B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 238 through 253 Processing helix chain 'B' and resid 253 through 274 Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.926A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 332 removed outlier: 3.724A pdb=" N GLU B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.894A pdb=" N VAL B 367 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 74 through 89 Processing helix chain 'C' and resid 89 through 110 Processing helix chain 'C' and resid 113 through 119 Processing helix chain 'C' and resid 123 through 136 removed outlier: 3.766A pdb=" N LEU C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 169 Proline residue: C 158 - end of helix removed outlier: 3.591A pdb=" N MET C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 213 through 217 Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.962A pdb=" N ILE C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 253 Processing helix chain 'C' and resid 253 through 274 Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'C' and resid 287 through 298 removed outlier: 3.912A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 332 removed outlier: 3.784A pdb=" N GLU C 332 " --> pdb=" O ASN C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.855A pdb=" N VAL C 367 " --> pdb=" O LEU C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 382 537 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2383 1.34 - 1.46: 1501 1.46 - 1.57: 4435 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 8439 Sorted by residual: bond pdb=" C ILE C 226 " pdb=" N PRO C 227 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.36e-02 5.41e+03 4.94e-01 bond pdb=" C ILE B 226 " pdb=" N PRO B 227 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.17e-01 bond pdb=" C ILE A 226 " pdb=" N PRO A 227 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.15e-01 bond pdb=" CG PRO C 341 " pdb=" CD PRO C 341 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.98e-01 bond pdb=" CG PRO B 341 " pdb=" CD PRO B 341 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.83e-01 ... (remaining 8434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 11180 1.14 - 2.29: 186 2.29 - 3.43: 61 3.43 - 4.57: 2 4.57 - 5.71: 13 Bond angle restraints: 11442 Sorted by residual: angle pdb=" CA LEU C 148 " pdb=" C LEU C 148 " pdb=" N PRO C 149 " ideal model delta sigma weight residual 118.44 121.35 -2.91 1.59e+00 3.96e-01 3.35e+00 angle pdb=" N THR B 305 " pdb=" CA THR B 305 " pdb=" C THR B 305 " ideal model delta sigma weight residual 109.14 106.84 2.30 1.49e+00 4.50e-01 2.38e+00 angle pdb=" N THR A 305 " pdb=" CA THR A 305 " pdb=" C THR A 305 " ideal model delta sigma weight residual 109.14 107.00 2.14 1.49e+00 4.50e-01 2.07e+00 angle pdb=" CA TYR A 369 " pdb=" CB TYR A 369 " pdb=" CG TYR A 369 " ideal model delta sigma weight residual 113.90 116.45 -2.55 1.80e+00 3.09e-01 2.01e+00 angle pdb=" C GLY A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta sigma weight residual 120.42 118.42 2.00 1.42e+00 4.96e-01 1.99e+00 ... (remaining 11437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 3963 11.82 - 23.64: 566 23.64 - 35.46: 235 35.46 - 47.28: 77 47.28 - 59.11: 43 Dihedral angle restraints: 4884 sinusoidal: 1902 harmonic: 2982 Sorted by residual: dihedral pdb=" CA LYS B 139 " pdb=" CB LYS B 139 " pdb=" CG LYS B 139 " pdb=" CD LYS B 139 " ideal model delta sinusoidal sigma weight residual -180.00 -121.48 -58.52 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CG LYS B 355 " pdb=" CD LYS B 355 " pdb=" CE LYS B 355 " pdb=" NZ LYS B 355 " ideal model delta sinusoidal sigma weight residual 180.00 121.57 58.43 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS A 50 " pdb=" CB LYS A 50 " pdb=" CG LYS A 50 " pdb=" CD LYS A 50 " ideal model delta sinusoidal sigma weight residual 60.00 118.43 -58.43 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 791 0.026 - 0.052: 292 0.052 - 0.078: 148 0.078 - 0.104: 64 0.104 - 0.130: 13 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CA PRO C 370 " pdb=" N PRO C 370 " pdb=" C PRO C 370 " pdb=" CB PRO C 370 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA PRO A 370 " pdb=" N PRO A 370 " pdb=" C PRO A 370 " pdb=" CB PRO A 370 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO B 370 " pdb=" N PRO B 370 " pdb=" C PRO B 370 " pdb=" CB PRO B 370 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 1305 not shown) Planarity restraints: 1386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 162 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C SER A 162 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 162 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 163 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 161 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C