Starting phenix.real_space_refine on Thu Jun 19 12:43:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fnq_50602/06_2025/9fnq_50602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fnq_50602/06_2025/9fnq_50602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fnq_50602/06_2025/9fnq_50602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fnq_50602/06_2025/9fnq_50602.map" model { file = "/net/cci-nas-00/data/ceres_data/9fnq_50602/06_2025/9fnq_50602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fnq_50602/06_2025/9fnq_50602.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 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 56 5.16 5 C 14294 2.51 5 N 3871 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22589 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3227 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 24, 'TRANS': 385} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 9.02, per 1000 atoms: 0.40 Number of scatterers: 22589 At special positions: 0 Unit cell: (175.13, 172.64, 116.2, 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 56 16.00 O 4368 8.00 N 3871 7.00 C 14294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 159 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 164 " distance=2.03 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: 4.99 Conformation dependent library (CDL) restraints added in 3.0 seconds 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 16 sheets defined 19.3% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 372 through 381 removed outlier: 3.635A pdb=" N THR A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 112 through 123 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.635A pdb=" N THR B 376 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 112 through 123 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.635A pdb=" N THR C 376 " --> pdb=" O ASP C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 393 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 35 through 41 Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 112 through 123 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 372 through 381 removed outlier: 3.635A pdb=" N THR D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 393 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 97 through 107 Processing helix chain 'E' and resid 112 through 123 Processing helix chain 'E' and resid 354 through 361 Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 372 through 381 removed outlier: 3.634A pdb=" N THR E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 393 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 27 through 34 Processing helix chain 'F' and resid 35 through 41 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 372 through 381 removed outlier: 3.636A pdb=" N THR F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 393 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 27 through 34 Processing helix chain 'G' and resid 35 through 41 Processing helix chain 'G' and resid 97 through 107 Processing helix chain 'G' and resid 112 through 123 Processing helix chain 'G' and resid 354 through 361 Processing helix chain 'G' and resid 364 through 368 Processing helix chain 'G' and resid 372 through 381 removed outlier: 3.635A pdb=" N THR G 376 " --> pdb=" O ASP G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 393 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.761A pdb=" N THR A 73 " --> pdb=" O PHE A 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 96 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 91 through 96 current: chain 'A' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 169 through 179 current: chain 'A' and resid 289 through 321 removed outlier: 3.506A pdb=" N TYR A 314 " --> pdb=" O ILE A 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 338 through 345 current: chain 'B' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 169 through 179 current: chain 'B' and resid 289 through 321 removed outlier: 3.506A pdb=" N TYR B 314 " --> pdb=" O ILE B 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 338 through 345 current: chain 'C' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 169 through 179 current: chain 'C' and resid 289 through 321 removed outlier: 3.507A pdb=" N TYR C 314 " --> pdb=" O ILE C 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 338 through 345 current: chain 'D' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 179 current: chain 'D' and resid 289 through 321 removed outlier: 3.506A pdb=" N TYR D 314 " --> pdb=" O ILE D 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 338 through 345 current: chain 'E' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 179 current: chain 'E' and resid 289 through 321 removed outlier: 3.506A pdb=" N TYR E 314 " --> pdb=" O ILE E 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 338 through 345 current: chain 'F' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 179 current: chain 'F' and resid 289 through 321 removed outlier: 3.506A pdb=" N TYR F 314 " --> pdb=" O ILE F 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 338 through 345 current: chain 'G' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 169 through 179 current: chain 'G' and resid 289 through 321 removed outlier: 3.506A pdb=" N TYR G 314 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 215 through 247 removed outlier: 7.283A pdb=" N GLU A 252 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA B 244 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 220 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLU B 252 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA C 244 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 220 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU C 252 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA D 244 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 220 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU D 252 " --> pdb=" O ALA E 244 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA