Starting phenix.real_space_refine on Wed Sep 17 10:09:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdf_38276/09_2025/8xdf_38276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdf_38276/09_2025/8xdf_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_38276/09_2025/8xdf_38276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdf_38276/09_2025/8xdf_38276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xdf_38276/09_2025/8xdf_38276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdf_38276/09_2025/8xdf_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-2.0-5805/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: 1.99, per 1000 atoms: 0.25 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: 0.67 Conformation dependent library (CDL) restraints added in 473.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.96 Time building geometry restraints manager: 0.91 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: 0.02 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- 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 aren 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 : 0.311 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 352 MET cc_start: 0.8675 (ttp) cc_final: 0.8475 (ttp) 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: 0.3825 time to fit residues: 59.9214 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 : 0.281 ------------------------------------------------------------------------------- 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: 4.9990 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: 1.0582 ------------------------------------------------------------------------------- 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 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 = 0.3266 r_free = 0.3266 target = 0.112090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.090197 restraints weight = 9064.662| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.43 r_work: 0.2915 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8253 Z= 0.148 Angle : 0.564 5.945 11280 Z= 0.291 Chirality : 0.041 0.139 1323 Planarity : 0.006 0.066 1368 Dihedral : 4.289 15.854 1092 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.61 % Allowed : 13.49 % 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 aren not related in a simple way. whole: 2.29 (0.26), residues: 1044 helix: 1.91 (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 C 374 TYR 0.016 0.002 TYR A 194 PHE 0.014 0.002 PHE A 301 TRP 0.013 0.001 TRP B 340 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8253) covalent geometry : angle 0.56356 (11280) hydrogen bonds : bond 0.04645 ( 540) hydrogen bonds : angle 3.91772 ( 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 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.320 Fit side-chains REVERT: A 366 LYS cc_start: 0.8238 (mmtt) cc_final: 0.8031 (mmtp) REVERT: C 56 LEU cc_start: 0.7705 (mt) cc_final: 0.7468 (mt) outliers start: 14 outliers final: 8 residues processed: 108 average time/residue: 0.4881 time to fit residues: 56.6070 Evaluate side-chains 107 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 2.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 ** 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 = 0.3236 r_free = 0.3236 target = 0.109897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.088075 restraints weight = 9004.127| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.42 r_work: 0.2888 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8253 Z= 0.167 Angle : 0.569 5.966 11280 Z= 0.292 Chirality : 0.042 0.141 1323 Planarity : 0.006 0.065 1368 Dihedral : 4.415 16.825 1092 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.42 % Allowed : 13.03 % 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 aren not related in a simple way. whole: 2.33 (0.26), residues: 1044 helix: 1.96 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.61 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.015 0.002 TYR A 194 PHE 0.014 0.002 PHE A 301 TRP 0.015 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8253) covalent geometry : angle 0.56918 (11280) hydrogen bonds : bond 0.04791 ( 540) hydrogen bonds : angle 3.92886 ( 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 123 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.318 Fit side-chains REVERT: A 366 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8007 (mmtp) REVERT: C 56 LEU cc_start: 0.7753 (mt) cc_final: 0.7530 (mp) REVERT: C 364 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8168 (mp) outliers start: 21 outliers final: 13 residues processed: 114 average time/residue: 0.4817 time to fit residues: 58.9048 Evaluate side-chains 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 56 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 204 ILE 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: 0.9980 chunk 54 optimal weight: 0.0170 chunk 94 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 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 = 0.3264 r_free = 0.3264 target = 0.111891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.090114 restraints weight = 9213.191| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.44 r_work: 0.2902 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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= 0.120 Angle : 0.513 5.845 11280 Z= 0.262 Chirality : 0.039 0.136 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.194 16.342 1092 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.96 % Allowed : 13.84 % 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 aren not related in a simple way. whole: 2.54 (0.26), residues: 1044 helix: 2.10 (0.18), residues: 753 sheet: None (None), residues: 0 loop : 0.72 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 114 TYR 0.012 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 0.00274 ( 8253) covalent geometry : angle 0.51270 (11280) hydrogen bonds : bond 0.04209 ( 540) hydrogen bonds : angle 3.73814 ( 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: 17 poor density : 102 time to evaluate : 0.432 Fit side-chains REVERT: A 366 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7991 (mmtp) REVERT: C 56 LEU cc_start: 0.7722 (mt) cc_final: 0.7499 (mp) REVERT: C 364 