Starting phenix.real_space_refine on Tue Jun 10 12:26:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v21_31633/06_2025/7v21_31633.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v21_31633/06_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_31633/06_2025/7v21_31633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v21_31633/06_2025/7v21_31633.map" model { file = "/net/cci-nas-00/data/ceres_data/7v21_31633/06_2025/7v21_31633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v21_31633/06_2025/7v21_31633.cif" } resolution = 3.08 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 ------------------------------------------------------------------------------- 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.46, per 1000 atoms: 0.63 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: 2.57 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.45 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: 3.94 Time building geometry restraints manager: 3.10 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: 0.880 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 28.740 Find NCS groups from input model: 0.600 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.022 0.002 TRP A 178 HIS 0.003 0.001 HIS D 419 PHE 0.014 0.002 PHE A 357 TYR 0.015 0.002 TYR B 262 ARG 0.003 0.000 ARG C 106 Details of bonding type rmsd hydrogen bonds : bond 0.13977 ( 535) hydrogen bonds : angle 5.63849 ( 1491) covalent geometry : bond 0.00388 (12177) covalent geometry : angle 0.73164 (16482) *********************** 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 : 1.419 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: 0.3031 time to fit residues: 58.5073 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 : 1.365 ------------------------------------------------------------------------------- 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 124 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.110073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.086864 restraints weight = 17732.716| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.70 r_work: 0.2872 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0974 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= 0.115 Angle : 0.500 6.090 16482 Z= 0.267 Chirality : 0.043 0.131 1813 Planarity : 0.003 0.040 2090 Dihedral : 4.361 38.204 1654 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.47 % Allowed : 3.96 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.16 (0.22), residues: 1493 helix: 1.90 (0.23), residues: 504 sheet: 0.75 (0.39), residues: 186 loop : 0.11 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.012 0.001 HIS B 191 PHE 0.010 0.001 PHE B 308 TYR 0.025 0.001 TYR A 201 ARG 0.002 0.000 ARG C 106 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 535) hydrogen bonds : angle 4.76507 ( 1491) covalent geometry : bond 0.00265 (12177) covalent geometry : angle 0.50003 (16482) *********************** 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 124 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 1.228 Fit side-chains REVERT: A 211 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8283 (ptp-110) REVERT: C 411 ARG cc_start: 0.7956 (ttt90) cc_final: 0.6953 (ptp-170) REVERT: D 248 PHE cc_start: 0.8106 (t80) cc_final: 0.7685 (t80) outliers start: 6 outliers final: 2 residues processed: 121 average time/residue: 0.2447 time to fit residues: 42.2251 Evaluate side-chains 113 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 105 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.107393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.084004 restraints weight = 17903.075| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.70 r_work: 0.2774 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 12177 Z= 0.228 Angle : 0.589 6.755 16482 Z= 0.310 Chirality : 0.047 0.160 1813 Planarity : 0.004 0.042 2090 Dihedral : 4.533 19.611 1651 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.70 % Allowed : 6.52 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.89 (0.21), residues: 1493 helix: 1.56 (0.23), residues: 520 sheet: 0.82 (0.38), residues: 185 loop : -0.07 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 398 HIS 0.012 0.001 HIS B 191 PHE 0.015 0.002 PHE B 308 TYR 0.015 0.002 TYR C 262 ARG 0.005 0.001 ARG B 316 Details of bonding type rmsd hydrogen bonds : bond 0.05325 ( 535) hydrogen bonds : angle 4.91107 ( 1491) covalent geometry : bond 0.00564 (12177) covalent geometry : angle 0.58936 (16482) *********************** 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 121 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.291 Fit side-chains REVERT: A 211 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8340 (ptp-110) REVERT: D 419 HIS cc_start: 0.9232 (OUTLIER) cc_final: 0.8763 (t70) outliers start: 9 outliers final: 6 residues processed: 119 average time/residue: 0.2607 time to fit residues: 44.0898 Evaluate side-chains 113 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 376 MET Chi-restraints excluded: chain C residue 292 THR 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 125 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 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 B 419 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.086634 restraints weight = 17635.637| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.64 r_work: 0.2816 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12177 Z= 0.128 Angle : 0.500 5.824 16482 Z= 0.266 Chirality : 0.043 0.126 1813 Planarity : 0.003 0.042 2090 Dihedral : 4.352 19.756 1651 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.78 % Allowed : 8.23 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.13 (0.22), residues: 1493 helix: 1.87 (0.24), residues: 508 sheet: 0.84 (0.39), residues: 192 loop : 0.05 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.011 0.001 HIS B 191 PHE 0.012 0.001 PHE B 308 TYR 0.020 0.001 TYR A 201 ARG 0.005 0.000 ARG C 411 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 535) hydrogen bonds : angle 4.68489 ( 1491) covalent geometry : bond 0.00306 (12177) covalent geometry : angle 0.49960 (16482) *********************** 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 118 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.239 Fit side-chains REVERT: A 211 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8304 (ptp-110) outliers start: 10 outliers final: 7 residues processed: 115 average time/residue: 0.2610 time to fit residues: 42.6653 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 : 1.419 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 122 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.109593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.086876 restraints weight = 17705.982| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.65 r_work: 0.2827 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1455 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= 0.123 Angle : 0.486 5.530 16482 Z= 0.259 Chirality : 0.043 0.126 1813 Planarity : 0.003 0.041 2090 Dihedral : 4.230 18.580 1651 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.24 % Allowed : 8.07 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.22 (0.22), residues: 1493 helix: 1.98 (0.24), residues: 508 sheet: 0.93 (0.39), residues: 192 loop : 0.07 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.008 0.001 HIS B 191 PHE 0.011 0.001 PHE B 308 TYR 0.017 0.001 TYR A 201 ARG 0.006 0.000 ARG C 411 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 535) hydrogen bonds : angle 4.56183 ( 1491) covalent geometry : bond 0.00295 (12177) covalent geometry : angle 0.48579 (16482) *********************** 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 126 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.323 Fit side-chains REVERT: A 211 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8298 (ptp-110) REVERT: D 419 HIS cc_start: 0.9152 (OUTLIER) cc_final: 0.8709 (t70) outliers start: 16 outliers final: 11 residues processed: 122 average time/residue: 0.2430 time to fit residues: 43.1786 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 : 1.302 ------------------------------------------------------------------------------- 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 377 MET 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 9 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.110982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.088980 restraints weight = 17775.858| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.61 r_work: 0.2851 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12177 Z= 0.102 Angle : 0.459 5.206 16482 Z= 0.245 Chirality : 0.042 0.126 1813 Planarity : 0.003 0.040 2090 Dihedral : 4.094 18.251 1651 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.16 % Allowed : 8.85 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.34 (0.22), residues: 1493 helix: 2.09 (0.24), residues: 508 sheet: 1.01 (0.40), residues: 192 loop : 0.13 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 178 HIS 0.006 0.001 HIS B 191 PHE 0.010 0.001 PHE B 308 TYR 0.012 0.001 TYR C 262 ARG 0.006 0.000 ARG C 411 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 535) hydrogen bonds : angle 4.43956 ( 1491) covalent geometry : bond 0.00239 (12177) covalent geometry : angle 0.45891 (16482) *********************** 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 130 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 2.214 Fit side-chains REVERT: A 211 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8300 (ptp-110) REVERT: D 419 HIS cc_start: 0.9076 (OUTLIER) cc_final: 0.8580 (t70) outliers start: 15 outliers final: 9 residues processed: 127 average time/residue: 0.2911 time to fit residues: 54.7139 Evaluate side-chains 121 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.0070 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.9604 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.110204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087452 restraints weight = 17832.929| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.65 r_work: 0.2824 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12177 Z= 0.116 Angle : 0.478 8.361 16482 Z= 0.253 Chirality : 0.042 0.155 1813 Planarity : 0.003 0.040 2090 Dihedral : 4.101 17.175 1651 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.93 % Allowed : 9.78 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.33 (0.22), residues: 1493 helix: 2.08 (0.24), residues: 508 sheet: 1.10 (0.40), residues: 189 loop : 0.10 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 178 HIS 0.006 0.001 HIS B 191 PHE 0.010 0.001 PHE B 308 TYR 0.013 0.001 TYR C 262 ARG 0.006 0.000 ARG C 411 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 535) hydrogen bonds : angle 4.45300 ( 1491) covalent geometry : bond 0.00279 (12177) covalent geometry : angle 0.47758 (16482) *********************** 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 122 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.204 Fit side-chains REVERT: D 419 HIS cc_start: 0.9119 (OUTLIER) cc_final: 0.8610 (t70) outliers start: 12 outliers final: 8 residues processed: 120 average time/residue: 0.2784 time to fit residues: 48.5737 Evaluate side-chains 115 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.107153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.084301 restraints weight = 17918.779| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.63 r_work: 0.2766 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12177 Z= 0.200 Angle : 0.558 6.144 16482 