Starting phenix.real_space_refine on Tue Feb 3 23:41:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdf_38276/02_2026/8xdf_38276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdf_38276/02_2026/8xdf_38276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xdf_38276/02_2026/8xdf_38276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdf_38276/02_2026/8xdf_38276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xdf_38276/02_2026/8xdf_38276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdf_38276/02_2026/8xdf_38276.map" } resolution = 2.4 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= 0.041 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 69 5.16 5 C 5331 2.51 5 N 1239 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 8025 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 330} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 330} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 330} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.21, per 1000 atoms: 0.15 Number of scatterers: 8025 At special positions: 0 Unit cell: (100.04, 94.3, 73.8, 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 69 16.00 O 1386 8.00 N 1239 7.00 C 5331 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: 0.71 Conformation dependent library (CDL) restraints added in 200.8 milliseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 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 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: 3.852A pdb=" N THR A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.691A pdb=" N LEU A 217 " --> pdb=" O TRP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.854A 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 removed outlier: 3.623A pdb=" N SER A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 274 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.501A pdb=" N ILE A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 305 through 332 removed outlier: 3.684A 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 369 through 383 Processing helix chain 'B' and resid 34 through 38 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 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: 3.852A pdb=" N THR B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix 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 removed outlier: 3.691A pdb=" N LEU B 217 " --> pdb=" O TRP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.855A 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 removed outlier: 3.623A pdb=" N SER B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 274 Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 305 through 332 removed outlier: 3.683A 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 369 through 383 Processing helix chain 'C' and resid 34 through 38 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 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 removed outlier: 3.852A pdb=" N THR C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS C 157 " --> pdb=" O MET C 153 " (cutoff:3.500A) Proline residue: C 158 - end of helix 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 removed outlier: 3.691A pdb=" N LEU C 217 " --> pdb=" O TRP C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.855A 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 removed outlier: 3.623A pdb=" N SER C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 274 Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'C' and resid 288 through 298 Processing helix chain 'C' and resid 305 through 332 removed outlier: 3.682A 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 369 through 383 540 hydrogen bonds defined for protein. 1593 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: 0.95 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1427 1.33 - 1.45: 2109 1.45 - 1.57: 4603 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 8253 Sorted by residual: bond pdb=" CA ILE A 281 " pdb=" C ILE A 281 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.22e-02 6.72e+03 1.70e+01 bond pdb=" N GLU A 279 " pdb=" CA GLU A 279 " ideal model delta sigma weight residual 1.459 1.422 0.037 1.23e-02 6.61e+03 8.94e+00 bond pdb=" CA GLY A 284 " pdb=" C GLY A 284 " ideal model delta sigma weight residual 1.511 1.473 0.039 1.37e-02 5.33e+03 7.92e+00 bond pdb=" C GLY A 287 " pdb=" N PHE A 288 " ideal model delta sigma weight residual 1.332 1.295 0.036 1.35e-02 5.49e+03 7.27e+00 bond pdb=" N LEU A 285 " pdb=" CA LEU A 285 " ideal model delta sigma weight residual 1.458 1.423 0.035 1.33e-02 5.65e+03 6.86e+00 ... (remaining 8248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11108 2.00 - 3.99: 144 3.99 - 5.99: 26 5.99 - 7.99: 1 7.99 - 9.99: 1 Bond angle restraints: 11280 Sorted by residual: angle pdb=" N PHE A 283 " pdb=" CA PHE A 283 " pdb=" CB PHE A 283 " ideal model delta sigma weight residual 110.44 103.52 6.92 1.53e+00 4.27e-01 2.05e+01 angle pdb=" N GLY A 