Starting phenix.real_space_refine on Wed Sep 17 21:58:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v21_31633/09_2025/7v21_31633.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v21_31633/09_2025/7v21_31633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v21_31633/09_2025/7v21_31633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v21_31633/09_2025/7v21_31633.map" model { file = "/net/cci-nas-00/data/ceres_data/7v21_31633/09_2025/7v21_31633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v21_31633/09_2025/7v21_31633.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 7646 2.51 5 N 1996 2.21 5 O 2197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11903 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2986 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 360} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2990 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 360} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2959 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 356} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2968 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 357} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.59, per 1000 atoms: 0.30 Number of scatterers: 11903 At special positions: 0 Unit cell: (109.61, 90.21, 145.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2197 8.00 N 1996 7.00 C 7646 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: 1.03 Conformation dependent library (CDL) restraints added in 656.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 37.9% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 106 through 123 Processing helix chain 'A' and resid 164 through 180 removed outlier: 3.884A pdb=" N SER A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.697A pdb=" N SER A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 259 through 274 removed outlier: 3.552A pdb=" N THR A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.728A pdb=" N TRP A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 362 removed outlier: 4.973A pdb=" N GLY A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASN A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 464 through 478 Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 164 through 180 removed outlier: 3.846A pdb=" N SER B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.610A pdb=" N SER B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 337 through 354 Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'C' and resid 106 through 123 removed outlier: 3.526A pdb=" N SER C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 180 removed outlier: 3.834A pdb=" N SER C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.632A pdb=" N SER C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 259 through 274 removed outlier: 3.535A pdb=" N THR C 263 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 325 through 329 removed outlier: 3.692A pdb=" N TRP C 329 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 354 Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'D' and resid 106 through 123 removed outlier: 3.534A pdb=" N SER D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 180 removed outlier: 3.894A pdb=" N SER D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 209 through 215 removed outlier: 3.997A pdb=" N SER D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.556A pdb=" N THR D 263 " --> pdb=" O THR D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 Processing helix chain 'D' and resid 325 through 329 removed outlier: 3.834A pdb=" N TRP D 329 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 355 removed outlier: 4.572A pdb=" N GLY D 355 " --> pdb=" O GLY D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 464 through 479 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.474A pdb=" N VAL A 152 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 133 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162 removed outlier: 4.499A pdb=" N PHE A 334 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 201 removed outlier: 4.549A pdb=" N LYS A 199 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.564A pdb=" N VAL B 152 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 133 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 162 removed outlier: 4.044A pdb=" N PHE B 334 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 201 removed outlier: 4.538A pdb=" N LYS B 199 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 309 through 311 Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.591A pdb=" N VAL C 152 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL C 133 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.501A pdb=" N MET C 160 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE C 334 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 199 through 201 removed outlier: 4.381A pdb=" N LYS C 199 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 309 through 311 Processing sheet with id=AB4, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.571A pdb=" N VAL D 152 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL D 133 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 160 through 162 removed outlier: 3.944A pdb=" N PHE D 334 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AB7, first strand: chain 'D' and resid 309 through 311 535 hydrogen bonds defined for protein. 