E 244 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 220 " --> pdb=" O SER D 276 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU E 252 " --> pdb=" O ALA F 244 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA F 244 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG F 220 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU F 252 " --> pdb=" O ALA G 244 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA G 244 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG G 220 " --> pdb=" O SER F 276 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU G 252 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA A 244 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 220 " --> pdb=" O SER G 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.761A pdb=" N THR B 73 " --> pdb=" O PHE B 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.762A pdb=" N THR C 73 " --> pdb=" O PHE C 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.762A pdb=" N THR D 73 " --> pdb=" O PHE D 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 47 through 49 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.761A pdb=" N THR E 73 " --> pdb=" O PHE E 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AB4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.762A pdb=" N THR F 73 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AB6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.762A pdb=" N THR G 73 " --> pdb=" O PHE G 12 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 47 through 49 833 hydrogen bonds defined for protein. 2394 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: 7.19 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7131 1.34 - 1.46: 5653 1.46 - 1.58: 10372 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 23247 Sorted by residual: bond pdb=" N TYR D 304 " pdb=" CA TYR D 304 " ideal model delta sigma weight residual 1.456 1.474 -0.018 1.04e-02 9.25e+03 2.94e+00 bond pdb=" C ILE B 93 " pdb=" N PRO B 94 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.34e-02 5.57e+03 2.94e+00 bond pdb=" N TYR G 304 " pdb=" CA TYR G 304 " ideal model delta sigma weight residual 1.456 1.474 -0.018 1.04e-02 9.25e+03 2.92e+00 bond pdb=" N TYR F 304 " pdb=" CA TYR F 304 " ideal model delta sigma weight residual 1.456 1.474 -0.018 1.04e-02 9.25e+03 2.92e+00 bond pdb=" C ILE G 93 " pdb=" N PRO G 94 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.34e-02 5.57e+03 2.92e+00 ... (remaining 23242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 29060 0.94 - 1.87: 2188 1.87 - 2.81: 424 2.81 - 3.75: 80 3.75 - 4.68: 14 Bond angle restraints: 31766 Sorted by residual: angle pdb=" CA ASP B 301 " pdb=" C ASP B 301 " pdb=" N ILE B 302 " ideal model delta sigma weight residual 115.86 118.68 -2.82 1.24e+00 6.50e-01 5.18e+00 angle pdb=" CA ASP F 301 " pdb=" C ASP F 301 " pdb=" N ILE F 302 " ideal model delta sigma weight residual 115.86 118.68 -2.82 1.24e+00 6.50e-01 5.17e+00 angle pdb=" CA ASP D 301 " pdb=" C ASP D 301 " pdb=" N ILE D 302 " ideal model delta sigma weight residual 115.86 118.65 -2.79 1.24e+00 6.50e-01 5.06e+00 angle pdb=" CA ASP A 301 " pdb=" C ASP A 301 " pdb=" N ILE A 302 " ideal model delta sigma weight residual 115.86 118.65 -2.79 1.24e+00 6.50e-01 5.05e+00 angle pdb=" CA ASP G 301 " pdb=" C ASP G 301 " pdb=" N ILE G 302 " ideal model delta sigma weight residual 115.86 118.63 -2.77 1.24e+00 6.50e-01 5.00e+00 ... (remaining 31761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 12858 17.10 - 34.20: 484 34.20 - 51.30: 56 51.30 - 68.41: 28 68.41 - 85.51: 14 Dihedral angle restraints: 13440 sinusoidal: 5236 harmonic: 8204 Sorted by residual: dihedral pdb=" CA LEU F 179 " pdb=" C LEU F 179 " pdb=" N ASP F 180 " pdb=" CA ASP F 180 " ideal model delta harmonic sigma weight residual 180.00 164.28 15.72 0 5.00e+00 4.00e-02 9.88e+00 dihedral pdb=" CA LEU E 179 " pdb=" C LEU E 179 " pdb=" N ASP E 180 " pdb=" CA ASP E 180 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 dihedral pdb=" CA LEU A 179 " pdb=" C LEU A 179 " pdb=" N ASP A 180 " pdb=" CA ASP A 180 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.84e+00 ... (remaining 13437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2213 0.037 - 0.074: 728 0.074 - 0.111: 287 0.111 - 0.148: 78 0.148 - 0.185: 26 Chirality restraints: 3332 Sorted by residual: chirality pdb=" CA VAL D 172 " pdb=" N VAL D 172 " pdb=" C VAL D 172 " pdb=" CB VAL D 172 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA VAL C 172 " pdb=" N VAL C 172 " pdb=" C VAL C 172 " pdb=" CB VAL C 172 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CA VAL F 172 " pdb=" N VAL F 172 " pdb=" C VAL F 172 " pdb=" CB VAL F 172 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.32e-01 ... (remaining 3329 not shown) Planarity restraints: 4137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 249 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LEU B 249 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU B 249 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL B 250 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 249 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU G 249 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU G 249 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL G 250 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 249 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU F 249 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU F 249 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL F 250 " 0.019 2.00e-02 2.50e+03 ... (remaining 4134 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5236 2.80 - 3.32: 18805 3.32 - 3.85: 36399 3.85 - 4.37: 41258 4.37 - 4.90: 75223 Nonbonded interactions: 176921 Sorted by model distance: nonbonded pdb=" NH2 ARG A 28 " pdb=" OD1 ASP B 139 " model vdw 2.273 3.120 nonbonded pdb=" NH2 ARG D 28 " pdb=" OD1 ASP E 139 " model vdw 2.273 3.120 nonbonded pdb=" NH2 ARG E 28 " pdb=" OD1 ASP F 139 " model vdw 2.273 3.120 nonbonded pdb=" NH2 ARG C 28 " pdb=" OD1 ASP D 139 " model vdw 2.273 3.120 nonbonded pdb=" NH2 ARG B 28 " pdb=" OD1 ASP C 139 " model vdw 2.273 3.120 ... (remaining 176916 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.900 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 45.110 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 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:15.