Starting phenix.real_space_refine on Wed Feb 12 14:40:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukd_26577/02_2025/7ukd_26577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukd_26577/02_2025/7ukd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ukd_26577/02_2025/7ukd_26577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukd_26577/02_2025/7ukd_26577.map" model { file = "/net/cci-nas-00/data/ceres_data/7ukd_26577/02_2025/7ukd_26577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukd_26577/02_2025/7ukd_26577.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 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: 5.50, per 1000 atoms: 0.69 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: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.56 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: 1.86 Time building geometry restraints manager: 2.24 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.960 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.120 ------------------------------------------------------------------------------- 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= 0.289 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP C 362 HIS 0.004 0.001 HIS C 306 PHE 0.017 0.001 PHE C 295 TYR 0.018 0.002 TYR C 273 ARG 0.006 0.000 ARG B 293 *********************** 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 : 0.904 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: 0.6980 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 1.0611 time to fit residues: 181.3900 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.184431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114896 restraints weight = 9627.418| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.56 r_work: 0.3232 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8188 Z= 0.232 Angle : 0.577 13.279 11124 Z= 0.299 Chirality : 0.041 0.151 1320 Planarity : 0.004 0.047 1360 Dihedral : 3.876 13.386 1148 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.90 % Allowed : 11.73 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.26), residues: 1028 helix: 1.44 (0.18), residues: 812 sheet: None (None), residues: 0 loop : 0.22 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 362 HIS 0.003 0.001 HIS A 306 PHE 0.013 0.001 PHE C 295 TYR 0.012 0.001 TYR B 188 ARG 0.005 0.000 ARG B 293 *********************** 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 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.915 Fit side-chains REVERT: A 303 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: C 230 PHE cc_start: 0.7534 (t80) cc_final: 0.7301 (t80) REVERT: C 303 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: D 246 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.6147 (mp) outliers start: 16 outliers final: 3 residues processed: 145 average time/residue: 1.0385 time to fit residues: 161.5002 Evaluate side-chains 129 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 303 PHE 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 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.185619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114338 restraints weight = 9788.279| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.61 r_work: 0.3245 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1334 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= 0.229 Angle : 0.553 12.355 11124 Z= 0.289 Chirality : 0.043 0.491 1320 Planarity : 0.004 0.051 1360 Dihedral : 3.796 13.913 1148 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.78 % Allowed : 13.63 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.27), residues: 1028 helix: 1.50 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.34 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.004 0.001 HIS A 306 PHE 0.011 0.001 PHE A 257 TYR 0.020 0.001 TYR C 273 ARG 0.005 0.000 ARG D 293 *********************** 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 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.856 Fit side-chains REVERT: A 418 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7341 (mtm-85) REVERT: B 310 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6927 (mp) REVERT: C 415 GLN cc_start: 0.7336 (mm-40) cc_final: 0.6769 (mm-40) REVERT: C 418 ARG cc_start: 0.7512 (mtp180) cc_final: 0.6860 (mtm-85) REVERT: D 310 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6980 (mp) outliers start: 15 outliers final: 6 residues processed: 146 average time/residue: 0.9616 time to fit residues: 150.9395 Evaluate side-chains 134 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL 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 316 THR 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 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.185419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113864 restraints weight = 9781.302| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.62 r_work: 0.3229 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8188 Z= 0.236 Angle : 0.529 6.496 11124 Z= 0.284 Chirality : 0.041 0.182 1320 Planarity : 0.004 0.049 1360 Dihedral : 3.748 13.842 1148 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.78 % Allowed : 16.00 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.27), residues: 1028 helix: 1.54 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.39 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.005 0.001 HIS C 306 PHE 0.014 0.001 PHE A 257 TYR 0.021 0.001 TYR