1491 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: 2.13 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3336 1.33 - 1.45: 1992 1.45 - 1.57: 6741 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 12177 Sorted by residual: bond pdb=" C LEU B 365 " pdb=" N PRO B 366 " ideal model delta sigma weight residual 1.330 1.362 -0.032 1.22e-02 6.72e+03 6.76e+00 bond pdb=" C LEU A 365 " pdb=" N PRO A 366 " ideal model delta sigma weight residual 1.331 1.361 -0.030 1.31e-02 5.83e+03 5.29e+00 bond pdb=" C LYS B 370 " pdb=" N PRO B 371 " ideal model delta sigma weight residual 1.335 1.363 -0.029 1.28e-02 6.10e+03 4.96e+00 bond pdb=" CA PRO C 447 " pdb=" C PRO C 447 " ideal model delta sigma weight residual 1.517 1.531 -0.014 6.70e-03 2.23e+04 4.32e+00 bond pdb=" N ASN B 359 " pdb=" CA ASN B 359 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.05e+00 ... (remaining 12172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16073 1.99 - 3.97: 336 3.97 - 5.96: 49 5.96 - 7.94: 17 7.94 - 9.93: 7 Bond angle restraints: 16482 Sorted by residual: angle pdb=" N ASN B 363 " pdb=" CA ASN B 363 " pdb=" C ASN B 363 " ideal model delta sigma weight residual 113.16 103.23 9.93 1.24e+00 6.50e-01 6.41e+01 angle pdb=" N ALA A 163 " pdb=" CA ALA A 163 " pdb=" C ALA A 163 " ideal model delta sigma weight residual 111.36 119.81 -8.45 1.09e+00 8.42e-01 6.01e+01 angle pdb=" N ASN A 363 " pdb=" CA ASN A 363 " pdb=" C ASN A 363 " ideal model delta sigma weight residual 111.71 103.14 8.57 1.34e+00 5.57e-01 4.09e+01 angle pdb=" N SER A 360 " pdb=" CA SER A 360 " pdb=" C SER A 360 " ideal model delta sigma weight residual 111.14 117.40 -6.26 1.08e+00 8.57e-01 3.36e+01 angle pdb=" N ALA B 105 " pdb=" CA ALA B 105 " pdb=" C ALA B 105 " ideal model delta sigma weight residual 111.07 117.09 -6.02 1.07e+00 8.73e-01 3.16e+01 ... (remaining 16477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 6588 18.00 - 36.00: 582 36.00 - 53.99: 89 53.99 - 71.99: 21 71.99 - 89.99: 4 Dihedral angle restraints: 7284 sinusoidal: 2927 harmonic: 4357 Sorted by residual: dihedral pdb=" C ASN B 359 " pdb=" N ASN B 359 " pdb=" CA ASN B 359 " pdb=" CB ASN B 359 " ideal model delta harmonic sigma weight residual -122.60 -131.42 8.82 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" CA ASP C 476 " pdb=" CB ASP C 476 " pdb=" CG ASP C 476 " pdb=" OD1 ASP C 476 " ideal model delta sinusoidal sigma weight residual -30.00 -89.32 59.32 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP B 324 " pdb=" CB ASP B 324 " pdb=" CG ASP B 324 " pdb=" OD1 ASP B 324 " ideal model delta sinusoidal sigma weight residual -30.00 -88.42 58.42 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 7281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1447 0.060 - 0.120: 296 0.120 - 0.180: 57 0.180 - 0.240: 11 0.240 - 0.300: 2 Chirality restraints: 1813 Sorted by residual: chirality pdb=" CA ALA A 163 " pdb=" N ALA A 163 " pdb=" C ALA A 163 " pdb=" CB ALA A 163 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ASN B 359 " pdb=" N ASN B 359 " pdb=" C ASN B 359 " pdb=" CB ASN B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA MET D 396 " pdb=" N MET D 396 " pdb=" C MET D 396 " pdb=" CB MET D 396 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1810 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 155 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO D 156 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 155 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 156 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 155 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO B 156 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.021 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2838 2.79 - 3.32: 10843 3.32 - 3.85: 19360 3.85 - 4.37: 24340 4.37 - 4.90: 41144 Nonbonded interactions: 98525 Sorted by model distance: nonbonded pdb=" NH2 ARG D 106 " pdb=" OE1 GLU D 474 " model vdw 2.266 3.120 nonbonded pdb=" O PHE A 260 " pdb=" OG1 THR A 263 " model vdw 2.283 3.040 nonbonded pdb=" O PHE C 260 " pdb=" OG1 THR C 263 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR A 223 " pdb=" OD2 ASP A 245 " model vdw 2.308 3.040 nonbonded pdb=" O PHE D 260 " pdb=" OG1 THR D 263 " model vdw 2.313 3.040 ... (remaining 98520 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 103 through 357 or resid 362 through 480)) selection = (chain 'B' and (resid 103 through 357 or (resid 362 and (name N or name CA or na \ me C or name O or name CB )) or resid 363 through 480)) selection = (chain 'C' and (resid 103 through 357 or (resid 362 and (name N or name CA or na \ me C or name O or name CB )) or resid 363 through 480)) selection = (chain 'D' and (resid 103 through 357 or (resid 362 and (name N or name CA or na \ me C or name O or name CB )) or resid 363 through 480)) } 