Starting phenix.real_space_refine on Tue Mar 3 18:32:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukd_26577/03_2026/7ukd_26577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukd_26577/03_2026/7ukd_26577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ukd_26577/03_2026/7ukd_26577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukd_26577/03_2026/7ukd_26577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ukd_26577/03_2026/7ukd_26577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukd_26577/03_2026/7ukd_26577.map" } resolution = 2.88 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= 0.005 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 56 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.93, per 1000 atoms: 0.24 Number of scatterers: 8000 At special positions: 0 Unit cell: (114.814, 116.466, 83.426, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 56 16.00 O 1356 8.00 N 1332 7.00 C 5252 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: 0.85 Conformation dependent library (CDL) restraints added in 288.6 milliseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 84.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 225 through 251 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.574A pdb=" N THR A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 320 through 347 Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.947A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 400 through 424 removed outlier: 4.196A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 251 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.560A pdb=" N GLU B 283 " --> pdb=" O THR B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.636A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.978A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 398 Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 225 through 251 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.574A pdb=" N THR C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 311 through 320 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.947A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 400 through 424 removed outlier: 4.196A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 251 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 280 through 283 removed outlier: 3.559A pdb=" N GLU D 283 " --> pdb=" O THR D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.635A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.977A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 398 Processing helix chain 'D' and resid 401 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.724A pdb=" N LEU A 219 " --> pdb=" O CYS A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.724A pdb=" N LEU C 219 " --> pdb=" O CYS C 209 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2440 1.34 - 1.46: 1869 1.46 - 1.58: 3791 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8188 Sorted by residual: bond pdb=" CG1 ILE A 270 " pdb=" CD1 ILE A 270 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.15e+00 bond pdb=" CG1 ILE C 270 " pdb=" CD1 ILE C 270 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.10e+00 bond pdb=" CG LEU B 271 " pdb=" CD1 LEU B 271 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CG LEU D 271 " pdb=" CD1 LEU D 271 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB LEU A 371 " pdb=" CG LEU A 371 " ideal model delta sigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 8.71e-01 ... (remaining 8183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 10738 1.41 - 2.81: 295 2.81 - 4.22: 62 4.22 - 5.62: 23 5.62 - 7.03: 6 Bond angle restraints: 11124 Sorted by residual: angle pdb=" CA MET B 279 " pdb=" CB MET B 279 " pdb=" CG MET B 279 " ideal model delta sigma weight residual 114.10 121.13 -7.03 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CA MET D 279 " pdb=" CB MET D 279 " pdb=" CG MET D 279 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.22e+01 angle pdb=" N LEU A 271 " pdb=" CA LEU A 271 " pdb=" C LEU A 271 " ideal model delta sigma weight residual 113.57 116.62 -3.05 1.38e+00 5.25e-01 4.88e+00 angle pdb=" N LEU C 271 " pdb=" CA LEU C 271 " pdb=" C LEU C 271 " ideal model delta sigma weight residual 113.57 116.60 -3.03 1.38e+00 5.25e-01 4.82e+00 angle pdb=" N LEU D 271 " pdb=" CA LEU D 271 " pdb=" C LEU D 271 " ideal model delta sigma weight residual 113.16 116.25 -3.09 1.42e+00 4.96e-01 4.72e+00 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 4316 15.06 - 30.12: 376 30.12 - 45.19: 90 45.19 - 60.25: 4 60.25 - 75.31: 6 Dihedral