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8162 (mp) outliers start: 17 outliers final: 13 residues processed: 115 average time/residue: 0.4630 time to fit residues: 57.2541 Evaluate side-chains 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL 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 204 ILE 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: 5.9990 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN 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 = 0.3258 r_free = 0.3258 target = 0.111497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.089701 restraints weight = 9128.451| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.43 r_work: 0.2913 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2009 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 : 0.529 5.849 11280 Z= 0.271 Chirality : 0.040 0.136 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.201 16.164 1092 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.19 % Allowed : 13.03 % 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 aren not related in a simple way. whole: 2.57 (0.26), residues: 1044 helix: 2.14 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.69 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 114 TYR 0.011 0.002 TYR A 194 PHE 0.012 0.001 PHE C 301 TRP 0.019 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8253) covalent geometry : angle 0.52872 (11280) hydrogen bonds : bond 0.04248 ( 540) hydrogen bonds : angle 3.71977 ( 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: 19 poor density : 101 time to evaluate : 0.339 Fit side-chains REVERT: A 204 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.8007 (pt) REVERT: A 366 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7978 (mmtp) REVERT: B 256 MET cc_start: 0.8805 (mtp) cc_final: 0.8443 (mtp) REVERT: C 56 LEU cc_start: 0.7710 (mt) cc_final: 0.7491 (mp) REVERT: C 213 SER cc_start: 0.7916 (t) cc_final: 0.7678 (m) REVERT: C 364 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8184 (mp) outliers start: 19 outliers final: 13 residues processed: 114 average time/residue: 0.4928 time to fit residues: 60.2890 Evaluate side-chains 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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=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: 1.9990 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN 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 = 0.3226 r_free = 0.3226 target = 0.109156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.087355 restraints weight = 9129.873| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.42 r_work: 0.2879 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8253 Z= 0.169 Angle : 0.570 5.983 11280 Z= 0.292 Chirality : 0.042 0.143 1323 Planarity : 0.006 0.066 1368 Dihedral : 4.447 16.649 1092 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.31 % Allowed : 12.46 % Favored : 85.24 % 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 aren not related in a simple way. whole: 2.37 (0.26), residues: 1044 helix: 1.98 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.65 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 114 TYR 0.013 0.002 TYR A 194 PHE 0.014 0.002 PHE A 301 TRP 0.019 0.001 TRP A 171 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8253) covalent geometry : angle 0.57011 (11280) hydrogen bonds : bond 0.04693 ( 540) hydrogen bonds : angle 3.85450 ( 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 118 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.336 Fit side-chains REVERT: A 366 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7983 (mmtp) REVERT: B 302 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8285 (mtm) REVERT: C 56 LEU cc_start: 0.7697 (mt) cc_final: 0.7470 (mp) REVERT: C 364 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8166 (mp) outliers start: 20 outliers final: 14 residues processed: 112 average time/residue: 0.4694 time to fit residues: 56.5851 Evaluate side-chains 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU 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 302 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.089555 restraints weight = 9134.006| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.42 r_work: 0.2885 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2106 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= 0.125 Angle : 0.522 5.841 11280 Z= 0.267 Chirality : 0.040 0.140 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.239 16.127 1092 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.96 % Allowed : 12.69 % Favored : 85.35 % 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 aren not related in a simple way. whole: 2.52 (0.26), residues: 1044 helix: 2.07 (0.18), residues: 753 sheet: None (None), residues: 0 loop : 0.77 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 114 TYR 0.011 0.002 TYR C 369 PHE 0.012 0.001 PHE C 288 TRP 0.022 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8253) covalent geometry : angle 0.52202 (11280) hydrogen bonds : bond 0.04237 ( 540) hydrogen bonds : angle 3.72043 ( 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 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.317 Fit side-chains REVERT: A 204 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8007 (pt) REVERT: A 366 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7984 (mmtp) REVERT: B 256 MET cc_start: 0.8791 (mtp) cc_final: 0.8432 (mtp) REVERT: C 56 LEU cc_start: 0.7740 (mt) cc_final: 0.7509 (mp) REVERT: C 364 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8172 (mp) outliers start: 17 outliers final: 14 residues processed: 110 average time/residue: 0.4769 time to fit residues: 56.4709 Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 94 optimal weight: 0.0870 chunk 82 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.091205 restraints weight = 9076.428| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.42 r_work: 0.2910 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8253 Z= 0.111 Angle : 0.504 5.771 11280 Z= 0.257 Chirality : 0.039 0.135 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.112 15.466 1092 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.85 % Allowed : 12.92 % Favored : 85.24 % 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 