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.660 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: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 12177 Z= 0.207 Angle : 0.732 9.930 16482 Z= 0.451 Chirality : 0.054 0.300 1813 Planarity : 0.004 0.039 2090 Dihedral : 13.476 89.992 4506 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 0.31 % Allowed : 1.48 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.22), residues: 1493 helix: 1.73 (0.24), residues: 499 sheet: 0.66 (0.39), residues: 187 loop : -0.01 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 106 TYR 0.015 0.002 TYR B 262 PHE 0.014 0.002 PHE A 357 TRP 0.022 0.002 TRP A 178 HIS 0.003 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00388 (12177) covalent geometry : angle 0.73164 (16482) hydrogen bonds : bond 0.13977 ( 535) hydrogen bonds : angle 5.63849 ( 1491) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.496 Fit side-chains REVERT: C 396 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7588 (mtp) REVERT: C 411 ARG cc_start: 0.7367 (ttt90) cc_final: 0.7026 (ptp-170) outliers start: 4 outliers final: 0 residues processed: 141 average time/residue: 0.1464 time to fit residues: 28.1912 Evaluate side-chains 105 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 HIS C 413 GLN C 419 HIS D 325 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.087637 restraints weight = 17756.972| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.66 r_work: 0.2811 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12177 Z= 0.149 Angle : 0.534 6.449 16482 Z= 0.284 Chirality : 0.044 0.133 1813 Planarity : 0.004 0.041 2090 Dihedral : 4.479 36.650 1654 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.54 % Allowed : 4.81 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.22), residues: 1493 helix: 1.79 (0.23), residues: 504 sheet: 0.73 (0.39), residues: 185 loop : 0.07 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 411 TYR 0.024 0.001 TYR A 201 PHE 0.012 0.001 PHE B 308 TRP 0.013 0.001 TRP A 178 HIS 0.012 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00357 (12177) covalent geometry : angle 0.53372 (16482) hydrogen bonds : bond 0.04621 ( 535) hydrogen bonds : angle 4.84097 ( 1491) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.491 Fit side-chains REVERT: A 211 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8313 (ptp-110) REVERT: C 411 ARG cc_start: 0.7984 (ttt90) cc_final: 0.7009 (ptp-170) REVERT: D 248 PHE cc_start: 0.8206 (t80) cc_final: 0.7767 (t80) outliers start: 7 outliers final: 4 residues processed: 120 average time/residue: 0.1178 time to fit residues: 20.5165 Evaluate side-chains 111 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 296 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 114 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.106842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.084402 restraints weight = 17889.275| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.61 r_work: 0.2758 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 12177 Z= 0.241 Angle : 0.609 7.182 16482 Z= 0.320 Chirality : 0.048 0.172 1813 Planarity : 0.004 0.044 2090 Dihedral : 4.648 20.004 1651 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.09 % Allowed : 6.52 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.21), residues: 1493 helix: 1.46 (0.23), residues: 520 sheet: 0.73 (0.38), residues: 190 loop : -0.12 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 316 TYR 0.016 0.002 TYR A 201 PHE 0.016 0.002 PHE B 308 TRP 0.016 0.002 TRP C 398 HIS 0.013 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00598 (12177) covalent geometry : angle 0.60883 (16482) hydrogen bonds : bond 0.05529 ( 535) hydrogen bonds : angle 4.96041 ( 1491) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.500 Fit side-chains REVERT: C 444 ASN cc_start: 0.7583 (t0) cc_final: 0.7208 (t0) REVERT: D 419 HIS cc_start: 0.9250 (OUTLIER) cc_final: 0.8850 (t70) outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 0.1230 time to fit residues: 22.0025 Evaluate side-chains 115 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 106 optimal weight: 0.0010 chunk 116 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.087040 restraints weight = 17626.179| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.65 r_work: 0.2828 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12177 Z= 0.116 Angle : 0.491 6.055 16482 Z= 0.262 Chirality : 0.042 0.132 1813 Planarity : 0.003 0.044 2090 Dihedral : 4.315 19.780 1651 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.78 % Allowed : 8.39 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.22), residues: 1493 helix: 1.88 (0.24), residues: 508 sheet: 0.92 (0.39), residues: 192 loop : 0.03 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 411 TYR 0.014 0.001 TYR A 201 PHE 0.012 0.001 PHE B 308 TRP 0.013 0.001 TRP A 178 HIS 0.012 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00273 (12177) covalent geometry : angle 0.49090 (16482) hydrogen bonds : bond 0.03940 ( 535) hydrogen bonds : angle 4.63444 ( 1491) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.488 Fit side-chains REVERT: A 211 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8312 (ptp-110) outliers start: 10 outliers final: 5 residues processed: 119 average time/residue: 0.1250 time to fit residues: 21.4741 Evaluate side-chains 110 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 292 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 117 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.082998 restraints weight = 17989.954| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.61 r_work: 0.2733 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 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 : 0.007 0.075 12177 Z= 0.285 Angle : 0.639 8.041 16482 Z= 0.334 Chirality : 0.049 0.193 1813 Planarity : 0.004 0.044 2090 Dihedral : 4.766 20.702 1651 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.40 % Allowed : 9.08 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.21), residues: 1493 helix: 1.39 (0.23), residues: 520 sheet: 0.90 (0.38), residues: 190 loop : -0.28 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 316 TYR 0.018 0.002 TYR B 262 PHE 0.018 0.002 PHE B 308 TRP 0.017 0.002 TRP C 398 HIS 0.010 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00704 (12177) covalent geometry : angle 0.63857 (16482) hydrogen bonds : bond 0.05818 ( 535) hydrogen bonds : angle 4.96182 ( 1491) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.488 Fit side-chains REVERT: B 221 ARG cc_start: 0.8019 (ptt-90) cc_final: 0.7816 (ptt90) REVERT: B 358 LYS cc_start: 0.6485 (mttt) cc_final: 0.6217 (mmtt) REVERT: C 396 MET cc_start: 0.8725 (mtp) cc_final: 0.8523 (mtp) REVERT: D 419 HIS cc_start: 0.9349 (OUTLIER) cc_final: 0.8997 (t70) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 0.1248 time to fit residues: 20.7503 Evaluate side-chains 115 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 79 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS D 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.086827 restraints weight = 17771.682| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.60 r_work: 0.2810 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12177 Z= 0.113 Angle : 0.490 6.346 16482 Z= 0.262 Chirality : 0.042 0.125 1813 Planarity : 0.003 0.045 2090 Dihedral : 4.385 19.672 1651 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.01 % Allowed : 10.09 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.22), residues: 1493 helix: 1.76 (0.24), residues: 520 sheet: 0.98 (0.39), residues: 193 loop : -0.11 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 411 TYR 0.015 0.001 TYR A 201 PHE 0.012 0.001 PHE B 308 TRP 0.011 0.001 TRP A 329 HIS 0.011 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00267 (12177) covalent geometry : angle 0.49032 (16482) hydrogen bonds : bond 0.03938 ( 535) hydrogen bonds : angle 4.61037 ( 1491) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.478 Fit side-chains REVERT: A 211 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8293 (ptp-110) REVERT: C 396 MET cc_start: 0.8715 (mtp) cc_final: 0.8491 (mtp) outliers start: 13 outliers final: 7 residues processed: 117 average time/residue: 0.1216 time to fit residues: 20.4755 Evaluate side-chains 112 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 77 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 130 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087396 restraints weight = 17667.345| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.63 r_work: 0.2856 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12177 Z= 0.101 Angle : 0.472 8.698 16482 Z= 0.251 Chirality : 0.042 0.145 1813 Planarity : 0.003 0.043 2090 Dihedral : 4.150 17.933 1651 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.93 % Allowed : 10.48 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.22), residues: 1493 helix: 2.03 (0.24), residues: 508 sheet: 1.02 (0.40), residues: 193 loop : 0.05 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 411 TYR 0.012 0.001 TYR C 262 PHE 0.011 0.001 PHE B 308 TRP 0.019 0.001 TRP A 178 HIS 0.009 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00236 (12177) covalent geometry : angle 0.47193 (16482) hydrogen bonds : bond 0.03547 ( 535) hydrogen bonds : angle 4.46140 ( 1491) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.515 Fit side-chains REVERT: A 211 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8281 (ptp-110) REVERT: C 396 MET cc_start: 0.8699 (mtp) cc_final: 0.8467 (mtp) REVERT: D 419 HIS cc_start: 0.9069 (OUTLIER) cc_final: 0.8561 (t70) outliers start: 12 outliers final: 6 residues processed: 118 average time/residue: 0.1249 time to fit residues: 21.2275 Evaluate side-chains 112 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 8 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 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 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.088487 restraints weight = 17669.490| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.59 r_work: 0.2860 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12177 Z= 0.102 Angle : 0.470 8.864 16482 Z= 0.249 Chirality : 0.042 0.129 1813 Planarity : 0.003 0.041 2090 Dihedral : 