angle restraints: 4792 sinusoidal: 1760 harmonic: 3032 Sorted by residual: dihedral pdb=" CA THR C 370 " pdb=" C THR C 370 " pdb=" N LEU C 371 " pdb=" CA LEU C 371 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA THR A 370 " pdb=" C THR A 370 " pdb=" N LEU A 371 " pdb=" CA LEU A 371 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PHE B 298 " pdb=" C PHE B 298 " pdb=" N ARG B 299 " pdb=" CA ARG B 299 " ideal model delta harmonic sigma weight residual 180.00 164.89 15.11 0 5.00e+00 4.00e-02 9.14e+00 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 969 0.045 - 0.089: 293 0.089 - 0.134: 54 0.134 - 0.179: 0 0.179 - 0.224: 4 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA LEU B 271 " pdb=" N LEU B 271 " pdb=" C LEU B 271 " pdb=" CB LEU B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA LEU D 271 " pdb=" N LEU D 271 " pdb=" C LEU D 271 " pdb=" CB LEU D 271 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LEU A 271 " pdb=" N LEU A 271 " pdb=" C LEU A 271 " pdb=" CB LEU A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1317 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 271 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO A 272 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 271 " -0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO C 272 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 272 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 272 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 346 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" CD GLU C 346 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU C 346 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 346 " -0.009 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 1985 2.78 - 3.37: 9798 3.37 - 3.96: 15076 3.96 - 4.55: 21844 4.55 - 5.14: 30941 Nonbonded interactions: 79644 Sorted by model distance: nonbonded pdb=" O SER D 260 " pdb=" OG SER D 263 " model vdw 2.195 3.040 nonbonded pdb=" O SER B 260 " pdb=" OG SER B 263 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR D 188 " pdb=" O ARG D 305 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR B 188 " pdb=" O ARG B 305 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" O HIS A 306 " model vdw 2.280 3.040 ... (remaining 79639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 166 through 424) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.510 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8188 Z= 0.192 Angle : 0.623 7.030 11124 Z= 0.353 Chirality : 0.042 0.224 1320 Planarity : 0.004 0.040 1360 Dihedral : 12.078 75.310 2840 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 1.30 (0.26), residues: 1028 helix: 1.20 (0.18), residues: 802 sheet: None (None), residues: 0 loop : -0.07 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 293 TYR 0.018 0.002 TYR C 273 PHE 0.017 0.001 PHE C 295 TRP 0.009 0.001 TRP C 362 HIS 0.004 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8188) covalent geometry : angle 0.62264 (11124) hydrogen bonds : bond 0.10781 ( 625) hydrogen bonds : angle 5.17180 ( 1821) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.277 Fit side-chains REVERT: A 262 MET cc_start: 0.7759 (tpp) cc_final: 0.7497 (tpp) REVERT: A 401 PRO cc_start: 0.7274 (Cg_exo) cc_final: 0.6979 (Cg_endo) REVERT: C 262 MET cc_start: 0.7807 (tpp) cc_final: 0.7358 (tpp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.4858 time to fit residues: 82.6914 Evaluate side-chains 123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.0000 chunk 45 optimal weight: 0.1980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN D 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.186164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116953 restraints weight = 9746.752| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.59 r_work: 0.3257 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8188 Z= 0.131 Angle : 0.559 13.040 11124 Z= 0.289 Chirality : 0.040 0.148 1320 Planarity : 0.004 0.046 1360 Dihedral : 3.819 13.148 1148 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.42 % Allowed : 11.37 % Favored : 87.20 % 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: 1.74 (0.26), residues: 1028 helix: 1.44 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.25 (0.49), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 293 TYR 0.012 0.001 TYR B 188 PHE 0.017 0.001 PHE C 295 TRP 0.007 0.001 TRP A 362 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8188) covalent geometry : angle 0.55909 (11124) hydrogen bonds : bond 0.04189 ( 625) hydrogen bonds : angle 4.26006 ( 