C 273 ARG 0.005 0.000 ARG D 293 *********************** 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 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.869 Fit side-chains REVERT: A 262 MET cc_start: 0.7613 (tpp) cc_final: 0.7189 (tpp) REVERT: A 303 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6292 (m-80) REVERT: A 415 GLN cc_start: 0.7271 (mm-40) cc_final: 0.6911 (mm-40) REVERT: A 418 ARG cc_start: 0.7673 (mtp180) cc_final: 0.7261 (mtm-85) REVERT: B 310 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6919 (mp) REVERT: B 346 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8188 (mm-30) REVERT: C 230 PHE cc_start: 0.7627 (t80) cc_final: 0.7339 (t80) REVERT: C 262 MET cc_start: 0.7568 (tpp) cc_final: 0.7173 (tpp) REVERT: C 415 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6741 (mm-40) REVERT: C 418 ARG cc_start: 0.7526 (mtp180) cc_final: 0.6981 (mtp180) REVERT: D 310 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6971 (mp) outliers start: 15 outliers final: 7 residues processed: 145 average time/residue: 1.0299 time to fit residues: 160.2449 Evaluate side-chains 138 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 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 9 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.0020 chunk 89 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.184027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114384 restraints weight = 9641.405| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.53 r_work: 0.3235 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1564 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= 0.268 Angle : 0.542 6.970 11124 Z= 0.292 Chirality : 0.041 0.189 1320 Planarity : 0.005 0.053 1360 Dihedral : 3.772 13.891 1148 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.37 % Allowed : 17.30 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.26), residues: 1028 helix: 1.55 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.40 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 362 HIS 0.005 0.001 HIS C 306 PHE 0.008 0.001 PHE A 295 TYR 0.018 0.001 TYR C 273 ARG 0.006 0.000 ARG D 256 *********************** 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 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.907 Fit side-chains REVERT: A 303 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.6351 (m-80) REVERT: A 415 GLN cc_start: 0.7337 (mm-40) cc_final: 0.7029 (mm-40) REVERT: A 418 ARG cc_start: 0.7690 (mtp180) cc_final: 0.7456 (mtp-110) REVERT: B 293 ARG cc_start: 0.7581 (mtt90) cc_final: 0.7370 (mtp85) REVERT: B 310 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6955 (mp) REVERT: C 230 PHE cc_start: 0.7696 (t80) cc_final: 0.7406 (t80) REVERT: C 262 MET cc_start: 0.7658 (tpp) cc_final: 0.7297 (tpp) REVERT: C 303 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6420 (m-80) REVERT: C 415 GLN cc_start: 0.7503 (mm-40) cc_final: 0.6881 (mm-40) REVERT: C 418 ARG cc_start: 0.7537 (mtp180) cc_final: 0.6942 (mtm-85) REVERT: D 262 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6965 (mmm) REVERT: D 310 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6955 (mp) REVERT: D 346 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8224 (mm-30) outliers start: 20 outliers final: 9 residues processed: 143 average time/residue: 0.9498 time to fit residues: 146.3784 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 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 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 2 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.184311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114760 restraints weight = 9731.260| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.54 r_work: 0.3232 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8188 Z= 0.250 Angle : 0.535 7.520 11124 Z= 0.287 Chirality : 0.041 0.211 1320 Planarity : 0.005 0.053 1360 Dihedral : 3.747 14.005 1148 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.37 % Allowed : 18.01 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.26), residues: 1028 helix: 1.61 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.40 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.005 0.001 HIS A 306 PHE 0.020 0.001 PHE A 257 TYR 0.017 0.001 TYR C 273 ARG 0.005 0.000 ARG D 256 *********************** 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 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.950 Fit side-chains REVERT: A 262 MET cc_start: 0.7778 (tpp) cc_final: 0.7383 (tpp) REVERT: A 303 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6378 (m-80) REVERT: A 328 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7428 (tm) REVERT: A 415 GLN cc_start: 0.7316 (mm-40) cc_final: 0.7023 (mm-40) REVERT: A 418 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7432 (mtp-110) REVERT: B 293 ARG cc_start: 0.7550 (mtt90) cc_final: 0.7338 (mtp85) REVERT: B 310 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6911 (mp) REVERT: B 346 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8168 (mm-30) REVERT: C 230 PHE cc_start: 0.7691 (t80) cc_final: 0.7438 (t80) REVERT: C 271 LEU cc_start: 0.8296 (pp) cc_final: 0.7802 (mm) REVERT: C 275 ILE cc_start: 0.8121 (mt) cc_final: 0.7905 (mp) REVERT: C 303 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6410 (m-80) REVERT: C 415 GLN cc_start: 0.7461 (mm-40) cc_final: 0.6814 (mm-40) REVERT: C 418 ARG cc_start: 0.7538 (mtp180) cc_final: 0.6976 (mtp180) REVERT: D 310 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6935 (mp) outliers start: 20 outliers final: 12 residues processed: 146 average time/residue: 0.9459 time to fit residues: 149.3314 Evaluate side-chains 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 328 LEU 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 B residue 412 ILE Chi-restraints excluded: chain C residue 227 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 316 THR 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 73 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.186937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116015 restraints weight = 9776.754| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.57 r_work: 0.3266 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8188 Z= 0.195 Angle : 0.524 7.284 11124 Z= 0.279 Chirality : 0.040 0.206 1320 Planarity : 0.004 0.052 1360 Dihedral : 3.662 14.300 1148 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.54 % Allowed : 20.02 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.27), residues: 1028 helix: 1.76 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.43 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 362 HIS 0.004 0.001 HIS C 306 PHE 0.013 0.001 PHE A 257 TYR 0.014 0.001 TYR C 273 ARG 0.005 0.000 ARG D 256 *********************** 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 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.072 Fit side-chains REVERT: A 230 PHE cc_start: 0.7866 (t80) cc_final: 0.7609 (t80) REVERT: A 271 LEU cc_start: 0.8241 (pp) cc_final: 0.7777 (mm) REVERT: A 275 ILE cc_start: 0.8100 (mt) cc_final: 0.7893 (mp) REVERT: A 303 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6350 (m-80) REVERT: A 415 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7024 (mm-40) REVERT: A 418 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7490 (mtp-110) REVERT: B 310 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6966 (mp) REVERT: B 346 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8144 (mt-10) REVERT: C 230 PHE cc_start: 0.7673 (t80) cc_final: 0.7425 (t80) REVERT: C 262 MET cc_start: 0.7685 (tpp) cc_final: 0.7348 (tpp) REVERT: C 271 LEU cc_start: 0.8222 (pp) cc_final: 0.7794 (mm) REVERT: C 275 ILE cc_start: 0.8148 (mt) cc_final: 0.7928 (mp) REVERT: C 303 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6369 (m-80) REVERT: C 415 GLN cc_start: 0.7469 (mm-40) cc_final: 0.6857 (mm-40) REVERT: C 418 ARG cc_start: 0.7517 (mtp180) cc_final: 0.6986 (mtp180) REVERT: D 310 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6920 (mp) outliers start: 13 outliers final: 7 residues processed: 144 average time/residue: 1.0519 time to fit residues: 164.8622 Evaluate side-chains 144 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 B residue 412 ILE Chi-restraints excluded: chain C residue 197 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.186564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115215 restraints weight = 9848.585| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.63 r_work: 0.3251 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8188 Z= 0.222 Angle : 0.560 8.433 11124 Z= 0.293 Chirality : 0.041 0.236 1320 Planarity : 0.004 0.051 1360 Dihedral : 3.649 14.239 1148 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.66 % Allowed : 21.33 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.27), residues: 1028 helix: 1.73 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.45 (0.49), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 362 HIS 0.005 0.001 HIS C 306 PHE 0.028 0.001 PHE A 257 TYR 0.022 0.001 TYR C 273 ARG 0.007 0.000 ARG B 256 *********************** 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 147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.826 Fit side-chains REVERT: A 230 PHE cc_start: 0.7900 (t80) cc_final: 0.7647 (t80) REVERT: A 262 MET cc_start: 0.7745 (tpp) cc_final: 0.7182 (tpp) REVERT: A 271 LEU cc_start: 0.8160 (pp) cc_final: 0.7757 (mm) REVERT: A 275 ILE cc_start: 0.8129 (mt) cc_final: 0.7908 (mp) REVERT: A 303 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: A 415 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7022 (mm-40) REVERT: A 418 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7471 (mtp-110) REVERT: B 310 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6954 (mp) REVERT: C 230 PHE cc_start: 0.7731 (t80) cc_final: 0.7469 (t80) REVERT: C 262 MET cc_start: 0.7699 (tpp) cc_final: 0.7204 (tpp) REVERT: C 271 LEU cc_start: 0.8137 (pp) cc_final: 0.7737 (mm) REVERT: C 275 ILE cc_start: 0.8144 (mt) cc_final: 0.7921 (mp) REVERT: C 303 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: C 328 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7377 (tm) REVERT: C 415 GLN cc_start: 0.7471 (mm-40) cc_final: 0.6901 (mm-40) REVERT: C 418 ARG cc_start: 0.7553 (mtp180) cc_final: 0.7016 (mtp180) REVERT: D 262 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6857 (mmm) REVERT: D 310 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6899 (mp) outliers start: 14 outliers final: 6 residues processed: 140 average time/residue: 0.9545 time to fit residues: 143.8749 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 : 0.918 ------------------------------------------------------------------------------- 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 310 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 303 PHE Chi-restraints excluded: chain C residue 328 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 0.0010 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.187679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116917 restraints weight = 10006.747| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.65 r_work: 0.3274 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8188 Z= 0.199 Angle : 0.548 8.528 11124 Z= 0.287 Chirality : 0.040 0.256 1320 Planarity : 0.004 0.049 1360 Dihedral : 3.621 14.400 1148 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.66 % Allowed : 21.