SER A 161 " 0.023 2.00e-02 2.50e+03 pdb=" O SER A 161 " -0.009 2.00e-02 2.50e+03 pdb=" N SER A 162 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 160 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C PHE A 160 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE A 160 " -0.009 2.00e-02 2.50e+03 pdb=" N SER A 161 " -0.008 2.00e-02 2.50e+03 ... (remaining 1383 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 764 2.74 - 3.28: 8213 3.28 - 3.82: 14722 3.82 - 4.36: 18261 4.36 - 4.90: 30814 Nonbonded interactions: 72774 Sorted by model distance: nonbonded pdb=" OH TYR C 124 " pdb=" O PHE C 176 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 124 " pdb=" O PHE A 176 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR B 124 " pdb=" O PHE B 176 " model vdw 2.221 3.040 nonbonded pdb=" O GLY C 40 " pdb=" ND2 ASN C 74 " model vdw 2.274 3.120 nonbonded pdb=" O CYS B 157 " pdb=" OG SER B 161 " model vdw 2.294 3.040 ... (remaining 72769 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 36 through 408) selection = chain 'B' selection = chain 'C' } 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: 1.150 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.690 Find NCS groups from input model: 0.320 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.002 0.026 8439 Z= 0.101 Angle : 0.440 5.714 11442 Z= 0.224 Chirality : 0.038 0.130 1308 Planarity : 0.004 0.033 1386 Dihedral : 15.028 59.106 2976 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.03 % Allowed : 16.78 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.27), residues: 1035 helix: 1.75 (0.19), residues: 738 sheet: None (None), residues: 0 loop : 0.76 (0.41), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 374 TYR 0.012 0.001 TYR A 124 PHE 0.011 0.001 PHE B 288 TRP 0.008 0.001 TRP A 340 HIS 0.002 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8439) covalent geometry : angle 0.43965 (11442) hydrogen bonds : bond 0.14774 ( 537) hydrogen bonds : angle 4.97166 ( 1584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.271 Fit side-chains outliers start: 26 outliers final: 24 residues processed: 126 average time/residue: 0.4665 time to fit residues: 63.3801 Evaluate side-chains 126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN B 57 GLN C 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.092375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.078272 restraints weight = 10878.317| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 1.31 r_work: 0.2616 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8439 Z= 0.105 Angle : 0.449 5.806 11442 Z= 0.227 Chirality : 0.038 0.134 1308 Planarity : 0.004 0.039 1386 Dihedral : 7.842 57.812 1286 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.40 % Allowed : 17.25 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.26), residues: 1035 helix: 2.10 (0.19), residues: 741 sheet: None (None), residues: 0 loop : 0.65 (0.41), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 64 TYR 0.011 0.001 TYR C 124 PHE 0.009 0.001 PHE B 288 TRP 0.008 0.001 TRP B 306 HIS 0.002 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8439) covalent geometry : angle 0.44906 (11442) hydrogen bonds : bond 0.04234 ( 537) hydrogen bonds : angle 3.68026 ( 1584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.329 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 110 average time/residue: 0.5214 time to fit residues: 61.4570 Evaluate side-chains 104 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 305 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.2987 r_free = 0.2987 target = 0.095693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.082008 restraints weight = 10172.845| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.25 r_work: 0.2640 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8439 Z= 0.120 Angle : 0.461 5.822 11442 Z= 0.233 Chirality : 0.039 0.138 1308 Planarity : 0.004 0.044 1386 Dihedral : 7.241 59.053 1252 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.63 % Allowed : 16.55 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.26), residues: 1035 helix: 2.03 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.47 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 64 TYR 0.011 0.001 TYR A 124 PHE 0.010 0.001 PHE B 288 TRP 0.008 0.001 TRP A 306 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8439) covalent geometry : angle 0.46141 (11442) hydrogen bonds : bond 0.04329 ( 537) hydrogen bonds : angle 3.68082 ( 1584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.295 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 109 average time/residue: 0.4897 time to fit residues: 57.2885 Evaluate side-chains 110 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 305 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3000 r_free = 