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.003 0.024 23254 Z= 0.230 Angle : 0.559 4.682 31780 Z= 0.342 Chirality : 0.047 0.185 3332 Planarity : 0.004 0.032 4137 Dihedral : 10.077 85.507 8211 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.16 % Allowed : 2.61 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 2842 helix: 0.42 (0.23), residues: 490 sheet: 1.62 (0.15), residues: 1064 loop : -0.13 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 329 HIS 0.003 0.001 HIS F 186 PHE 0.009 0.001 PHE G 321 TYR 0.014 0.001 TYR E 76 ARG 0.002 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.22699 ( 833) hydrogen bonds : angle 7.26466 ( 2394) SS BOND : bond 0.00133 ( 7) SS BOND : angle 0.62896 ( 14) covalent geometry : bond 0.00334 (23247) covalent geometry : angle 0.55926 (31766) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 439 time to evaluate : 2.244 Fit side-chains REVERT: A 29 GLU cc_start: 0.5028 (mp0) cc_final: 0.4806 (mp0) REVERT: A 66 LYS cc_start: 0.5869 (pttt) cc_final: 0.5542 (pttp) REVERT: A 152 ARG cc_start: 0.7439 (ttm170) cc_final: 0.7184 (ttp-170) REVERT: A 171 LYS cc_start: 0.7977 (mttt) cc_final: 0.7496 (mttp) REVERT: A 185 LYS cc_start: 0.7722 (mttt) cc_final: 0.7217 (mtpp) REVERT: A 236 SER cc_start: 0.7338 (t) cc_final: 0.6922 (p) REVERT: A 255 LEU cc_start: 0.5930 (tp) cc_final: 0.5423 (tm) REVERT: A 258 GLU cc_start: 0.7074 (tt0) cc_final: 0.5924 (tp30) REVERT: A 259 ILE cc_start: 0.7521 (mt) cc_final: 0.7153 (mt) REVERT: A 309 LYS cc_start: 0.6985 (mtpp) cc_final: 0.6668 (ttmt) REVERT: A 378 GLN cc_start: 0.7012 (mt0) cc_final: 0.6295 (pt0) REVERT: A 394 ARG cc_start: 0.7484 (ttt180) cc_final: 0.7253 (ttt180) REVERT: A 415 GLU cc_start: 0.8216 (tt0) cc_final: 0.8012 (tt0) REVERT: B 64 GLU cc_start: 0.6356 (tt0) cc_final: 0.5780 (tt0) REVERT: B 171 LYS cc_start: 0.8038 (mttt) cc_final: 0.7488 (mtmt) REVERT: B 185 LYS cc_start: 0.7868 (mttt) cc_final: 0.7474 (mtpp) REVERT: B 188 ASP cc_start: 0.7096 (m-30) cc_final: 0.6891 (m-30) REVERT: B 236 SER cc_start: 0.7349 (t) cc_final: 0.6794 (m) REVERT: B 258 GLU cc_start: 0.7128 (tt0) cc_final: 0.5956 (tp30) REVERT: B 259 ILE cc_start: 0.7629 (mt) cc_final: 0.6881 (mm) REVERT: B 299 LYS cc_start: 0.8002 (mttt) cc_final: 0.7000 (mtpt) REVERT: B 309 LYS cc_start: 0.6971 (mtpp) cc_final: 0.6692 (tttt) REVERT: B 378 GLN cc_start: 0.7055 (mt0) cc_final: 0.6228 (mm-40) REVERT: B 415 GLU cc_start: 0.8263 (tt0) cc_final: 0.8047 (tt0) REVERT: C 57 MET cc_start: 0.5576 (mtp) cc_final: 0.5167 (mtm) REVERT: C 64 GLU cc_start: 0.6314 (tt0) cc_final: 0.5812 (tt0) REVERT: C 171 LYS cc_start: 0.8087 (mttt) cc_final: 0.7600 (mtmt) REVERT: C 185 LYS cc_start: 0.7911 (mttt) cc_final: 0.7565 (mtpp) REVERT: C 236 SER cc_start: 0.7389 (t) cc_final: 0.6890 (m) REVERT: C 258 GLU cc_start: 0.7311 (tt0) cc_final: 0.6152 (tp30) REVERT: C 259 ILE cc_start: 0.7663 (mt) cc_final: 0.7229 (mt) REVERT: C 309 LYS cc_start: 0.7087 (mtpp) cc_final: 0.6878 (ttmm) REVERT: C 378 GLN cc_start: 0.7060 (mt0) cc_final: 0.6435 (mm110) REVERT: C 394 ARG cc_start: 0.7671 (ttt180) cc_final: 0.7299 (ttt180) REVERT: C 415 GLU cc_start: 0.8199 (tt0) cc_final: 0.7944 (tt0) REVERT: D 41 MET cc_start: 0.6748 (mtm) cc_final: 0.6486 (mtp) REVERT: D 66 LYS cc_start: 0.5824 (pttt) cc_final: 0.5449 (pttp) REVERT: D 185 LYS cc_start: 0.7627 (mttt) cc_final: 0.7289 (mtpp) REVERT: D 236 SER cc_start: 0.7245 (t) cc_final: 0.6927 (p) REVERT: D 258 GLU cc_start: 0.7141 (tt0) cc_final: 0.5946 (tp30) REVERT: D 259 ILE cc_start: 0.7528 (mt) cc_final: 0.7095 (mt) REVERT: D 309 LYS cc_start: 0.6807 (mtpp) cc_final: 0.6546 (tptt) REVERT: D 311 ASP cc_start: 0.7515 (m-30) cc_final: 0.7134 (m-30) REVERT: D 378 GLN cc_start: 0.6947 (mt0) cc_final: 0.6159 (pt0) REVERT: D 394 ARG cc_start: 0.7352 (ttt180) cc_final: 0.7099 (ttt180) REVERT: E 29 GLU cc_start: 0.5020 (mp0) cc_final: 0.4763 (mp0) REVERT: E 64 GLU cc_start: 0.6201 (tt0) cc_final: 0.5905 (tt0) REVERT: E 185 LYS cc_start: 0.7915 (mttt) cc_final: 0.7455 (mtpp) REVERT: E 229 LYS cc_start: 0.7819 (mttt) cc_final: 0.7609 (mttp) REVERT: E 236 SER cc_start: 0.7357 (t) cc_final: 0.6953 (p) REVERT: E 258 GLU cc_start: 0.7216 (tt0) cc_final: 0.6100 (tp30) REVERT: E 259 ILE cc_start: 0.7539 (mt) cc_final: 0.7145 (mt) REVERT: E 309 LYS cc_start: 0.6939 (mtpp) cc_final: 0.6536 (tptt) REVERT: E 378 GLN cc_start: 0.7023 (mt0) cc_final: 0.6194 (mm-40) REVERT: E 385 MET cc_start: 0.7794 (mmm) cc_final: 0.7582 (mmm) REVERT: E 394 ARG cc_start: 0.7519 (ttt180) cc_final: 0.7297 (ttt180) REVERT: F 64 GLU cc_start: 0.6282 (tt0) cc_final: 0.5714 (tt0) REVERT: F 185 LYS cc_start: 0.7832 (mttt) cc_final: 0.7397 (mtpp) REVERT: F 236 SER cc_start: 0.7237 (t) cc_final: 0.6715 (m) REVERT: F 243 ASN cc_start: 0.6236 (m-40) cc_final: 0.6027 (m110) REVERT: F 257 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6397 (mp) REVERT: F 258 GLU cc_start: 0.7106 (tt0) cc_final: 0.5913 (tp30) REVERT: F 259 ILE cc_start: 0.7627 (mt) cc_final: 0.7075 (mm) REVERT: F 309 LYS cc_start: 0.6934 (mtpp) cc_final: 0.6502 (tptt) REVERT: F 378 GLN cc_start: 0.6822 (mt0) cc_final: 0.5939 (mm-40) REVERT: F 394 ARG cc_start: 0.7553 (ttt180) cc_final: 0.7332 (ttt180) REVERT: G 152 ARG cc_start: 0.7530 (ttm170) cc_final: 0.7301 (ttp-170) REVERT: G 178 ASN cc_start: 0.7102 (t0) cc_final: 0.6789 (t0) REVERT: G 185 LYS cc_start: 0.7784 (mttt) cc_final: 0.7423 (mtpp) REVERT: G 236 SER cc_start: 0.7282 (t) cc_final: 0.6810 (p) REVERT: G 255 LEU cc_start: 0.5764 (tp) cc_final: 0.5200 (tm) REVERT: G 258 GLU cc_start: 0.7178 (tt0) cc_final: 0.6013 (tp30) REVERT: G 259 ILE cc_start: 0.7516 (mt) cc_final: 0.7050 (mt) REVERT: G 309 LYS cc_start: 0.6925 (mtpp) cc_final: 