287 " pdb=" CA GLY A 287 " pdb=" C GLY A 287 " ideal model delta sigma weight residual 113.18 123.17 -9.99 2.37e+00 1.78e-01 1.78e+01 angle pdb=" N ASN A 280 " pdb=" CA ASN A 280 " pdb=" C ASN A 280 " ideal model delta sigma weight residual 111.36 115.20 -3.84 1.09e+00 8.42e-01 1.24e+01 angle pdb=" N THR C 177 " pdb=" CA THR C 177 " pdb=" C THR C 177 " ideal model delta sigma weight residual 113.19 108.07 5.12 1.58e+00 4.01e-01 1.05e+01 angle pdb=" N THR B 177 " pdb=" CA THR B 177 " pdb=" C THR B 177 " ideal model delta sigma weight residual 113.19 108.09 5.10 1.58e+00 4.01e-01 1.04e+01 ... (remaining 11275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 3908 11.91 - 23.82: 523 23.82 - 35.73: 220 35.73 - 47.64: 68 47.64 - 59.55: 36 Dihedral angle restraints: 4755 sinusoidal: 1746 harmonic: 3009 Sorted by residual: dihedral pdb=" N PHE A 283 " pdb=" C PHE A 283 " pdb=" CA PHE A 283 " pdb=" CB PHE A 283 " ideal model delta harmonic sigma weight residual 122.80 113.57 9.23 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" CA LEU C 304 " pdb=" C LEU C 304 " pdb=" N THR C 305 " pdb=" CA THR C 305 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA LEU A 304 " pdb=" C LEU A 304 " pdb=" N THR A 305 " pdb=" CA THR A 305 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 4752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1229 0.081 - 0.162: 90 0.162 - 0.243: 2 0.243 - 0.324: 1 0.324 - 0.405: 1 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA ASN A 280 " pdb=" N ASN A 280 " pdb=" C ASN A 280 " pdb=" CB ASN A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA LEU A 285 " pdb=" N LEU A 285 " pdb=" C LEU A 285 " pdb=" CB LEU A 285 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA TRP A 286 " pdb=" N TRP A 286 " pdb=" C TRP A 286 " pdb=" CB TRP A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1320 not shown) Planarity restraints: 1368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 283 " 0.028 2.00e-02 2.50e+03 2.02e-02 7.11e+00 pdb=" CG PHE A 283 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 283 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 283 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 283 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 283 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 283 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 281 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C ILE A 281 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE A 281 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR A 282 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 369 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 370 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.033 5.00e-02 4.00e+02 ... (remaining 1365 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1943 2.79 - 3.32: 8069 3.32 - 3.84: 14269 3.84 - 4.37: 17284 4.37 - 4.90: 28366 Nonbonded interactions: 69931 Sorted by model distance: nonbonded pdb=" O GLY C 263 " pdb=" OG SER C 290 " model vdw 2.262 3.040 nonbonded pdb=" O GLY B 263 " pdb=" OG SER B 290 " model vdw 2.263 3.040 nonbonded pdb=" O GLY A 263 " pdb=" OG SER A 290 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR A 100 " pdb=" OG1 THR A 127 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR C 100 " pdb=" OG1 THR C 127 " model vdw 2.291 3.040 ... (remaining 69926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8253 Z= 0.230 Angle : 0.566 9.987 11280 Z= 0.315 Chirality : 0.044 0.405 1323 Planarity : 0.006 0.059 1368 Dihedral : 14.784 59.549 2829 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 15.80 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.26), residues: 1044 helix: 1.60 (0.19), residues: 735 sheet: None (None), residues: 0 loop : 0.43 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 374 TYR 0.017 0.002 TYR C 194 PHE 0.042 0.002 PHE A 283 TRP 0.012 0.001 TRP B 306 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8253) covalent geometry : angle 0.56643 (11280) hydrogen bonds : bond 0.14683 ( 540) hydrogen bonds : angle 5.32111 ( 1593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.304 Fit side-chains REVERT: B 167 VAL cc_start: 0.8053 (t) cc_final: 0.7680 (t) REVERT: C 56 LEU cc_start: 0.7869 (mt) cc_final: 0.7669 (mp) REVERT: C 362 MET cc_start: 0.8457 (mmm) cc_final: 0.8206 (mmm) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.3371 time to fit residues: 52.7704 Evaluate side-chains 110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.093722 restraints weight = 8837.597| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.41 r_work: 0.2935 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8253 Z= 0.126 Angle : 0.535 5.831 11280 Z= 0.276 Chirality : 0.039 0.137 1323 Planarity : 0.006 0.065 1368 Dihedral : 4.139 15.409 1092 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.27 % Allowed : 13.84 % Favored : 84.89 % 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: 2.36 (0.26), residues: 1044 helix: 1.96 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.66 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.014 0.002 TYR B 194 PHE 0.012 0.001 PHE A 301 TRP 0.014 0.001 TRP A 171 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8253) covalent geometry : angle 0.53544 (11280) hydrogen bonds : bond 0.04459 ( 540) hydrogen bonds : angle 3.85095 ( 1593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.239 Fit side-chains REVERT: A 366 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7881 (mmtm) REVERT: B 167 VAL cc_start: 0.8172 (t) cc_final: 0.7901 (t) REVERT: C 56 LEU cc_start: 0.7702 (mt) cc_final: 0.7462 (mt) outliers start: 11 outliers final: 4 residues processed: 104 average time/residue: 0.4010 time to fit residues: 45.0033 Evaluate side-chains 100 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 308 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 60 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.0470 chunk 38 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.091196 restraints weight = 8992.306| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.43 r_work: 0.2928 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8253 Z= 0.124 Angle : 0.521 5.845 11280 Z= 0.266 Chirality : 0.040 0.135 1323 Planarity : 0.005 0.063 1368 Dihedral : 4.110 15.331 1092 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.73 % Allowed : 13.96 % Favored : 84.31 % 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: 2.60 (0.26), residues: 1044 helix: 2.16 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.70 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.013 0.002 TYR A 194 PHE 0.012 0.001 PHE A 301 TRP 0.017 0.001 TRP A 171 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8253) covalent geometry : angle 0.52082 (11280) hydrogen bonds : bond 0.04290 ( 540) hydrogen bonds : angle 3.75805 ( 1593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.255 Fit side-chains REVERT: A 204 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7995 (pt) REVERT: A 366 LYS cc_start: 0.8228 (mmtt) cc_final: 0.8017 (mmtp) REVERT: B 56 LEU cc_start: 0.7726 (mt) cc_final: 0.7475 (mp) REVERT: C 56 LEU cc_start: 0.7707 (mt) cc_final: 0.7467 (mp) REVERT: C 237 ASP cc_start: 0.8886 (p0) cc_final: 0.8545 (p0) REVERT: C 364 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8213 (mp) outliers start: 15 outliers final: 9 residues processed: 112 average time/residue: 0.3978 time to fit residues: 47.9046 Evaluate side-chains 111 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 0.0870 chunk 39 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.092181 restraints weight = 9219.001| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.44 r_work: 0.2924 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8253 Z= 0.110 Angle : 0.503 5.793 11280 Z= 0.257 Chirality : 0.039 0.132 1323 Planarity : 0.005 0.064 1368 Dihedral : 4.012 14.819 1092 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.50 % Allowed : 14.07 % Favored : 84.43 % 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: 2.70 (0.26), residues: 1044 helix: 2.18 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.89 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.011 0.001 TYR A 194 PHE 0.011 0.001 PHE A 301 TRP 0.018 0.001 TRP A 171 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8253) covalent geometry : angle 0.50350 (11280) hydrogen bonds : bond 0.04038 ( 540) hydrogen bonds : angle 3.65057 ( 1593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.330 Fit side-chains REVERT: A 204 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8016 (pt) REVERT: A 366 LYS cc_start: 0.8232 (mmtt) cc_final: 0.8016 (mmtp) REVERT: B 56 LEU cc_start: 0.7745 (mt) cc_final: 0.7502 (mp) REVERT: C 56 LEU cc_start: 0.7701 (mt) cc_final: 0.7467 (mp) REVERT: C 213 SER cc_start: 0.7938 (t) cc_final: 0.7703 (m) REVERT: C 237 ASP cc_start: 0.8925 (p0) cc_final: 0.8574 (p0) REVERT: C 364 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8195 (mp) outliers start: 13 outliers final: 7 residues processed: 115 average time/residue: 0.4253 time to fit residues: 52.4305 Evaluate side-chains 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 104 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.090954 restraints weight = 9129.220| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.43 r_work: 0.2904 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8253 Z= 0.119 Angle : 0.514 5.818 11280 Z= 0.262 Chirality : 0.039 0.135 1323 Planarity : 0.005 0.064 1368 Dihedral : 4.073 14.950 1092 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.96 % Allowed : 13.61 % Favored : 84.43 % 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: 2.69 (0.26), residues: 1044 helix: 2.20 (0.18), residues: 753 sheet: None (None), residues: 0 loop : 0.83 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.011 0.002 TYR C 369 PHE 0.011 0.001 PHE A 288 TRP 0.020 0.001 TRP