0.3000 target = 0.096448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.082747 restraints weight = 10349.164| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 1.27 r_work: 0.2637 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8439 Z= 0.116 Angle : 0.456 5.826 11442 Z= 0.230 Chirality : 0.039 0.138 1308 Planarity : 0.004 0.045 1386 Dihedral : 7.233 59.059 1252 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.75 % Allowed : 16.32 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.26), residues: 1035 helix: 2.08 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.37 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 64 TYR 0.012 0.001 TYR C 124 PHE 0.010 0.001 PHE B 288 TRP 0.008 0.001 TRP A 306 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8439) covalent geometry : angle 0.45610 (11442) hydrogen bonds : bond 0.04204 ( 537) hydrogen bonds : angle 3.63851 ( 1584) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.265 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.4401 time to fit residues: 53.0486 Evaluate side-chains 114 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 305 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 81 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.2897 r_free = 0.2897 target = 0.090646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.076489 restraints weight = 10951.604| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 1.35 r_work: 0.2595 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8439 Z= 0.117 Angle : 0.457 5.828 11442 Z= 0.231 Chirality : 0.039 0.138 1308 Planarity : 0.004 0.046 1386 Dihedral : 7.255 57.798 1252 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.63 % Allowed : 16.55 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.26), residues: 1035 helix: 2.12 (0.18), residues: 747 sheet: None (None), residues: 0 loop : 0.53 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 64 TYR 0.012 0.001 TYR C 124 PHE 0.011 0.001 PHE B 288 TRP 0.008 0.001 TRP A 306 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8439) covalent geometry : angle 0.45718 (11442) hydrogen bonds : bond 0.04207 ( 537) hydrogen bonds : angle 3.63095 ( 1584) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.211 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 111 average time/residue: 0.4419 time to fit residues: 52.6378 Evaluate side-chains 112 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 305 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.2904 r_free = 0.2904 target = 0.091117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.077060 restraints weight = 10821.710| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 1.34 r_work: 0.2610 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8439 Z= 0.111 Angle : 0.450 5.800 11442 Z= 0.227 Chirality : 0.038 0.137 1308 Planarity : 0.004 0.046 1386 Dihedral : 7.174 56.802 1252 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.86 % Allowed : 16.90 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.26), residues: 1035 helix: 2.16 (0.18), residues: 747 sheet: None (None), residues: 0 loop : 0.53 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 64 TYR 0.012 0.001 TYR C 124 PHE 0.011 0.001 PHE B 288 TRP 0.008 0.001 TRP A 340 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8439) covalent geometry : angle 0.45047 (11442) hydrogen bonds : bond 0.04108 ( 537) hydrogen bonds : angle 3.59952 ( 1584) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.195 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 108 average time/residue: 0.5058 time to fit residues: 58.2739 Evaluate side-chains 108 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 305 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.2874 r_free = 0.2874 target = 0.089218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.075110 restraints weight = 10975.211| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 1.34 r_work: 0.2567 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8439 Z= 0.139 Angle : 0.480 5.889 11442 Z= 0.243 Chirality : 0.040 0.142 1308 Planarity : 0.004 0.046 1386 Dihedral : 7.557 56.427 1252 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.75 % Allowed : 16.78 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.26), residues: 1035 helix: 2.05 (0.18), residues: 747 sheet: None (None), residues: 0 loop : 0.50 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 64 TYR 0.013 0.001 TYR A 124 PHE 0.012 0.001 PHE B 288 TRP 0.008 0.001 TRP A 306 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8439) covalent geometry : angle 0.48000 (11442) hydrogen bonds : bond 0.04472 ( 537) hydrogen bonds : angle 3.70925 ( 1584) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.298 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 113 average time/residue: 0.4336 