0.6603 (tttt) REVERT: G 378 GLN cc_start: 0.6829 (mt0) cc_final: 0.6060 (mm-40) REVERT: G 415 GLU cc_start: 0.8097 (tt0) cc_final: 0.7890 (tt0) outliers start: 28 outliers final: 7 residues processed: 453 average time/residue: 1.3778 time to fit residues: 706.6777 Evaluate side-chains 278 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 270 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain G residue 250 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 74 optimal weight: 0.0970 chunk 146 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 224 optimal weight: 0.0020 chunk 87 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN B 174 ASN C 174 ASN D 174 ASN E 174 ASN F 174 ASN G 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.164495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130638 restraints weight = 19280.602| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.53 r_work: 0.3363 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 23254 Z= 0.145 Angle : 0.529 4.593 31780 Z= 0.297 Chirality : 0.046 0.144 3332 Planarity : 0.004 0.031 4137 Dihedral : 4.660 32.156 3124 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.82 % Allowed : 5.13 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 2842 helix: 0.66 (0.22), residues: 504 sheet: 1.73 (0.15), residues: 1092 loop : -0.01 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 329 HIS 0.003 0.001 HIS F 186 PHE 0.012 0.001 PHE G 321 TYR 0.009 0.001 TYR F 215 ARG 0.003 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.05186 ( 833) hydrogen bonds : angle 4.96730 ( 2394) SS BOND : bond 0.00267 ( 7) SS BOND : angle 0.82411 ( 14) covalent geometry : bond 0.00239 (23247) covalent geometry : angle 0.52880 (31766) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 287 time to evaluate : 2.457 Fit side-chains REVERT: A 84 GLU cc_start: 0.7479 (tt0) cc_final: 0.7160 (tp30) REVERT: A 138 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.6501 (mm-30) REVERT: A 258 GLU cc_start: 0.7766 (tt0) cc_final: 0.7193 (tp30) REVERT: A 259 ILE cc_start: 0.8487 (mt) cc_final: 0.8224 (mm) REVERT: A 378 GLN cc_start: 0.7903 (mt0) cc_final: 0.7685 (pt0) REVERT: B 138 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: B 258 GLU cc_start: 0.7665 (tt0) cc_final: 0.7153 (tp30) REVERT: B 259 ILE cc_start: 0.8532 (mt) cc_final: 0.8216 (mm) REVERT: B 299 LYS cc_start: 0.8705 (mttt) cc_final: 0.8006 (mmmt) REVERT: B 378 GLN cc_start: 0.7898 (mt0) cc_final: 0.7517 (mm-40) REVERT: C 258 GLU cc_start: 0.7842 (tt0) cc_final: 0.7367 (tp30) REVERT: D 66 LYS cc_start: 0.6422 (pttt) cc_final: 0.6199 (pttp) REVERT: D 258 GLU cc_start: 0.7724 (tt0) cc_final: 0.7172 (tp30) REVERT: D 378 GLN cc_start: 0.7936 (mt0) cc_final: 0.7598 (mm-40) REVERT: E 35 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6706 (tptt) REVERT: E 258 GLU cc_start: 0.7852 (tt0) cc_final: 0.7385 (tp30) REVERT: F 29 GLU cc_start: 0.6426 (mp0) cc_final: 0.6187 (mp0) REVERT: F 35 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6574 (tppt) REVERT: F 258 GLU cc_start: 0.7797 (tt0) cc_final: 0.7217 (tp30) REVERT: F 259 ILE cc_start: 0.8499 (mt) cc_final: 0.8235 (mm) REVERT: F 277 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7580 (tt) REVERT: G 178 ASN cc_start: 0.8237 (t0) cc_final: 0.7952 (t0) REVERT: G 258 GLU cc_start: 0.7787 (tt0) cc_final: 0.7258 (tp30) REVERT: G 277 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7855 (tp) REVERT: G 299 LYS cc_start: 0.8642 (mttt) cc_final: 0.8284 (mttm) outliers start: 44 outliers final: 17 residues processed: 312 average time/residue: 1.3435 time to fit residues: 483.2746 Evaluate side-chains 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 172 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 217 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN B 174 ASN B 195 GLN C 174 ASN C 378 GLN D 174 ASN D 195 GLN E 195 GLN E 378 GLN F 174 ASN F 378 GLN G 174 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.163860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130895 restraints weight = 19281.731| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.49 r_work: 0.3365 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 23254 Z= 0.141 Angle : 0.516 4.611 31780 Z= 0.288 Chirality : 0.045 0.140 3332 Planarity : 0.004 0.031 4137 Dihedral : 4.449 30.033 3119 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.90 % Allowed : 6.54 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.15), residues: 2842 helix: 1.01 (0.22), residues: 504 sheet: 1.74 (0.14), residues: 1078 loop : 0.04 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 329 HIS 0.003 0.001 HIS F 186 PHE 0.013 0.002 PHE G 321 TYR 0.008 0.001 TYR D 177 ARG 0.002 0.000 ARG F 282 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 833) hydrogen bonds : angle 4.70833 ( 2394) SS BOND : bond 0.00201 ( 7) SS BOND : angle 0.55599 ( 14) covalent geometry : bond 0.00229 (23247) covalent geometry : angle 0.51585 (31766) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 2.257 Fit side-chains REVERT: A 84 GLU cc_start: 0.7467 (tt0) cc_final: 0.7150 (tp30) REVERT: A 138 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.6621 (mm-30) REVERT: A 207 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8036 (t0) REVERT: A 258 GLU cc_start: 0.7668 (tt0) cc_final: 0.7119 (tp30) REVERT: A 259 ILE cc_start: 0.8451 (mt) cc_final: 0.8198 (mm) REVERT: A 277 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7800 (tt) REVERT: A 309 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7702 (ttmt) REVERT: B 138 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.6717 (mm-30) REVERT: B 258 GLU cc_start: 0.7674 (tt0) cc_final: 0.7179 (tp30) REVERT: B 259 ILE cc_start: 0.8516 (mt) cc_final: 0.8140 (mm) REVERT: B 299 LYS cc_start: 0.8655 (mttt) cc_final: 0.7964 (mmmt) REVERT: B 378 GLN cc_start: 0.7835 (mt0) cc_final: 0.7469 (mm-40) REVERT: C 258 GLU cc_start: 0.7712 (tt0) cc_final: 0.7275 (tp30) REVERT: D 35 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6087 (tppp) REVERT: D 258 GLU