Starting phenix.real_space_refine on Tue Feb 13 22:51:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukd_26577/02_2024/7ukd_26577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukd_26577/02_2024/7ukd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukd_26577/02_2024/7ukd_26577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukd_26577/02_2024/7ukd_26577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukd_26577/02_2024/7ukd_26577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukd_26577/02_2024/7ukd_26577.pdb" } 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 Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.65, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 3.55 Conformation dependent library (CDL) restraints added in 1.6 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: 0.68 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: 2.18 Time building geometry restraints manager: 3.82 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: 99.71 - 106.58: 196 106.58 - 113.46: 4533 113.46 - 120.33: 3307 120.33 - 127.20: 3024 127.20 - 134.07: 64 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 2.440 nonbonded pdb=" O SER B 260 " pdb=" OG SER B 263 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR D 188 " pdb=" O ARG D 305 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR B 188 " pdb=" O ARG B 305 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR A 188 " pdb=" O HIS A 306 " model vdw 2.280 2.440 ... (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 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: 1.920 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: 9.230 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.230 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.350 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.850 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: 1.1182 time to fit residues: 190.8153 Evaluate side-chains 126 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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: 4.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN D 408 ASN D 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8188 Z= 0.251 Angle : 0.569 13.934 11124 Z= 0.294 Chirality : 0.040 0.142 1320 Planarity : 0.004 0.047 1360 Dihedral : 3.918 13.345 1148 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.01 % Allowed : 12.56 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.26), residues: 1028 helix: 1.44 (0.18), residues: 812 sheet: None (None), residues: 0 loop : 0.14 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 362 HIS 0.004 0.001 HIS A 306 PHE 0.011 0.001 PHE C 295 TYR 0.012 0.001 TYR B 188 ARG 0.005 0.000 ARG D 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 fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 0.963 Fit side-chains REVERT: A 303 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: C 303 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7123 (m-80) outliers start: 17 outliers final: 4 residues processed: 144 average time/residue: 0.9929 time to fit residues: 153.1506 Evaluate side-chains 126 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN D 408 ASN D 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8188 Z= 0.243 Angle : 0.530 10.893 11124 Z= 0.280 Chirality : 0.042 0.418 1320 Planarity : 0.004 0.051 1360 Dihedral : 3.832 13.675 1148 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.54 % Allowed : 14.81 % Favored : 83.65 % 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: 1.90 (0.26), residues: 1028 helix: 1.59 (0.18), residues: 812 sheet: None (None), residues: 0 loop : 0.23 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 362 HIS 0.005 0.001 HIS C 306 PHE 0.012 0.001 PHE A 257 TYR 0.012 0.001 TYR C 188 ARG 0.006 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 151 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 0.884 Fit side-chains REVERT: B 310 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7619 (mp) REVERT: C 303 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: D 262 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7204 (mmm) outliers start: 13 outliers final: 6 residues processed: 144 average time/residue: 0.9868 time to fit residues: 152.8433 Evaluate side-chains 134 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.0040 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 0.0170 chunk 54 optimal weight: 0.9980 overall best weight: 0.5630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 408 ASN B 417 GLN D 408 ASN D 417 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8188 Z= 0.188 Angle : 0.505 11.618 11124 Z= 0.267 Chirality : 0.041 0.485 1320 Planarity : 0.004 0.049 1360 Dihedral : 3.724 13.604 1148 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.66 % Allowed : 17.18 % Favored : 81.16 % 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: 2.03 (0.27), residues: 1028 helix: 1.65 (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 0.005 0.001 TRP C 362 HIS 0.005 0.001 HIS A 306 PHE 0.014 0.001 PHE A 257 TYR 0.018 0.001 TYR A 273 ARG 0.004 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 152 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 0.955 Fit side-chains REVERT: A 303 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: B 310 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7615 (mp) REVERT: C 230 PHE cc_start: 0.8213 (t80) cc_final: 0.7839 (t80) REVERT: D 346 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7936 (mm-30) outliers start: 14 outliers final: 4 residues processed: 143 average time/residue: 0.9910 time to fit residues: 152.0600 Evaluate side-chains 136 