Starting phenix.real_space_refine on Sun Dec 29 23:33:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v21_31633/12_2024/7v21_31633.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v21_31633/12_2024/7v21_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_31633/12_2024/7v21_31633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v21_31633/12_2024/7v21_31633.map" model { file = "/net/cci-nas-00/data/ceres_data/7v21_31633/12_2024/7v21_31633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v21_31633/12_2024/7v21_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-5532/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: 7.49, 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: 2.64 Conformation dependent library (CDL) restraints added in 1.7 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: 1.64 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: 4.53 Time building geometry restraints manager: 3.12 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: 1.220 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.250 Find NCS groups from input model: 0.590 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.720 ------------------------------------------------------------------------------- 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= 0.247 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 *********************** 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 : 1.427 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: 0.3084 time to fit residues: 59.4814 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 : 1.476 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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= 0.169 Angle : 0.500 6.090 16482 Z= 0.267 Chirality : 0.043 0.131 1813 Planarity : 0.003 0.040 2090 Dihedral : 4.361 38.207 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 *********************** 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 : 1.445 Fit side-chains REVERT: A 211 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8138 (ptp-110) REVERT: C 411 ARG cc_start: 0.7600 (ttt90) cc_final: 0.7009 (ptp-170) REVERT: D 248 PHE cc_start: 0.7881 (t80) cc_final: 0.7492 (t80) outliers start: 6 outliers final: 2 residues processed: 121 average time/residue: 0.2575 time to fit residues: 44.7638 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 : 1.339 ------------------------------------------------------------------------------- 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 74 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 0.0040 chunk 108 optimal weight: 2.9990 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12177 Z= 0.324 Angle : 0.574 6.640 16482 Z= 0.303 Chirality : 0.046 0.155 1813 Planarity : 0.004 0.041 2090 Dihedral : 4.490 19.163 1651 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.70 % Allowed : 6.91 % 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 (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 (0.21), residues: 1493 helix: 1.62 (0.23), residues: 520 sheet: 0.83 (0.39), residues: 187 loop : -0.03 (0.21), residues: 786 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 0.014 0.002 PHE B 308 TYR 0.015 0.002 TYR C 262 ARG 0.004 0.001 ARG B 316 *********************** 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 122 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.441 Fit side-chains REVERT: A 211 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8218 (ptp-110) REVERT: C 444 ASN cc_start: 0.7300 (t0) cc_final: 0.6996 (t0) REVERT: D 419 HIS cc_start: 0.9151 (OUTLIER) cc_final: 0.8704 (t70) outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 0.2816 time to fit residues: 47.9638 Evaluate side-chains 114 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 133 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12177 Z= 0.284 Angle : 0.544 6.478 16482 Z= 0.287 Chirality : 0.045 0.128 1813 Planarity : 0.004 0.043 2090 Dihedral : 4.491 20.313 1651 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.09 % Allowed : 8.23 % 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: 0.94 (0.21), residues: 1493 helix: 1.64 (0.23), residues: 520 sheet: 0.85 (0.38), residues: 189 loop : -0.08 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 178 HIS 0.011 0.001 HIS B 191 PHE 0.014 0.001 PHE B 308 TYR 0.019 0.002 TYR A 201 ARG 0.004 0.000 ARG C 411 *********************** 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 120 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.330 Fit side-chains REVERT: A 211 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8154 (ptp-110) REVERT: C 396 MET cc_start: 0.8415 (mtp) cc_final: 0.8150 (mtp) REVERT: D 