cc_start: 0.7626 (tt0) cc_final: 0.7109 (tp30) REVERT: D 378 GLN cc_start: 0.7923 (mt0) cc_final: 0.7595 (mm-40) REVERT: E 35 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6711 (tptt) REVERT: E 97 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7920 (p0) REVERT: E 258 GLU cc_start: 0.7689 (tt0) cc_final: 0.7215 (tp30) REVERT: E 309 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8168 (tptt) REVERT: F 29 GLU cc_start: 0.6455 (mp0) cc_final: 0.6234 (mp0) REVERT: F 35 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6566 (tppt) REVERT: F 84 GLU cc_start: 0.7580 (tt0) cc_final: 0.7325 (tp30) REVERT: F 207 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8056 (t0) REVERT: F 258 GLU cc_start: 0.7683 (tt0) cc_final: 0.7142 (tp30) REVERT: F 259 ILE cc_start: 0.8460 (mt) cc_final: 0.8176 (mm) REVERT: F 277 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7622 (tt) REVERT: G 178 ASN cc_start: 0.8266 (t0) cc_final: 0.7990 (t0) REVERT: G 258 GLU cc_start: 0.7699 (tt0) cc_final: 0.7189 (tp30) REVERT: G 277 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7898 (tt) REVERT: G 299 LYS cc_start: 0.8600 (mttt) cc_final: 0.8246 (mttm) outliers start: 46 outliers final: 19 residues processed: 272 average time/residue: 1.0668 time to fit residues: 339.1612 Evaluate side-chains 266 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 166 optimal weight: 2.9990 chunk 211 optimal weight: 0.0770 chunk 35 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 234 optimal weight: 0.0370 chunk 246 optimal weight: 0.0770 overall best weight: 0.6454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 195 GLN B 174 ASN B 195 GLN C 174 ASN C 378 GLN D 174 ASN E 195 GLN E 378 GLN F 174 ASN F 378 GLN G 174 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.166041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133449 restraints weight = 19592.638| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.12 r_work: 0.3384 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 23254 Z= 0.119 Angle : 0.477 4.600 31780 Z= 0.264 Chirality : 0.044 0.135 3332 Planarity : 0.004 0.030 4137 Dihedral : 4.220 25.429 3119 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.57 % Allowed : 7.12 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.15), residues: 2842 helix: 1.30 (0.23), residues: 504 sheet: 1.66 (0.14), residues: 1120 loop : 0.14 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 359 HIS 0.002 0.001 HIS A 186 PHE 0.013 0.001 PHE B 321 TYR 0.007 0.001 TYR E 304 ARG 0.001 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 833) hydrogen bonds : angle 4.51907 ( 2394) SS BOND : bond 0.00168 ( 7) SS BOND : angle 0.42806 ( 14) covalent geometry : bond 0.00194 (23247) covalent geometry : angle 0.47678 (31766) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 2.744 Fit side-chains REVERT: A 84 GLU cc_start: 0.7484 (tt0) cc_final: 0.7152 (tp30) REVERT: A 138 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.6578 (mm-30) REVERT: A 207 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8068 (t0) REVERT: A 258 GLU cc_start: 0.7629 (tt0) cc_final: 0.7030 (tp30) REVERT: A 259 ILE cc_start: 0.8346 (mt) cc_final: 0.8034 (mm) REVERT: A 277 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7692 (tt) REVERT: A 309 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7623 (ttmt) REVERT: B 258 GLU cc_start: 0.7638 (tt0) cc_final: 0.7116 (tp30) REVERT: B 299 LYS cc_start: 0.8570 (mttt) cc_final: 0.8165 (mtpt) REVERT: B 378 GLN cc_start: 0.7771 (mt0) cc_final: 0.7386 (mm-40) REVERT: C 84 GLU cc_start: 0.7612 (tt0) cc_final: 0.7249 (tp30) REVERT: C 258 GLU cc_start: 0.7711 (tt0) cc_final: 0.7202 (tp30) REVERT: D 258 GLU cc_start: 0.7591 (tt0) cc_final: 0.7043 (tp30) REVERT: D 378 GLN cc_start: 0.7886 (mt0) cc_final: 0.7536 (mm-40) REVERT: E 35 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6637 (tptt) REVERT: E 258 GLU cc_start: 0.7674 (tt0) cc_final: 0.7125 (tp30) REVERT: E 299 LYS cc_start: 0.8503 (mttt) cc_final: 0.8222 (mttm) REVERT: F 35 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6565 (tppt) REVERT: F 84 GLU cc_start: 0.7597 (tt0) cc_final: 0.7317 (tp30) REVERT: F 258 GLU cc_start: 0.7670 (tt0) cc_final: 0.7094 (tp30) REVERT: F 259 ILE cc_start: 0.8329 (mt) cc_final: 0.8041 (mm) REVERT: F 277 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7539 (tt) REVERT: G 178 ASN cc_start: 0.8255 (t0) cc_final: 0.7959 (t0) REVERT: G 258 GLU cc_start: 0.7686 (tt0) cc_final: 0.7134 (tp30) REVERT: G 277 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7894 (tp) REVERT: G 299 LYS cc_start: 0.8538 (mttt) cc_final: 0.8167 (mttm) outliers start: 38 outliers final: 16 residues processed: 270 average time/residue: 1.4533 time to fit residues: 458.8642 Evaluate side-chains 266 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 258 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN B 174 ASN C 174 ASN C 378 GLN D 174 ASN E 195 GLN E 378 GLN F 132 HIS F 174 ASN F 378 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126633 restraints weight = 19282.043| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.09 r_work: 0.3284 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23254 Z= 0.198 Angle : 0.608 4.894 31780 Z= 0.344 Chirality : 0.048 0.151 3332 Planarity : 0.005 0.032 4137 Dihedral : 4.715 23.260 3118 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.95 % Allowed : 7.12 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.15), residues: 2842 helix: 0.80 (0.22), residues: 504 sheet: 1.74 (0.14), residues: 1078 loop : -0.01 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 329 HIS 0.005 0.002 HIS D 186 PHE 0.010 0.002 PHE G 343 TYR 0.012 0.002 TYR G 76 ARG 0.005 0.001 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.05934 ( 833) hydrogen bonds : angle 4.80761 ( 2394) SS BOND : bond 0.00347 ( 7) SS BOND : angle 0.44842 ( 14) covalent geometry : bond 0.00337 (23247) covalent geometry : angle 0.60818 (31766) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 2.604 Fit side-chains REVERT: A 84 GLU