1821) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.236 Fit side-chains REVERT: C 303 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: D 246 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6228 (mp) outliers start: 12 outliers final: 0 residues processed: 144 average time/residue: 0.4680 time to fit residues: 71.9121 Evaluate side-chains 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.184878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115522 restraints weight = 9701.995| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.57 r_work: 0.3242 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8188 Z= 0.156 Angle : 0.542 10.791 11124 Z= 0.287 Chirality : 0.042 0.398 1320 Planarity : 0.004 0.049 1360 Dihedral : 3.775 13.746 1148 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.66 % Allowed : 14.10 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.27), residues: 1028 helix: 1.53 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.37 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 293 TYR 0.020 0.001 TYR C 273 PHE 0.011 0.001 PHE A 257 TRP 0.007 0.001 TRP C 362 HIS 0.004 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8188) covalent geometry : angle 0.54214 (11124) hydrogen bonds : bond 0.04215 ( 625) hydrogen bonds : angle 4.17699 ( 1821) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.303 Fit side-chains REVERT: A 303 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6291 (m-80) REVERT: A 418 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7339 (mtm-85) REVERT: B 310 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6927 (mp) REVERT: C 415 GLN cc_start: 0.7278 (mm-40) cc_final: 0.6747 (mm-40) REVERT: C 418 ARG cc_start: 0.7478 (mtp180) cc_final: 0.6816 (mtm-85) REVERT: D 310 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6952 (mp) outliers start: 14 outliers final: 5 residues processed: 143 average time/residue: 0.4196 time to fit residues: 64.3894 Evaluate side-chains 137 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.183468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113674 restraints weight = 9841.462| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.54 r_work: 0.3219 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8188 Z= 0.197 Angle : 0.558 6.564 11124 Z= 0.299 Chirality : 0.042 0.204 1320 Planarity : 0.005 0.050 1360 Dihedral : 3.818 13.723 1148 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.25 % Allowed : 15.40 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.26), residues: 1028 helix: 1.47 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.35 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 293 TYR 0.021 0.002 TYR C 273 PHE 0.014 0.001 PHE A 257 TRP 0.007 0.001 TRP A 362 HIS 0.004 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 8188) covalent geometry : angle 0.55833 (11124) hydrogen bonds : bond 0.04402 ( 625) hydrogen bonds : angle 4.16043 ( 1821) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.321 Fit side-chains REVERT: A 262 MET cc_start: 0.7692 (tpp) cc_final: 0.7297 (tpp) REVERT: A 303 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: A 415 GLN cc_start: 0.7261 (mm-40) cc_final: 0.6897 (mm-40) REVERT: A 418 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7273 (mtm-85) REVERT: B 262 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6730 (mmt) REVERT: B 310 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6964 (mp) REVERT: C 303 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6397 (m-80) REVERT: C 415 GLN cc_start: 0.7378 (mm-40) cc_final: 0.6656 (mm-40) REVERT: C 418 ARG cc_start: 0.7553 (mtp180) cc_final: 0.7003 (mtp180) REVERT: D 262 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6927 (mmm) REVERT: D 310 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6987 (mp) outliers start: 19 outliers final: 9 residues processed: 145 average time/residue: 0.4489 time to fit residues: 69.5912 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.185493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116242 restraints weight = 9796.272| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.57 r_work: 0.3252 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8188 Z= 0.134 Angle : 0.515 6.902 11124 Z= 0.277 Chirality : 0.040 0.185 1320 Planarity : 0.004 0.053 1360 Dihedral : 3.721 13.658 1148 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.54 % Allowed : 18.25 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.27), residues: 1028 helix: 1.66 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.43 