4.074 17.126 1651 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.16 % Allowed : 10.25 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.22), residues: 1493 helix: 2.08 (0.24), residues: 508 sheet: 0.78 (0.38), residues: 213 loop : 0.09 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 411 TYR 0.012 0.001 TYR C 262 PHE 0.013 0.001 PHE B 249 TRP 0.024 0.001 TRP A 178 HIS 0.008 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00240 (12177) covalent geometry : angle 0.47028 (16482) hydrogen bonds : bond 0.03512 ( 535) hydrogen bonds : angle 4.41662 ( 1491) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.496 Fit side-chains REVERT: A 211 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8308 (ptp-110) REVERT: C 249 PHE cc_start: 0.7853 (m-10) cc_final: 0.7652 (m-10) REVERT: C 396 MET cc_start: 0.8675 (mtp) cc_final: 0.8428 (mtp) REVERT: D 419 HIS cc_start: 0.9076 (OUTLIER) cc_final: 0.8587 (t70) outliers start: 15 outliers final: 10 residues processed: 122 average time/residue: 0.1186 time to fit residues: 21.0838 Evaluate side-chains 117 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 88 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.086779 restraints weight = 17491.851| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.60 r_work: 0.2828 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12177 Z= 0.128 Angle : 0.500 9.478 16482 Z= 0.264 Chirality : 0.043 0.146 1813 Planarity : 0.003 0.040 2090 Dihedral : 4.132 17.139 1651 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.01 % Allowed : 10.64 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.22), residues: 1493 helix: 1.93 (0.24), residues: 520 sheet: 0.77 (0.38), residues: 213 loop : 0.02 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 411 TYR 0.014 0.001 TYR C 262 PHE 0.012 0.001 PHE B 308 TRP 0.029 0.001 TRP A 178 HIS 0.008 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00310 (12177) covalent geometry : angle 0.50027 (16482) hydrogen bonds : bond 0.03869 ( 535) hydrogen bonds : angle 4.47163 ( 1491) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.534 Fit side-chains REVERT: C 396 MET cc_start: 0.8709 (mtp) cc_final: 0.8461 (mtp) REVERT: D 282 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7967 (mm-40) REVERT: D 419 HIS cc_start: 0.9136 (OUTLIER) cc_final: 0.8691 (t70) outliers start: 13 outliers final: 9 residues processed: 114 average time/residue: 0.1206 time to fit residues: 19.9934 Evaluate side-chains 110 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 142 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.087655 restraints weight = 17651.060| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.62 r_work: 0.2812 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12177 Z= 0.109 Angle : 0.482 9.897 16482 Z= 0.255 Chirality : 0.042 0.141 1813 Planarity : 0.003 0.041 2090 Dihedral : 4.073 16.808 1651 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.85 % Allowed : 10.95 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.22), residues: 1493 helix: 2.07 (0.24), residues: 508 sheet: 0.83 (0.38), residues: 213 loop : 0.11 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 411 TYR 0.013 0.001 TYR C 277 PHE 0.011 0.001 PHE B 308 TRP 0.036 0.001 TRP A 178 HIS 0.009 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00259 (12177) covalent geometry : angle 0.48208 (16482) hydrogen bonds : bond 0.03575 ( 535) hydrogen bonds : angle 4.41733 ( 1491) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.492 Fit side-chains REVERT: A 474 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7705 (mm-30) REVERT: C 396 MET cc_start: 0.8669 (mtp) cc_final: 0.8415 (mtt) REVERT: D 282 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7937 (mm-40) REVERT: D 419 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8576 (t70) outliers start: 11 outliers final: 9 residues processed: 112 average time/residue: 0.1130 time to fit residues: 18.7915 Evaluate side-chains 111 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN B 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.088847 restraints weight = 17602.631| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.64 r_work: 0.2878 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12177 Z= 0.095 Angle : 0.463 9.672 16482 Z= 0.246 Chirality : 0.042 0.138 1813 Planarity : 0.003 0.041 2090 Dihedral : 3.964 15.887 1651 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.85 % Allowed : 11.02 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.22), residues: 1493 helix: 2.13 (0.24), residues: 509 sheet: 0.88 (0.39), residues: 213 loop : 0.13 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 411 TYR 0.014 0.001 TYR C 277 PHE 0.010 0.001 PHE B 308 TRP 0.032 0.001 TRP A 178 HIS 0.010 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00220 (12177) covalent geometry : angle 0.46286 (16482) hydrogen bonds : bond 0.03292 ( 535) hydrogen bonds : angle 4.31602 ( 1491) =============================================================================== Job complete usr+sys time: 3104.06 seconds wall clock time: 54 minutes 6.98 seconds (3246.98 seconds total)