cc_start: 0.7510 (tt0) cc_final: 0.7128 (tp30) REVERT: A 138 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.6596 (mm-30) REVERT: A 258 GLU cc_start: 0.7896 (tt0) cc_final: 0.7203 (tp30) REVERT: A 259 ILE cc_start: 0.8542 (mt) cc_final: 0.8335 (mm) REVERT: A 277 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7984 (tt) REVERT: A 309 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7754 (ttmt) REVERT: B 138 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.6790 (mm-30) REVERT: B 258 GLU cc_start: 0.7765 (tt0) cc_final: 0.7208 (tp30) REVERT: B 299 LYS cc_start: 0.8759 (mttt) cc_final: 0.8116 (mmmt) REVERT: B 378 GLN cc_start: 0.7895 (mt0) cc_final: 0.7474 (mm-40) REVERT: C 84 GLU cc_start: 0.7610 (tt0) cc_final: 0.7249 (tp30) REVERT: C 258 GLU cc_start: 0.7922 (tt0) cc_final: 0.7388 (tp30) REVERT: C 311 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: D 35 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6421 (tppp) REVERT: D 47 ILE cc_start: 0.6149 (OUTLIER) cc_final: 0.5933 (mp) REVERT: D 258 GLU cc_start: 0.7803 (tt0) cc_final: 0.7195 (tp30) REVERT: D 378 GLN cc_start: 0.7994 (mt0) cc_final: 0.7584 (mm-40) REVERT: E 35 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6954 (tptt) REVERT: E 258 GLU cc_start: 0.7885 (tt0) cc_final: 0.7244 (tp30) REVERT: F 35 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6800 (tppt) REVERT: F 84 GLU cc_start: 0.7606 (tt0) cc_final: 0.7272 (tp30) REVERT: F 207 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8183 (t0) REVERT: F 258 GLU cc_start: 0.7819 (tt0) cc_final: 0.7177 (tp30) REVERT: F 259 ILE cc_start: 0.8498 (mt) cc_final: 0.8261 (mm) REVERT: F 277 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7853 (tt) REVERT: G 138 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7014 (mm-30) REVERT: G 178 ASN cc_start: 0.8396 (t0) cc_final: 0.8090 (t0) REVERT: G 258 GLU cc_start: 0.7785 (tt0) cc_final: 0.7211 (tp30) REVERT: G 277 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8119 (tt) REVERT: G 299 LYS cc_start: 0.8760 (mttt) cc_final: 0.8023 (mmmt) outliers start: 47 outliers final: 21 residues processed: 272 average time/residue: 1.1524 time to fit residues: 365.2456 Evaluate side-chains 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 285 optimal weight: 0.9980 chunk 191 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN B 174 ASN C 174 ASN C 378 GLN D 174 ASN E 174 ASN E 195 GLN E 378 GLN F 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124429 restraints weight = 19121.462| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.10 r_work: 0.3263 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23254 Z= 0.235 Angle : 0.682 5.530 31780 Z= 0.386 Chirality : 0.051 0.196 3332 Planarity : 0.005 0.037 4137 Dihedral : 5.010 20.501 3117 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.03 % Allowed : 7.04 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 2842 helix: 0.47 (0.21), residues: 504 sheet: 1.60 (0.14), residues: 1113 loop : -0.28 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 370 HIS 0.006 0.002 HIS F 186 PHE 0.014 0.003 PHE G 321 TYR 0.014 0.002 TYR G 76 ARG 0.007 0.001 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.06628 ( 833) hydrogen bonds : angle 5.02386 ( 2394) SS BOND : bond 0.00432 ( 7) SS BOND : angle 0.59271 ( 14) covalent geometry : bond 0.00411 (23247) covalent geometry : angle 0.68185 (31766) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 2.579 Fit side-chains REVERT: A 84 GLU cc_start: 0.7477 (tt0) cc_final: 0.7119 (tp30) REVERT: A 138 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: A 258 GLU cc_start: 0.7981 (tt0) cc_final: 0.7265 (tp30) REVERT: A 277 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8036 (tt) REVERT: A 309 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7791 (ttmt) REVERT: B 62 ASN cc_start: 0.7163 (m-40) cc_final: 0.6948 (m-40) REVERT: B 138 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: B 207 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8397 (m-30) REVERT: B 258 GLU cc_start: 0.7889 (tt0) cc_final: 0.7247 (tp30) REVERT: B 277 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7750 (tt) REVERT: B 378 GLN cc_start: 0.7909 (mt0) cc_final: 0.7480 (mm-40) REVERT: C 84 GLU cc_start: 0.7591 (tt0) cc_final: 0.7242 (tp30) REVERT: C 138 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.6827 (mm-30) REVERT: C 258 GLU cc_start: 0.7983 (tt0) cc_final: 0.7454 (tp30) REVERT: C 311 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8349 (m-30) REVERT: D 35 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6611 (tppp) REVERT: D 47 ILE cc_start: 0.6140 (OUTLIER) cc_final: 0.5922 (mp) REVERT: D 258 GLU cc_start: 0.7848 (tt0) cc_final: 0.7242 (tp30) REVERT: D 378 GLN cc_start: 0.7993 (mt0) cc_final: 0.7552 (mm-40) REVERT: E 35 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7087 (tppt) REVERT: E 258 GLU cc_start: 0.7972 (tt0) cc_final: 0.7319 (tp30) REVERT: E 277 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8029 (tt) REVERT: F 35 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6881 (tppt) REVERT: F 84 GLU cc_start: 0.7594 (tt0) cc_final: 0.7262 (tp30) REVERT: F 207 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8169 (t0) REVERT: F 258 GLU cc_start: 0.7885 (tt0) cc_final: 0.7212 (tp30) REVERT: F 259 ILE cc_start: 0.8549 (mt) cc_final: 0.8307 (mm) REVERT: F 277 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7955 (tt) REVERT: F 311 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: G 138 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.6999 (mm-30) REVERT: G 207 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: G 258 GLU cc_start: 0.7856 (tt0) cc_final: 0.7275 (tp30) REVERT: G 277 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8159 (tt) outliers start: 49 outliers final: 21 residues processed: 260 average time/residue: 1.1477 time to fit residues: 348.1631 Evaluate side-chains 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN B 174 ASN C 174 ASN C 378 GLN D 174 ASN E 174 ASN E 195 GLN E 263 