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 256 TYR 0.019 0.001 TYR C 273 PHE 0.008 0.001 PHE A 295 TRP 0.004 0.001 TRP A 362 HIS 0.005 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8188) covalent geometry : angle 0.51518 (11124) hydrogen bonds : bond 0.04010 ( 625) hydrogen bonds : angle 4.00523 ( 1821) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.286 Fit side-chains REVERT: A 303 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6370 (m-80) REVERT: A 415 GLN cc_start: 0.7298 (mm-40) cc_final: 0.7009 (mm-40) REVERT: A 418 ARG cc_start: 0.7648 (mtp180) cc_final: 0.7427 (mtp-110) REVERT: B 310 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6896 (mp) REVERT: B 346 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8128 (mm-30) REVERT: B 347 LYS cc_start: 0.7882 (ptmt) cc_final: 0.7669 (ptmm) REVERT: C 230 PHE cc_start: 0.7611 (t80) cc_final: 0.7324 (t80) REVERT: C 262 MET cc_start: 0.7581 (tpp) cc_final: 0.7245 (tpp) REVERT: C 303 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: C 415 GLN cc_start: 0.7457 (mm-40) cc_final: 0.6813 (mm-40) REVERT: C 418 ARG cc_start: 0.7522 (mtp180) cc_final: 0.6970 (mtp180) REVERT: D 262 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6877 (mmm) REVERT: D 310 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6893 (mp) REVERT: D 346 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8032 (mm-30) outliers start: 13 outliers final: 5 residues processed: 143 average time/residue: 0.4399 time to fit residues: 67.3317 Evaluate side-chains 139 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 412 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 7.9990 chunk 84 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.185906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114493 restraints weight = 9838.825| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.64 r_work: 0.3241 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8188 Z= 0.147 Angle : 0.531 7.359 11124 Z= 0.283 Chirality : 0.040 0.215 1320 Planarity : 0.004 0.053 1360 Dihedral : 3.699 13.639 1148 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.01 % Allowed : 18.84 % Favored : 79.15 % 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: 2.09 (0.27), residues: 1028 helix: 1.67 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.46 (0.49), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 256 TYR 0.017 0.001 TYR C 273 PHE 0.019 0.001 PHE A 257 TRP 0.005 0.001 TRP A 362 HIS 0.005 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8188) covalent geometry : angle 0.53086 (11124) hydrogen bonds : bond 0.04047 ( 625) hydrogen bonds : angle 4.01448 ( 1821) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.308 Fit side-chains REVERT: A 230 PHE cc_start: 0.7792 (t80) cc_final: 0.7516 (t80) REVERT: A 262 MET cc_start: 0.7731 (tpp) cc_final: 0.7409 (tpp) REVERT: A 271 LEU cc_start: 0.8248 (pp) cc_final: 0.7749 (mm) REVERT: A 275 ILE cc_start: 0.8091 (mt) cc_final: 0.7878 (mp) REVERT: A 303 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6344 (m-80) REVERT: A 415 GLN cc_start: 0.7326 (mm-40) cc_final: 0.7038 (mm-40) REVERT: A 418 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7415 (mtp-110) REVERT: B 310 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6905 (mp) REVERT: B 346 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8098 (mm-30) REVERT: C 230 PHE cc_start: 0.7657 (t80) cc_final: 0.7425 (t80) REVERT: C 303 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.6351 (m-80) REVERT: C 415 GLN cc_start: 0.7498 (mm-40) cc_final: 0.6881 (mm-40) REVERT: C 418 ARG cc_start: 0.7521 (mtp180) cc_final: 0.6914 (mtm-85) REVERT: D 310 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6936 (mp) outliers start: 17 outliers final: 8 residues processed: 144 average time/residue: 0.4013 time to fit residues: 62.2300 Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 412 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 54 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 71 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.187827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117756 restraints weight = 9945.315| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.62 r_work: 0.3290 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8188 Z= 0.126 Angle : 0.540 8.754 11124 Z= 0.280 Chirality : 0.040 0.231 1320 Planarity : 0.004 0.056 1360 Dihedral : 3.621 13.761 1148 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.18 % Allowed : 21.33 % Favored : 77.49 % 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: 2.24 (0.27), residues: 1028 helix: 1.78 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.48 (0.49), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 256 TYR 0.016 0.001 TYR C 273 PHE 0.015 0.001 PHE A 257 TRP 0.004 0.001 TRP C 362 HIS 0.004 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8188) covalent geometry : angle 0.54005 (11124) hydrogen bonds : bond 0.03834 ( 625) hydrogen bonds : angle 3.94867 ( 1821) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 230 PHE cc_start: 0.7878 (t80) cc_final: 0.7623 (t80) REVERT: A 262 MET cc_start: 0.7724 (tpp) cc_final: 0.7374 (tpp) REVERT: A 271 LEU cc_start: 0.8228 (pp) cc_final: 0.7751 (mm) REVERT: A 303 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6292 (m-80) REVERT: A 415 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7045 (mm-40) REVERT: A 418 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7476 (mtp-110) REVERT: B 347 LYS cc_start: 0.7828 (ptmt) cc_final: 0.7611 (ptmm) REVERT: C 230 PHE cc_start: 0.7694 (t80) cc_final: 0.7438 (t80) REVERT: C 262 MET cc_start: 0.7652 (tpp) cc_final: 0.7359 (tpp) REVERT: C 271 LEU cc_start: 0.8255 (pp) cc_final: 0.7772 (mm) REVERT: C 275 ILE cc_start: 0.8135 (mt) cc_final: 0.7913 (mp) REVERT: C 303 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6344 (m-80) REVERT: C 415 GLN cc_start: 0.7520 (mm-40) cc_final: 0.6932 (mm-40) REVERT: C 418 ARG cc_start: 0.7516 (mtp180) cc_final: 0.6922 (mtm-85) outliers start: 10 outliers final: 7 residues processed: 149 average time/residue: 0.4234 time to fit residues: 67.7094 Evaluate side-chains 138 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 412 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 0.0770 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.187387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116713 restraints weight = 9921.799| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.64 r_work: 0.3280 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8188 Z= 0.138 Angle : 0.559 9.379 11124 Z= 0.289 Chirality : 0.040 0.224 1320 Planarity : 0.004 0.050 1360 Dihedral : 3.621 14.021 1148 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.42 % Allowed : 21.45 % Favored : 77.13 % 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: 2.30 (0.27), residues: 1028 helix: 1.83 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.47 (0.49), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.023 0.001 TYR C 273 PHE 0.029 0.001 PHE A 257 TRP 0.004 0.001 TRP B 362 HIS 0.005 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8188) covalent geometry : angle 0.55870 (11124) hydrogen bonds : bond 0.03950 ( 625) hydrogen bonds : angle 3.96523 ( 1821) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.282 Fit side-chains REVERT: A 230 PHE cc_start: 0.7901 (t80) cc_final: 0.7643 (t80) REVERT: A 262 MET cc_start: 0.7758 (tpp) cc_final: 0.7230 (tpp) REVERT: A 303 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6344 (m-80) REVERT: A 415 GLN cc_start: 0.7344 (mm-40) cc_final: 0.7025 (mm-40) REVERT: A 418 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7493 (mtp-110) REVERT: C 230 PHE cc_start: 0.7739 (t80) cc_final: 0.7499 (t80) REVERT: C 262 MET cc_start: 0.7699 (tpp) cc_final: 0.7244 (tpp) REVERT: C 271 LEU cc_start: 0.8187 (pp) cc_final: 0.7770 (mm) REVERT: C 275 ILE cc_start: 0.8168 (mt) cc_final: 0.7929 (mp) REVERT: C 303 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6358 (m-80) REVERT: C 415 GLN cc_start: 0.7532 (mm-40) cc_final: 0.6932 (mm-40) REVERT: C 418 ARG cc_start: 0.7535 (mtp180) cc_final: 0.6984 (mtp180) REVERT: D 310 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6908 (mp) outliers start: 12 outliers final: 8 residues processed: 141 average time/residue: 0.4279 time to fit residues: 64.6576 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 0.0000 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.200804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136978 restraints weight = 9884.806| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.36 r_work: 0.3552 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8188 Z= 0.134 Angle : 0.556 8.157 11124 Z= 0.289 Chirality : 0.040 0.247 1320 Planarity : 0.004 0.049 1360 Dihedral : 3.579 14.068 1148 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.42 % Allowed : 21.21 % Favored : 77.37 % 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: 2.32 (0.27), residues: 1028 helix: 1.85 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.45 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 423 TYR 0.022 0.001 TYR C 273 PHE 