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN B 417 GLN D 408 ASN D 417 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8188 Z= 0.226 Angle : 0.502 5.160 11124 Z= 0.270 Chirality : 0.040 0.186 1320 Planarity : 0.004 0.053 1360 Dihedral : 3.697 13.414 1148 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.13 % Allowed : 18.25 % 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: 2.09 (0.27), residues: 1028 helix: 1.69 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.37 (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 0.007 0.001 PHE A 257 TYR 0.016 0.001 TYR A 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 157 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.843 Fit side-chains REVERT: A 303 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: B 310 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7624 (mp) REVERT: C 230 PHE cc_start: 0.8250 (t80) cc_final: 0.7880 (t80) REVERT: C 262 MET cc_start: 0.7821 (tpp) cc_final: 0.7581 (tpp) REVERT: C 303 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: D 310 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7606 (mp) REVERT: D 346 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7946 (mm-30) outliers start: 18 outliers final: 9 residues processed: 150 average time/residue: 0.9217 time to fit residues: 148.8168 Evaluate side-chains 145 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 391 SER 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 391 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 80 optimal weight: 0.0470 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN B 417 GLN D 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8188 Z= 0.207 Angle : 0.505 7.512 11124 Z= 0.268 Chirality : 0.040 0.199 1320 Planarity : 0.004 0.050 1360 Dihedral : 3.669 13.465 1148 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.73 % Allowed : 19.19 % Favored : 78.08 % 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: 1.75 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.43 (0.50), residues: 206 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 0.019 0.001 PHE A 257 TYR 0.019 0.001 TYR B 413 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 161 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 0.855 Fit side-chains REVERT: A 262 MET cc_start: 0.7640 (tpp) cc_final: 0.7404 (tpp) REVERT: A 271 LEU cc_start: 0.8466 (pp) cc_final: 0.8074 (mm) REVERT: A 303 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: A 328 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8136 (tm) REVERT: B 310 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7600 (mp) REVERT: C 230 PHE cc_start: 0.8267 (t80) cc_final: 0.7923 (t80) REVERT: C 271 LEU cc_start: 0.8538 (pp) cc_final: 0.8078 (mm) REVERT: C 303 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7039 (m-80) REVERT: C 328 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8122 (tm) REVERT: D 262 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7395 (mmm) REVERT: D 310 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7605 (mp) outliers start: 23 outliers final: 9 residues processed: 150 average time/residue: 0.8562 time to fit residues: 138.9935 Evaluate side-chains 152 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 391 SER 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 C residue 303 PHE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 238 MET 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 316 THR Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.1980 chunk 70 optimal weight: 0.3980 chunk 54 optimal weight: 0.0270 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN B 417 GLN D 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8188 Z= 0.189 Angle : 0.519 9.045 11124 Z= 0.272 Chirality : 0.039 0.217 1320 Planarity : 0.004 0.038 1360 Dihedral : 3.639 13.506 1148 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.90 % Allowed : 20.73 % 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 (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: 2.28 (0.27), residues: 1028 helix: 1.81 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.49 (0.50), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 172 HIS 0.005 0.001 HIS C 306 PHE 0.013 0.001 PHE A 257 TYR 0.020 0.001 TYR B 413 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 160 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8383 (t80) cc_final: 0.8089 (t80) REVERT: A 303 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: A 328 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8129 (tm) REVERT: B 310 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7603 (mp) REVERT: C 197 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8307 (t) REVERT: C 230 PHE cc_start: 0.8206 (t80) cc_final: 0.7916 (t80) REVERT: C 303 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: C 328 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8108 (tm) REVERT: D 262 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7348 (mmm) outliers start: 16 outliers final: 8 residues processed: 151 average time/residue: 0.9173 time to fit residues: 149.0868 Evaluate side-chains 150 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 391 SER 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 C residue 391 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 262 MET 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 29 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN B 417 GLN D 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8188 Z= 0.343 Angle : 0.575 6.148 11124 Z= 0.309 Chirality : 0.043 0.224 1320 Planarity : 0.004 0.039 1360 Dihedral : 3.735 14.155 1148 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.13 % Allowed : 21.80 % Favored : 76.07 % 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: 1.95 (0.26), residues: 1028 helix: 1.58 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.35 (0.50), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 362 HIS 0.005 0.001 HIS C 306 PHE 0.027 0.001 PHE A 257 TYR 0.020 0.001 TYR B 413 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 152 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 197 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8340 (t) REVERT: A 230 PHE cc_start: 0.8453 (t80) cc_final: 0.8138 (t80) REVERT: A 303 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.6956 (m-80) REVERT: B 310 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7634 (mp) REVERT: C 197 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8311 (t) REVERT: C 230 PHE cc_start: 0.8335 (t80) cc_final: 0.8006 (t80) REVERT: C 303 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: D 262 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7374 (mmm) REVERT: D 310 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7560 (mp) outliers start: 18 outliers final: 8 residues processed: 145 average time/residue: 0.9388 time to fit residues: 146.5476 Evaluate side-chains 147 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 391 SER 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 237 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 391 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN B 417 GLN D 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1891 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= 0.236 Angle : 0.548 7.642 11124 Z= 0.292 Chirality : 0.041 0.240 1320 Planarity : 0.004 0.038 1360 Dihedral : 3.702 14.490 1148 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.78 % Allowed : 22.75 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.04 (0.27), residues: 1028 helix: 1.64 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.42 (0.50), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 362 HIS 0.004 0.001 HIS C 306 PHE 0.021 0.001 PHE A 257 TYR 0.020 0.001 TYR B 413 ARG 0.005 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 153 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 0.833 Fit side-chains REVERT: A 197 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8330 (t) REVERT: A 230 PHE cc_start: 0.8429 (t80) cc_final: 0.8138 (t80) REVERT: A 303 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: B 310 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7617 (mp) REVERT: C 197 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8326 (t) REVERT: C 230 PHE cc_start: 0.8293 (t80) cc_final: 0.7993 (t80) REVERT: C 303 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7003 (m-80) outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 0.9021 time to fit residues: 140.0493 Evaluate side-chains 147 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 391 SER 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 237 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.0370 chunk 24 optimal weight: 0.9980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN B 417 GLN D 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8188 Z= 0.192 Angle : 0.530 7.476 11124 Z= 0.284 Chirality : 0.041 0.264 1320 Planarity : 0.004 0.038 1360 Dihedral : 3.602 14.722 1148 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.42 % Allowed : 23.34 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : 0.46 (0.50), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 172 HIS 0.006 0.001 HIS C 306 PHE 0.022 0.001 PHE A 257 TYR 0.021 0.001 TYR A 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 158 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.915 Fit side-chains REVERT: A 197 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8314 (t) REVERT: A 230 PHE cc_start: 0.8352 (t80) cc_final: 0.8106 (t80) REVERT: A 303 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: B 243 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 310 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7599 (mp) REVERT: C 197 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8318 (t) REVERT: C 230 PHE cc_start: 0.8235 (t80) cc_final: 0.8010 (t80) REVERT: C 303 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6997 (m-80) outliers start: 12 outliers final: 8 residues processed: 149 average time/residue: 0.8943 time to fit residues: 144.0547 Evaluate side-chains 151 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 271 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 237 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 0.0020 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.0170 chunk 57 optimal weight: 0.7980 overall best weight: 0.4426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN B 417 GLN D 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.200028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.136527 restraints weight = 9863.360| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.38 r_work: 0.3562 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.003 0.063 8188 Z= 0.205 Angle : 0.540 7.603 11124 Z= 0.287 Chirality : 0.041 0.286 1320 Planarity : 0.004 0.037 1360 Dihedral : 3.607 14.158 1148 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.30 % Allowed : 22.87 % Favored : 75.83 % 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: 1.81 (0.18), residues: 822 sheet: None (None), residues: 0 loop : 0.34 (0.49), residues: 206 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 0.030 0.001 PHE A 257 TYR 0.021 0.001 TYR A 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: 3280.91 seconds wall clock time: 59 minutes 14.93 seconds (3554.93 seconds total)