aren not related in a simple way. whole: 2.66 (0.26), residues: 1044 helix: 2.13 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.93 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 114 TYR 0.010 0.001 TYR C 369 PHE 0.012 0.001 PHE C 288 TRP 0.026 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8253) covalent geometry : angle 0.50384 (11280) hydrogen bonds : bond 0.04046 ( 540) hydrogen bonds : angle 3.63820 ( 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 120 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.379 Fit side-chains REVERT: A 204 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7988 (pt) REVERT: A 366 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7825 (mmtp) REVERT: B 256 MET cc_start: 0.8759 (mtp) cc_final: 0.8401 (mtp) REVERT: C 56 LEU cc_start: 0.7730 (mt) cc_final: 0.7498 (mp) REVERT: C 213 SER cc_start: 0.7923 (t) cc_final: 0.7696 (m) REVERT: C 364 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8169 (mp) outliers start: 16 outliers final: 10 residues processed: 117 average time/residue: 0.4873 time to fit residues: 61.1193 Evaluate side-chains 113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 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: 0.4980 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.111495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.089937 restraints weight = 9052.534| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.42 r_work: 0.2894 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2157 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= 0.125 Angle : 0.523 5.844 11280 Z= 0.266 Chirality : 0.040 0.136 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.210 15.515 1092 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.85 % Allowed : 12.80 % Favored : 85.35 % 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 aren not related in a simple way. whole: 2.58 (0.26), residues: 1044 helix: 2.06 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.94 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 114 TYR 0.012 0.002 TYR A 369 PHE 0.013 0.001 PHE A 301 TRP 0.029 0.002 TRP A 171 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8253) covalent geometry : angle 0.52337 (11280) hydrogen bonds : bond 0.04228 ( 540) hydrogen bonds : angle 3.68620 ( 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 117 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.322 Fit side-chains REVERT: A 204 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7997 (pt) REVERT: A 300 MET cc_start: 0.9093 (tpt) cc_final: 0.8880 (mmm) REVERT: A 366 LYS cc_start: 0.8263 (mmtt) cc_final: 0.8038 (mmtp) REVERT: C 56 LEU cc_start: 0.7730 (mt) cc_final: 0.7498 (mp) REVERT: C 213 SER cc_start: 0.7924 (t) cc_final: 0.7691 (m) REVERT: C 364 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8193 (mp) outliers start: 16 outliers final: 13 residues processed: 114 average time/residue: 0.4342 time to fit residues: 53.4143 Evaluate side-chains 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 0.0050 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.112389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.090863 restraints weight = 9083.896| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.41 r_work: 0.2912 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2181 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= 0.116 Angle : 0.514 5.816 11280 Z= 0.261 Chirality : 0.040 0.136 1323 Planarity : 0.005 0.065 1368 Dihedral : 4.150 15.222 1092 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.85 % Allowed : 12.80 % Favored : 85.35 % 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 aren not related in a simple way. whole: 2.64 (0.26), residues: 1044 helix: 2.12 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.94 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 114 TYR 0.011 0.001 TYR B 369 PHE 0.012 0.001 PHE C 288 TRP 0.033 0.002 TRP C 171 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8253) covalent geometry : angle 0.51372 (11280) hydrogen bonds : bond 0.04095 ( 540) hydrogen bonds : angle 3.64924 ( 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 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.312 Fit side-chains REVERT: A 204 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7992 (pt) REVERT: A 300 MET cc_start: 0.9058 (tpt) cc_final: 0.8855 (mmm) REVERT: A 366 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7823 (mmtp) REVERT: C 56 LEU cc_start: 0.7723 (mt) cc_final: 0.7486 (mp) REVERT: C 213 SER cc_start: 0.7915 (t) cc_final: 0.7687 (m) REVERT: C 364 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8200 (mp) outliers start: 16 outliers final: 14 residues processed: 110 average time/residue: 0.4477 time to fit residues: 53.2366 Evaluate side-chains 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 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: 0.7980 chunk 71 optimal weight: 0.0000 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.0270 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 0.0970 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 overall best weight: 0.2018 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.117978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.096896 restraints weight = 9026.233| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.41 r_work: 0.2998 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8253 Z= 0.096 Angle : 0.483 5.874 11280 Z= 0.245 Chirality : 0.038 0.130 1323 Planarity : 0.005 0.065 1368 Dihedral : 3.848 13.963 1092 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.58 % Allowed : 14.53 % 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 aren not related in a simple way. whole: 2.94 (0.26), residues: 1044 helix: 2.33 (0.18), residues: 753 sheet: None (None), residues: 0 loop : 1.08 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.009 0.001 TYR C 187 PHE 0.010 0.001 PHE C 288 TRP 0.030 0.002 TRP C 171 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 8253) covalent geometry : angle 0.48256 (11280) hydrogen bonds : bond 0.03670 ( 540) hydrogen bonds : angle 3.46997 ( 1593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2734.29 seconds wall clock time: 47 minutes 26.47 seconds (2846.47 seconds total)