0.023 0.001 PHE A 257 TRP 0.004 0.001 TRP D 362 HIS 0.005 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8188) covalent geometry : angle 0.55612 (11124) hydrogen bonds : bond 0.03920 ( 625) hydrogen bonds : angle 3.97017 ( 1821) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.189 Fit side-chains REVERT: A 230 PHE cc_start: 0.8393 (t80) cc_final: 0.8106 (t80) REVERT: A 262 MET cc_start: 0.7862 (tpp) cc_final: 0.7437 (tpp) REVERT: A 303 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: A 415 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7122 (mm-40) REVERT: A 418 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7553 (mtp180) REVERT: C 230 PHE cc_start: 0.8199 (t80) cc_final: 0.7981 (t80) REVERT: C 262 MET cc_start: 0.7920 (tpp) cc_final: 0.7499 (tpp) REVERT: C 271 LEU cc_start: 0.8382 (pp) cc_final: 0.7972 (mm) REVERT: C 275 ILE cc_start: 0.8525 (mt) cc_final: 0.8275 (mp) REVERT: C 303 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.6767 (m-80) REVERT: C 415 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7031 (mm-40) REVERT: C 418 ARG cc_start: 0.7635 (mtp180) cc_final: 0.7043 (mtp180) REVERT: D 310 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7241 (mp) outliers start: 12 outliers final: 10 residues processed: 137 average time/residue: 0.4097 time to fit residues: 60.3404 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 0.0020 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.187032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116393 restraints weight = 9872.054| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.62 r_work: 0.3279 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8188 Z= 0.148 Angle : 0.576 7.996 11124 Z= 0.298 Chirality : 0.041 0.274 1320 Planarity : 0.004 0.048 1360 Dihedral : 3.610 14.439 1148 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.78 % Allowed : 21.33 % Favored : 76.90 % 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: 2.22 (0.27), residues: 1028 helix: 1.78 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.44 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 423 TYR 0.022 0.001 TYR C 273 PHE 0.021 0.001 PHE A 257 TRP 0.006 0.001 TRP D 362 HIS 0.005 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8188) covalent geometry : angle 0.57626 (11124) hydrogen bonds : bond 0.04068 ( 625) hydrogen bonds : angle 4.00962 ( 1821) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.276 Fit side-chains REVERT: A 230 PHE cc_start: 0.7895 (t80) cc_final: 0.7649 (t80) REVERT: A 262 MET cc_start: 0.7604 (tpp) cc_final: 0.7174 (tpp) REVERT: A 301 PHE cc_start: 0.8241 (m-80) cc_final: 0.7767 (m-80) REVERT: A 303 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6316 (m-80) REVERT: A 415 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7076 (mm-40) REVERT: A 418 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7409 (mtp-110) REVERT: C 230 PHE cc_start: 0.7712 (t80) cc_final: 0.7508 (t80) REVERT: C 262 MET cc_start: 0.7672 (tpp) cc_final: 0.7214 (tpp) REVERT: C 271 LEU cc_start: 0.8130 (pp) cc_final: 0.7782 (mm) REVERT: C 275 ILE cc_start: 0.8121 (mt) cc_final: 0.7885 (mp) REVERT: C 303 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: C 415 GLN cc_start: 0.7520 (mm-40) cc_final: 0.6930 (mm-40) REVERT: C 418 ARG cc_start: 0.7486 (mtp180) cc_final: 0.6958 (mtp180) outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 0.3716 time to fit residues: 54.9998 Evaluate side-chains 139 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.186391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114933 restraints weight = 9831.991| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.62 r_work: 0.3253 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8188 Z= 0.166 Angle : 0.601 10.853 11124 Z= 0.312 Chirality : 0.042 0.262 1320 Planarity : 0.004 0.048 1360 Dihedral : 3.672 14.742 1148 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.54 % Allowed : 21.68 % Favored : 76.78 % 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: 2.09 (0.26), residues: 1028 helix: 1.68 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.40 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 423 TYR 0.022 0.001 TYR C 273 PHE 0.032 0.001 PHE A 257 TRP 0.006 0.001 TRP B 362 HIS 0.005 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8188) covalent geometry : angle 0.60129 (11124) hydrogen bonds : bond 0.04226 ( 625) hydrogen bonds : angle 4.08703 ( 1821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3310.32 seconds wall clock time: 57 minutes 0.28 seconds (3420.28 seconds total)