Z= 0.294 Chirality : 0.045 0.147 1813 Planarity : 0.004 0.039 2090 Dihedral : 4.440 18.787 1651 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.93 % Allowed : 9.86 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.22), residues: 1493 helix: 1.74 (0.23), residues: 520 sheet: 0.97 (0.39), residues: 191 loop : -0.09 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 178 HIS 0.006 0.001 HIS B 191 PHE 0.014 0.002 PHE B 308 TYR 0.016 0.002 TYR C 262 ARG 0.006 0.001 ARG B 316 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 535) hydrogen bonds : angle 4.72997 ( 1491) covalent geometry : bond 0.00494 (12177) covalent geometry : angle 0.55754 (16482) *********************** 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 117 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.249 Fit side-chains REVERT: C 396 MET cc_start: 0.8727 (mtp) cc_final: 0.8508 (mtp) REVERT: D 419 HIS cc_start: 0.9268 (OUTLIER) cc_final: 0.8921 (t70) outliers start: 12 outliers final: 8 residues processed: 116 average time/residue: 0.2441 time to fit residues: 41.4512 Evaluate side-chains 112 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 71 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 113 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.0670 chunk 123 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.110819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.088189 restraints weight = 17757.426| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.64 r_work: 0.2865 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12177 Z= 0.097 Angle : 0.470 10.605 16482 Z= 0.249 Chirality : 0.042 0.169 1813 Planarity : 0.003 0.041 2090 Dihedral : 4.095 15.673 1651 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.78 % Allowed : 9.70 % 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 (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: 1.31 (0.22), residues: 1493 helix: 2.07 (0.24), residues: 508 sheet: 1.11 (0.40), residues: 195 loop : 0.07 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 178 HIS 0.007 0.001 HIS B 191 PHE 0.009 0.001 PHE B 308 TYR 0.012 0.001 TYR D 262 ARG 0.005 0.000 ARG C 411 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 535) hydrogen bonds : angle 4.44647 ( 1491) covalent geometry : bond 0.00222 (12177) covalent geometry : angle 0.46956 (16482) *********************** 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 117 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.439 Fit side-chains REVERT: A 413 GLN cc_start: 0.8756 (mt0) cc_final: 0.8554 (mt0) REVERT: B 358 LYS cc_start: 0.6635 (mmmt) cc_final: 0.6280 (mmtt) REVERT: C 396 MET cc_start: 0.8701 (mtp) cc_final: 0.8480 (mtp) REVERT: D 282 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7953 (mm-40) outliers start: 10 outliers final: 8 residues processed: 115 average time/residue: 0.2415 time to fit residues: 41.6089 Evaluate side-chains 111 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 12 optimal weight: 0.0060 chunk 10 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.110657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.088138 restraints weight = 17532.021| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.62 r_work: 0.2866 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12177 Z= 0.103 Angle : 0.471 10.163 16482 Z= 0.250 Chirality : 0.042 0.166 1813 Planarity : 0.003 0.039 2090 Dihedral : 4.020 15.263 1651 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.70 % Allowed : 10.33 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.37 (0.22), residues: 1493 helix: 2.10 (0.24), residues: 508 sheet: 1.13 (0.40), residues: 195 loop : 0.11 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 178 HIS 0.008 0.001 HIS B 191 PHE 0.010 0.001 PHE C 248 TYR 0.013 0.001 TYR C 262 ARG 0.007 0.000 ARG C 411 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 535) hydrogen bonds : angle 4.39071 ( 1491) covalent geometry : bond 0.00243 (12177) covalent geometry : angle 0.47083 (16482) ********************** 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: 9 poor density : 105 time to evaluate : 1.412 Fit side-chains REVERT: A 413 GLN cc_start: 0.8757 (mt0) cc_final: 0.8549 (mt0) REVERT: A 474 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7732 (mm-30) REVERT: C 396 MET cc_start: 0.8690 (mtp) cc_final: 0.8456 (mtp) REVERT: D 282 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7937 (mm-40) outliers start: 9 outliers final: 8 residues processed: 112 average time/residue: 0.2267 time to fit residues: 38.0633 Evaluate side-chains 111 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 107 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.109058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.086475 restraints weight = 17627.989| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.60 r_work: 0.2819 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12177 Z= 0.141 Angle : 0.507 9.867 16482 Z= 0.269 Chirality : 0.043 0.166 1813 Planarity : 0.003 0.039 2090 Dihedral : 4.157 15.605 1651 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.78 % Allowed : 10.40 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.18 (0.22), residues: 1493 helix: 1.92 (0.24), residues: 520 sheet: 0.87 (0.38), residues: 209 loop : 0.02 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.008 0.001 HIS B 191 PHE 0.017 0.001 PHE C 248 TYR 0.014 0.001 TYR C 262 ARG 0.007 0.000 ARG C 411 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 535) hydrogen bonds : angle 4.51367 ( 1491) covalent geometry : bond 0.00346 (12177) covalent geometry : angle 0.50737 (16482) =============================================================================== Job complete usr+sys time: 6338.09 seconds wall clock time: 110 minutes 56.04 seconds (6656.04 seconds total)