419 HIS cc_start: 0.9171 (OUTLIER) cc_final: 0.8777 (t70) outliers start: 14 outliers final: 9 residues processed: 117 average time/residue: 0.2590 time to fit residues: 43.4818 Evaluate side-chains 113 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1492 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= 0.167 Angle : 0.475 5.601 16482 Z= 0.254 Chirality : 0.042 0.126 1813 Planarity : 0.003 0.042 2090 Dihedral : 4.229 18.653 1651 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.78 % Allowed : 8.93 % Favored : 90.30 % 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: 1.24 (0.22), residues: 1493 helix: 1.99 (0.24), residues: 508 sheet: 0.96 (0.40), residues: 192 loop : 0.08 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.009 0.001 HIS B 191 PHE 0.010 0.001 PHE B 308 TYR 0.017 0.001 TYR A 201 ARG 0.005 0.000 ARG C 411 *********************** 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 118 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.453 Fit side-chains REVERT: A 211 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8112 (ptp-110) REVERT: C 396 MET cc_start: 0.8399 (mtp) cc_final: 0.8146 (mtp) outliers start: 10 outliers final: 7 residues processed: 115 average time/residue: 0.2548 time to fit residues: 42.5478 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 : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1539 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= 0.187 Angle : 0.481 5.421 16482 Z= 0.256 Chirality : 0.042 0.126 1813 Planarity : 0.003 0.040 2090 Dihedral : 4.202 18.406 1651 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.32 % Allowed : 9.32 % Favored : 89.36 % 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: 1.25 (0.22), residues: 1493 helix: 2.01 (0.24), residues: 508 sheet: 1.01 (0.40), residues: 192 loop : 0.07 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.007 0.001 HIS B 191 PHE 0.011 0.001 PHE B 308 TYR 0.013 0.001 TYR C 262 ARG 0.005 0.000 ARG C 411 *********************** 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 127 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.450 Fit side-chains REVERT: A 211 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8136 (ptp-110) REVERT: A 270 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: C 396 MET cc_start: 0.8422 (mtp) cc_final: 0.8146 (mtp) REVERT: D 419 HIS cc_start: 0.9088 (OUTLIER) cc_final: 0.8662 (t70) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 0.2656 time to fit residues: 47.0128 Evaluate side-chains 117 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 270 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.0870 chunk 88 optimal weight: 0.7980 overall best weight: 0.5956 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12177 Z= 0.140 Angle : 0.457 8.454 16482 Z= 0.244 Chirality : 0.041 0.146 1813 Planarity : 0.003 0.040 2090 Dihedral : 4.053 17.095 1651 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: 1.37 (0.22), residues: 1493 helix: 2.12 (0.24), residues: 508 sheet: 1.07 (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 0.009 0.001 PHE B 308 TYR 0.012 0.001 TYR C 262 ARG 0.006 0.000 ARG C 411 *********************** 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 125 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.480 Fit side-chains REVERT: A 211 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8116 (ptp-110) REVERT: A 270 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: C 396 MET cc_start: 0.8377 (mtp) cc_final: 0.8121 (mtt) REVERT: D 419 HIS cc_start: 0.8984 (OUTLIER) cc_final: 0.8525 (t70) outliers start: 12 outliers final: 8 residues processed: 122 average time/residue: 0.2753 time to fit residues: 48.4979 Evaluate side-chains 122 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 270 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12177 Z= 0.150 Angle : 0.461 8.410 16482 Z= 0.245 Chirality : 0.042 0.145 1813 Planarity : 0.003 0.039 2090 Dihedral : 4.007 17.030 1651 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.09 % Allowed : 10.17 % Favored : 88.74 % 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: 1.40 (0.22), residues: 1493 helix: 2.14 (0.24), residues: 508 sheet: 1.10 (0.40), residues: 192 loop : 0.15 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 178 HIS 0.006 0.001 HIS B 191 PHE 0.009 0.001 PHE B 308 TYR 0.012 0.001 TYR C 262 ARG 0.006 0.000 ARG C 411 *********************** 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 128 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.562 Fit side-chains REVERT: A 178 TRP cc_start: 0.8587 (t60) cc_final: 0.8382 (t60) REVERT: A 211 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8116 (ptp-110) REVERT: A 270 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: A 446 VAL cc_start: 0.9073 (t) cc_final: 0.8744 (m) REVERT: A 474 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7013 (mm-30) REVERT: C 396 MET cc_start: 0.8354 (mtp) cc_final: 0.8099 (mtt) REVERT: D 419 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8553 (t70) outliers start: 14 outliers final: 7 residues processed: 126 average time/residue: 0.2578 time to fit residues: 47.2254 Evaluate side-chains 116 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 270 GLU 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 136 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1742 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= 0.159 Angle : 0.475 10.443 16482 Z= 0.250 Chirality : 0.042 0.147 1813 Planarity : 0.003 0.039 2090 Dihedral : 3.993 16.891 1651 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.93 % Allowed : 10.25 % 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: 1.42 (0.22), residues: 1493 helix: 2.15 (0.24), residues: 508 sheet: 1.09 (0.40), residues: 193 loop : 0.16 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 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 C 262 ARG 0.006 0.000 ARG C 411 *********************** 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: 12 poor density : 106 time to evaluate : 1.400 Fit side-chains REVERT: A 270 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: A 446 VAL cc_start: 0.9063 (t) cc_final: 0.8746 (m) REVERT: A 474 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6998 (mm-30) REVERT: C 248 PHE cc_start: 0.8229 (t80) cc_final: 0.7916 (t80) REVERT: C 396 MET cc_start: 0.8355 (mtp) cc_final: 0.8116 (mtt) REVERT: D 282 GLN cc_start: 0.7739 (tp-100) cc_final: 0.7494 (mm-40) REVERT: D 419 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8540 (t70) outliers start: 12 outliers final: 8 residues processed: 115 average time/residue: 0.2680 time to fit residues: 45.2319 Evaluate side-chains 116 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 270 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 85 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12177 Z= 0.151 Angle : 0.469 10.055 16482 Z= 0.247 Chirality : 0.042 0.151 1813 Planarity : 0.003 0.039 2090 Dihedral : 3.946 16.909 1651 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.93 % Allowed : 10.33 % Favored : 88.74 % 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: 1.44 (0.22), residues: 1493 helix: 2.16 (0.24), residues: 508 sheet: 1.11 (0.40), residues: 193 loop : 0.18 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 178 HIS 0.007 0.001 HIS B 191 PHE 0.009 0.001 PHE B 308 TYR 0.013 0.001 TYR C 277 ARG 0.007 0.000 ARG C 411 ********************** 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 119 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.306 Fit side-chains REVERT: A 270 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: A 446 VAL cc_start: 0.9028 (t) cc_final: 0.8701 (m) REVERT: A 474 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6928 (mm-30) REVERT: C 248 PHE cc_start: 0.8217 (t80) cc_final: 0.7914 (t80) REVERT: C 396 MET cc_start: 0.8360 (mtp) cc_final: 0.8125 (mtt) REVERT: D 282 GLN cc_start: 0.7732 (tp-100) cc_final: 0.7473 (mm-40) REVERT: D 419 HIS cc_start: 0.8938 (OUTLIER) cc_final: 0.8436 (t70) outliers start: 12 outliers final: 8 residues processed: 117 average time/residue: 0.2544 time to fit residues: 43.7787 Evaluate side-chains 115 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 270 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 35 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.111065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.088481 restraints weight = 17535.138| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.62 r_work: 0.2871 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1787 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= 0.164 Angle : 0.475 9.904 16482 Z= 0.251 Chirality : 0.042 0.138 1813 Planarity : 0.003 0.038 2090 Dihedral : 3.958 16.861 1651 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.93 % Allowed : 10.40 % Favored : 88.66 % 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: 1.44 (0.22), residues: 1493 helix: 2.15 (0.24), residues: 508 sheet: 1.12 (0.40), residues: 193 loop : 0.18 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 178 HIS 0.007 0.001 HIS B 191 PHE 0.011 0.001 PHE B 249 TYR 0.014 0.001 TYR C 277 ARG 0.007 0.000 ARG C 411 =============================================================================== Job complete usr+sys time: 2396.73 seconds wall clock time: 45 minutes 34.66 seconds (2734.66 seconds total)