time to fit residues: 52.5601 Evaluate side-chains 115 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 305 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.2887 r_free = 0.2887 target = 0.090066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.075959 restraints weight = 10905.113| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 1.34 r_work: 0.2582 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8439 Z= 0.126 Angle : 0.468 5.847 11442 Z= 0.236 Chirality : 0.039 0.141 1308 Planarity : 0.004 0.047 1386 Dihedral : 7.456 55.788 1252 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.63 % Allowed : 17.02 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.26), residues: 1035 helix: 2.08 (0.18), residues: 747 sheet: None (None), residues: 0 loop : 0.48 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 64 TYR 0.013 0.001 TYR C 124 PHE 0.011 0.001 PHE B 288 TRP 0.008 0.001 TRP A 340 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8439) covalent geometry : angle 0.46769 (11442) hydrogen bonds : bond 0.04314 ( 537) hydrogen bonds : angle 3.67721 ( 1584) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.220 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 111 average time/residue: 0.4974 time to fit residues: 59.2478 Evaluate side-chains 111 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 305 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.2863 r_free = 0.2863 target = 0.088478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.074446 restraints weight = 10885.872| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 1.32 r_work: 0.2560 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8439 Z= 0.158 Angle : 0.499 5.931 11442 Z= 0.253 Chirality : 0.041 0.145 1308 Planarity : 0.004 0.047 1386 Dihedral : 7.875 55.838 1252 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.98 % Allowed : 16.55 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.26), residues: 1035 helix: 1.97 (0.18), residues: 747 sheet: None (None), residues: 0 loop : 0.45 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 64 TYR 0.014 0.001 TYR A 124 PHE 0.012 0.001 PHE B 288 TRP 0.008 0.001 TRP A 306 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8439) covalent geometry : angle 0.49889 (11442) hydrogen bonds : bond 0.04673 ( 537) hydrogen bonds : angle 3.78725 ( 1584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.189 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 112 average time/residue: 0.4120 time to fit residues: 49.5143 Evaluate side-chains 115 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.2907 r_free = 0.2907 target = 0.091366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.077319 restraints weight = 10840.127| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 1.34 r_work: 0.2605 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8439 Z= 0.110 Angle : 0.451 5.777 11442 Z= 0.228 Chirality : 0.038 0.138 1308 Planarity : 0.004 0.047 1386 Dihedral : 7.317 54.688 1252 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.52 % Allowed : 17.13 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.26), residues: 1035 helix: 2.14 (0.18), residues: 747 sheet: None (None), residues: 0 loop : 0.48 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 64 TYR 0.012 0.001 TYR C 124 PHE 0.011 0.001 PHE B 288 TRP 0.010 0.001 TRP A 340 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8439) covalent geometry : angle 0.45126 (11442) hydrogen bonds : bond 0.04088 ( 537) hydrogen bonds : angle 3.62633 ( 1584) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.422 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.4675 time to fit residues: 54.1755 Evaluate side-chains 108 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.2911 r_free = 0.2911 target = 0.091632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.077553 restraints weight = 10895.259| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 1.34 r_work: 0.2603 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8439 Z= 0.107 Angle : 0.449 5.779 11442 Z= 0.227 Chirality : 0.038 0.136 1308 Planarity : 0.004 0.047 1386 Dihedral : 7.182 54.917 1252 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.28 % Allowed : 17.72 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.26), residues: 1035 helix: 2.19 (0.18), residues: 747 sheet: None (None), residues: 0 loop : 0.48 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 64 TYR 0.012 0.001 TYR C 124 PHE 0.011 0.001 PHE B 288 TRP 0.010 0.001 TRP C 340 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8439) covalent geometry : angle 0.44943 (11442) hydrogen bonds : bond 0.04063 ( 537) hydrogen bonds : angle 3.59486 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2069.26 seconds wall clock time: 36 minutes 7.13 seconds (2167.13 seconds total)