A 171 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8253) covalent geometry : angle 0.51391 (11280) hydrogen bonds : bond 0.04138 ( 540) hydrogen bonds : angle 3.66471 ( 1593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.326 Fit side-chains REVERT: A 204 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8028 (pt) REVERT: A 366 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7988 (mmtp) REVERT: B 56 LEU cc_start: 0.7735 (mt) cc_final: 0.7494 (mp) REVERT: B 256 MET cc_start: 0.8770 (mtp) cc_final: 0.8466 (mtp) REVERT: C 56 LEU cc_start: 0.7720 (mt) cc_final: 0.7498 (mp) REVERT: C 237 ASP cc_start: 0.8946 (p0) cc_final: 0.8586 (p0) REVERT: C 364 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8200 (mp) outliers start: 17 outliers final: 11 residues processed: 114 average time/residue: 0.4310 time to fit residues: 52.8605 Evaluate side-chains 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.091100 restraints weight = 9145.762| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.44 r_work: 0.2911 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8253 Z= 0.117 Angle : 0.508 5.815 11280 Z= 0.259 Chirality : 0.039 0.137 1323 Planarity : 0.005 0.064 1368 Dihedral : 4.078 14.990 1092 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.85 % Allowed : 13.73 % Favored : 84.43 % 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: 2.71 (0.26), residues: 1044 helix: 2.18 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.91 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 64 TYR 0.011 0.002 TYR C 369 PHE 0.011 0.001 PHE A 301 TRP 0.023 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8253) covalent geometry : angle 0.50766 (11280) hydrogen bonds : bond 0.04117 ( 540) hydrogen bonds : angle 3.64199 ( 1593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.233 Fit side-chains REVERT: A 366 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7983 (mmtp) REVERT: B 56 LEU cc_start: 0.7742 (mt) cc_final: 0.7479 (mp) REVERT: B 256 MET cc_start: 0.8772 (mtp) cc_final: 0.8407 (mtp) REVERT: C 56 LEU cc_start: 0.7712 (mt) cc_final: 0.7497 (mp) REVERT: C 213 SER cc_start: 0.7949 (t) cc_final: 0.7724 (m) REVERT: C 237 ASP cc_start: 0.8954 (p0) cc_final: 0.8626 (p0) REVERT: C 364 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8227 (mp) outliers start: 16 outliers final: 11 residues processed: 118 average time/residue: 0.4139 time to fit residues: 52.4087 Evaluate side-chains 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.111320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.089602 restraints weight = 9137.095| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.43 r_work: 0.2889 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8253 Z= 0.132 Angle : 0.524 5.861 11280 Z= 0.267 Chirality : 0.040 0.137 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.202 15.709 1092 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.85 % Allowed : 13.38 % Favored : 84.78 % 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: 2.63 (0.26), residues: 1044 helix: 2.14 (0.18), residues: 753 sheet: None (None), residues: 0 loop : 0.84 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.012 0.002 TYR A 369 PHE 0.012 0.001 PHE A 301 TRP 0.026 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8253) covalent geometry : angle 0.52395 (11280) hydrogen bonds : bond 0.04306 ( 540) hydrogen bonds : angle 3.71086 ( 1593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.302 Fit side-chains REVERT: A 366 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7986 (mmtp) REVERT: B 256 MET cc_start: 0.8762 (mtp) cc_final: 0.8361 (mtp) REVERT: C 56 LEU cc_start: 0.7701 (mt) cc_final: 0.7490 (mp) REVERT: C 237 ASP cc_start: 0.8966 (p0) cc_final: 0.8621 (p0) REVERT: C 364 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8211 (mp) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.4677 time to fit residues: 57.8942 Evaluate side-chains 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 94 optimal weight: 0.0670 chunk 82 optimal weight: 0.5980 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.088127 restraints weight = 9074.426| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.42 r_work: 0.2863 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8253 Z= 0.159 Angle : 0.559 5.956 11280 Z= 0.286 Chirality : 0.042 0.141 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.389 16.312 1092 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.96 % Allowed : 13.26 % Favored : 84.78 % 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: 2.45 (0.26), residues: 1044 helix: 2.03 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.71 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.013 0.002 TYR C 369 PHE 0.013 0.001 PHE A 301 TRP 0.029 0.002 TRP A 171 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8253) covalent geometry : angle 0.55941 (11280) hydrogen bonds : bond 0.04582 ( 540) hydrogen bonds : angle 3.80729 ( 1593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.313 Fit side-chains REVERT: A 366 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7982 (mmtp) REVERT: C 56 LEU cc_start: 0.7743 (mt) cc_final: 0.7540 (mp) REVERT: C 237 ASP cc_start: 0.8978 (p0) cc_final: 0.8599 (p0) REVERT: C 364 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8230 (mp) outliers start: 17 outliers final: 13 residues processed: 110 average time/residue: 0.4423 time to fit residues: 52.4250 Evaluate side-chains 111 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.091205 restraints weight = 9048.559| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.42 r_work: 0.2911 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8253 Z= 0.114 Angle : 0.509 5.782 11280 Z= 0.260 Chirality : 0.039 0.136 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.140 15.583 1092 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.50 % Allowed : 13.84 % Favored : 84.66 % 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: 2.62 (0.26), residues: 1044 helix: 2.11 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.88 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.011 0.001 TYR C 369 PHE 0.012 0.001 PHE C 288 TRP 0.030 0.001 TRP A 171 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8253) covalent geometry : angle 0.50945 (11280) hydrogen bonds : bond 0.04079 ( 540) hydrogen bonds : angle 3.65351 ( 1593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.211 Fit side-chains REVERT: A 204 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7996 (pt) REVERT: A 300 MET cc_start: 0.8997 (mmm) cc_final: 0.8791 (tpt) REVERT: A 366 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8016 (mmtp) REVERT: B 256 MET cc_start: 0.8759 (mtp) cc_final: 0.8426 (mtp) REVERT: C 56 LEU cc_start: 0.7705 (mt) cc_final: 0.7495 (mp) REVERT: C 237 ASP cc_start: 0.8956 (p0) cc_final: 0.8613 (p0) REVERT: C 364 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8218 (mp) REVERT: C 366 LYS cc_start: 0.8399 (mttp) cc_final: 0.8151 (mtpp) outliers start: 13 outliers final: 11 residues processed: 111 average time/residue: 0.4152 time to fit residues: 49.6251 Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 33 optimal weight: 0.0270 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.091552 restraints weight = 9078.401| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.42 r_work: 0.2919 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8253 Z= 0.113 Angle : 0.515 5.822 11280 Z= 0.263 Chirality : 0.039 0.135 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.113 15.310 1092 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.61 % Allowed : 13.96 % Favored : 84.43 % 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: 2.63 (0.26), residues: 1044 helix: 2.12 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.90 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.011 0.001 TYR A 369 PHE 0.012 0.001 PHE C 288 TRP 0.033 0.002 TRP A 171 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8253) covalent geometry : angle 0.51513 (11280) hydrogen bonds : bond 0.04055 ( 540) hydrogen bonds : angle 3.64301 ( 1593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.229 Fit side-chains REVERT: A 204 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7983 (pt) REVERT: A 366 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7771 (mmtp) REVERT: B 256 MET cc_start: 0.8758 (mtp) cc_final: 0.8419 (mtp) REVERT: C 56 LEU cc_start: 0.7685 (mt) cc_final: 0.7474 (mp) REVERT: C 213 SER cc_start: 0.7918 (t) cc_final: 0.7686 (m) REVERT: C 237 ASP cc_start: 0.8961 (p0) cc_final: 0.8623 (p0) REVERT: C 364 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8198 (mp) REVERT: C 366 LYS cc_start: 0.8416 (mttp) cc_final: 0.8171 (mtpp) outliers start: 14 outliers final: 12 residues processed: 113 average time/residue: 0.4431 time to fit residues: 53.9836 Evaluate side-chains 116 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.091380 restraints weight = 9018.560| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.41 r_work: 0.2915 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8253 Z= 0.116 Angle : 0.518 5.807 11280 Z= 0.264 Chirality : 0.040 0.135 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.122 15.060 1092 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.73 % Allowed : 13.73 % Favored : 84.54 % 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: 2.63 (0.26), residues: 1044 helix: 2.11 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.90 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.011 0.001 TYR A 369 PHE 0.011 0.001 PHE C 288 TRP 0.033 0.002 TRP A 171 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8253) covalent geometry : angle 0.51763 (11280) hydrogen bonds : bond 0.04076 ( 540) hydrogen bonds : angle 3.65016 ( 1593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2463.05 seconds wall clock time: 42 minutes 43.13 seconds (2563.13 seconds total)