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.27), residues: 1028 helix: 1.77 (0.18), residues: 824 sheet: None (None), residues: 0 loop : 0.37 (0.50), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 362 HIS 0.005 0.001 HIS A 306 PHE 0.024 0.001 PHE A 257 TYR 0.021 0.001 TYR C 273 ARG 0.006 0.000 ARG B 256 *********************** 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 151 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.838 Fit side-chains REVERT: A 230 PHE cc_start: 0.7912 (t80) cc_final: 0.7667 (t80) REVERT: A 262 MET cc_start: 0.7777 (tpp) cc_final: 0.7299 (tpp) REVERT: A 271 LEU cc_start: 0.8109 (pp) cc_final: 0.7832 (mm) REVERT: A 275 ILE cc_start: 0.8168 (mt) cc_final: 0.7957 (mp) REVERT: A 303 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: A 415 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7021 (mm-40) REVERT: A 418 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7454 (mtp-110) REVERT: C 230 PHE cc_start: 0.7743 (t80) cc_final: 0.7518 (t80) REVERT: C 262 MET cc_start: 0.7730 (tpp) cc_final: 0.7271 (tpp) REVERT: C 271 LEU cc_start: 0.8112 (pp) cc_final: 0.7755 (mm) REVERT: C 275 ILE cc_start: 0.8168 (mt) cc_final: 0.7955 (mp) REVERT: C 303 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: C 328 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7373 (tm) REVERT: C 415 GLN cc_start: 0.7524 (mm-40) cc_final: 0.6927 (mm-40) REVERT: C 418 ARG cc_start: 0.7490 (mtp180) cc_final: 0.6960 (mtp180) REVERT: D 310 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6925 (mp) outliers start: 14 outliers final: 8 residues processed: 143 average time/residue: 0.9276 time to fit residues: 143.1027 Evaluate side-chains 147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 237 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 328 LEU 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 95 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.187191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116551 restraints weight = 9815.619| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.61 r_work: 0.3271 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8188 Z= 0.213 Angle : 0.564 8.568 11124 Z= 0.294 Chirality : 0.041 0.273 1320 Planarity : 0.004 0.048 1360 Dihedral : 3.621 14.642 1148 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.18 % Allowed : 21.80 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.27), residues: 1028 helix: 1.78 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.45 (0.49), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 362 HIS 0.005 0.001 HIS A 306 PHE 0.023 0.001 PHE A 257 TYR 0.021 0.001 TYR C 273 ARG 0.006 0.000 ARG B 256 ********************** 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 144 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.853 Fit side-chains REVERT: A 230 PHE cc_start: 0.7915 (t80) cc_final: 0.7670 (t80) REVERT: A 262 MET cc_start: 0.7730 (tpp) cc_final: 0.7323 (tpp) REVERT: A 271 LEU cc_start: 0.8124 (pp) cc_final: 0.7834 (mm) REVERT: A 275 ILE cc_start: 0.8137 (mt) cc_final: 0.7925 (mp) REVERT: A 303 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6306 (m-80) REVERT: A 415 GLN cc_start: 0.7415 (mm-40) cc_final: 0.7051 (mm-40) REVERT: A 418 ARG cc_start: 0.7695 (mtp180) cc_final: 0.7382 (mtp180) REVERT: C 230 PHE cc_start: 0.7710 (t80) cc_final: 0.7508 (t80) REVERT: C 271 LEU cc_start: 0.8109 (pp) cc_final: 0.7785 (mm) REVERT: C 275 ILE cc_start: 0.8141 (mt) cc_final: 0.7928 (mp) REVERT: C 303 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6342 (m-80) REVERT: C 415 GLN cc_start: 0.7546 (mm-40) cc_final: 0.6966 (mm-40) REVERT: C 418 ARG cc_start: 0.7452 (mtp180) cc_final: 0.6947 (mtp180) REVERT: D 310 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6885 (mp) outliers start: 10 outliers final: 8 residues processed: 138 average time/residue: 0.8808 time to fit residues: 131.8198 Evaluate side-chains 140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 79 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.187465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117048 restraints weight = 9892.022| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.62 r_work: 0.3277 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8188 Z= 0.211 Angle : 0.586 13.592 11124 Z= 0.300 Chirality : 0.042 0.331 1320 Planarity : 0.004 0.047 1360 Dihedral : 3.628 14.763 1148 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.54 % Allowed : 21.21 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.27), residues: 1028 helix: 1.80 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.40 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 362 HIS 0.005 0.001 HIS A 306 PHE 0.021 0.001 PHE A 257 TYR 0.021 0.001 TYR C 273 ARG 0.006 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6757.54 seconds wall clock time: 119 minutes 49.09 seconds (7189.09 seconds total)