GLN F 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122279 restraints weight = 19241.166| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.12 r_work: 0.3219 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 23254 Z= 0.307 Angle : 0.808 6.119 31780 Z= 0.459 Chirality : 0.056 0.309 3332 Planarity : 0.006 0.050 4137 Dihedral : 5.372 19.394 3116 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.03 % Allowed : 7.25 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 2842 helix: 0.18 (0.21), residues: 504 sheet: 1.59 (0.14), residues: 1106 loop : -0.53 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 54 HIS 0.009 0.002 HIS F 186 PHE 0.016 0.004 PHE E 321 TYR 0.020 0.003 TYR G 76 ARG 0.010 0.001 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.07867 ( 833) hydrogen bonds : angle 5.30152 ( 2394) SS BOND : bond 0.00649 ( 7) SS BOND : angle 0.77250 ( 14) covalent geometry : bond 0.00568 (23247) covalent geometry : angle 0.80786 (31766) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 2.903 Fit side-chains REVERT: A 84 GLU cc_start: 0.7582 (tt0) cc_final: 0.7227 (tp30) REVERT: A 138 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: A 258 GLU cc_start: 0.8062 (tt0) cc_final: 0.7366 (tp30) REVERT: A 277 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8137 (tt) REVERT: B 138 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6998 (mm-30) REVERT: B 207 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8404 (m-30) REVERT: B 277 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7809 (tt) REVERT: B 378 GLN cc_start: 0.7980 (mt0) cc_final: 0.7568 (mm-40) REVERT: C 84 GLU cc_start: 0.7666 (tt0) cc_final: 0.7323 (tp30) REVERT: C 138 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: C 258 GLU cc_start: 0.8037 (tt0) cc_final: 0.7456 (tp30) REVERT: D 29 GLU cc_start: 0.6603 (mp0) cc_final: 0.6334 (mp0) REVERT: D 35 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.6757 (tppp) REVERT: D 47 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.6140 (mp) REVERT: D 258 GLU cc_start: 0.7931 (tt0) cc_final: 0.7344 (tp30) REVERT: D 378 GLN cc_start: 0.8113 (mt0) cc_final: 0.7766 (mm-40) REVERT: E 258 GLU cc_start: 0.8035 (tt0) cc_final: 0.7379 (tp30) REVERT: E 277 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8013 (tt) REVERT: F 35 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7161 (tppt) REVERT: F 84 GLU cc_start: 0.7739 (tt0) cc_final: 0.7404 (tp30) REVERT: F 258 GLU cc_start: 0.8006 (tt0) cc_final: 0.7325 (tp30) REVERT: F 259 ILE cc_start: 0.8667 (mt) cc_final: 0.8450 (mm) REVERT: F 277 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8089 (tt) REVERT: F 311 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8432 (m-30) REVERT: G 138 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7130 (mm-30) REVERT: G 207 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8349 (m-30) REVERT: G 277 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8253 (tp) outliers start: 49 outliers final: 19 residues processed: 255 average time/residue: 1.2320 time to fit residues: 364.3491 Evaluate side-chains 262 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 39 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 276 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN B 174 ASN C 174 ASN D 174 ASN E 174 ASN E 195 GLN F 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.157847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125995 restraints weight = 19220.264| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.07 r_work: 0.3265 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23254 Z= 0.205 Angle : 0.625 4.950 31780 Z= 0.354 Chirality : 0.048 0.152 3332 Planarity : 0.005 0.034 4137 Dihedral : 4.948 17.930 3115 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.86 % Allowed : 7.45 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 2842 helix: 0.47 (0.22), residues: 504 sheet: 1.41 (0.14), residues: 1141 loop : -0.31 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 370 HIS 0.006 0.002 HIS A 132 PHE 0.020 0.002 PHE G 321 TYR 0.011 0.002 TYR D 357 ARG 0.004 0.001 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.05910 ( 833) hydrogen bonds : angle 5.02165 ( 2394) SS BOND : bond 0.00319 ( 7) SS BOND : angle 0.52678 ( 14) covalent geometry : bond 0.00341 (23247) covalent geometry : angle 0.62531 (31766) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 2.353 Fit side-chains REVERT: A 84 GLU cc_start: 0.7584 (tt0) cc_final: 0.7238 (tp30) REVERT: A 138 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.6693 (mm-30) REVERT: A 258 GLU cc_start: 0.7995 (tt0) cc_final: 0.7331 (tp30) REVERT: A 277 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7991 (tt) REVERT: B 138 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: B 207 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8406 (m-30) REVERT: B 277 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7740 (tt) REVERT: B 378 GLN cc_start: 0.7895 (mt0) cc_final: 0.7547 (mm-40) REVERT: C 138 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: C 258 GLU cc_start: 0.8028 (tt0) cc_final: 0.7539 (tp30) REVERT: D 35 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6582 (tppp) REVERT: D 47 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.6099 (mp) REVERT: D 258 GLU cc_start: 0.7876 (tt0) cc_final: 0.7355 (tp30) REVERT: D 378 GLN cc_start: 0.8057 (mt0) cc_final: 0.7693 (mm-40) REVERT: E 35 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7116 (tppt) REVERT: E 258 GLU cc_start: 0.7991 (tt0) cc_final: 0.7360 (tp30) REVERT: E 277 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7980 (tt) REVERT: F 35 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6918 (tppt) REVERT: F 84 GLU cc_start: 0.7717 (tt0) cc_final: 0.7381 (tp30) REVERT: F 207 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8211 (t0) REVERT: F 258 GLU cc_start: 0.7895 (tt0) cc_final: 0.7259 (tp30) REVERT: F 259 ILE cc_start: 0.8530 (mt) cc_final: 0.8271 (mm) REVERT: F 277 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7889 (tt) REVERT: F 311 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8381 (m-30) REVERT: G 138 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7030 (mm-30) REVERT: G 277 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8162 (tt) outliers start: 45 outliers final: 22 residues processed: 243 average time/residue: 1.1660 time to fit residues: 330.7043 Evaluate side-chains 256 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 18 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 195 GLN B 174 ASN C 174 ASN D 174 ASN E 195 GLN F 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125421 restraints weight = 19155.696| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.09 r_work: 0.3257 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 23254 Z= 0.212 Angle : 0.638 4.923 31780 Z= 0.362 Chirality : 0.049 0.152 3332 Planarity : 0.005 0.034 4137 Dihedral : 4.959 17.773 3115 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.90 % Allowed : 7.45 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 2842 helix: 0.49 (0.22), residues: 504 sheet: 1.53 (0.14), residues: 1078 loop : -0.28 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 370 HIS 0.007 0.002 HIS A 132 PHE 0.018 0.002 PHE G 321 TYR 0.011 0.002 TYR D 177 ARG 0.004 0.001 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.06178 ( 833) hydrogen bonds : angle 5.01279 ( 2394) SS BOND : bond 0.00354 ( 7) SS BOND : angle 0.52628 ( 14) covalent geometry : bond 0.00358 (23247) covalent geometry : angle 0.63833 (31766) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 2.727 Fit side-chains REVERT: A 84 GLU cc_start: 0.7629 (tt0) cc_final: 0.7269 (tp30) REVERT: A 138 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: A 258 GLU cc_start: 0.8039 (tt0) cc_final: 0.7346 (tp30) REVERT: A 277 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8008 (tt) REVERT: B 138 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.6928 (mm-30) REVERT: B 207 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8398 (m-30) REVERT: B 277 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7742 (tt) REVERT: B 378 GLN cc_start: 0.7910 (mt0) cc_final: 0.7556 (mm-40) REVERT: C 138 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6952 (mm-30) REVERT: C 258 GLU cc_start: 0.8046 (tt0) cc_final: 0.7549 (tp30) REVERT: D 35 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6636 (tppp) REVERT: D 47 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.5954 (mp) REVERT: D 258 GLU cc_start: 0.7897 (tt0) cc_final: 0.7363 (tp30) REVERT: D 378 GLN cc_start: 0.8067 (mt0) cc_final: 0.7700 (mm-40) REVERT: E 35 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7089 (tptt) REVERT: E 258 GLU cc_start: 0.8004 (tt0) cc_final: 0.7370 (tp30) REVERT: E 277 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7992 (tt) REVERT: F 35 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6956 (tppt) REVERT: F 84 GLU cc_start: 0.7694 (tt0) cc_final: 0.7368 (tp30) REVERT: F 207 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8208 (t0) REVERT: F 258 GLU cc_start: 0.7901 (tt0) cc_final: 0.7267 (tp30) REVERT: F 259 ILE cc_start: 0.8538 (mt) cc_final: 0.8282 (mm) REVERT: F 277 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7947 (tt) REVERT: F 311 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8401 (m-30) REVERT: G 138 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7059 (mm-30) REVERT: G 277 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8173 (tt) outliers start: 46 outliers final: 23 residues processed: 244 average time/residue: 1.2428 time to fit residues: 360.1892 Evaluate side-chains 257 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 26 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 230 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 264 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 254 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 195 GLN B 174 ASN C 174 ASN D 174 ASN E 174 ASN E 195 GLN F 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.158069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125701 restraints weight = 19249.065| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.12 r_work: 0.3272 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23254 Z= 0.199 Angle : 0.614 4.689 31780 Z= 0.347 Chirality : 0.048 0.151 3332 Planarity : 0.005 0.033 4137 Dihedral : 4.877 18.047 3115 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.66 % Allowed : 7.74 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 2842 helix: 0.52 (0.22), residues: 504 sheet: 1.43 (0.14), residues: 1106 loop : -0.19 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 370 HIS 0.006 0.002 HIS A 132 PHE 0.020 0.002 PHE G 321 TYR 0.011 0.002 TYR D 357 ARG 0.004 0.001 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.05814 ( 833) hydrogen bonds : angle 4.95614 ( 2394) SS BOND : bond 0.00319 ( 7) SS BOND : angle 0.50214 ( 14) covalent geometry : bond 0.00334 (23247) covalent geometry : angle 0.61356 (31766) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 2.643 Fit side-chains REVERT: A 84 GLU cc_start: 0.7539 (tt0) cc_final: 0.7166 (tp30) REVERT: A 138 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.6592 (mm-30) REVERT: A 258 GLU cc_start: 0.7942 (tt0) cc_final: 0.7228 (tp30) REVERT: A 277 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7988 (tt) REVERT: B 138 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.6816 (mm-30) REVERT: B 207 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: B 258 GLU cc_start: 0.7885 (tt0) cc_final: 0.7257 (tp30) REVERT: B 277 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7758 (tt) REVERT: B 378 GLN cc_start: 0.7836 (mt0) cc_final: 0.7456 (mm-40) REVERT: C 138 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: C 258 GLU cc_start: 0.7967 (tt0) cc_final: 0.7441 (tp30) REVERT: D 35 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6512 (tppp) REVERT: D 47 ILE cc_start: 0.6222 (OUTLIER) cc_final: 0.6000 (mp) REVERT: D 258 GLU cc_start: 0.7813 (tt0) cc_final: 0.7246 (tp30) REVERT: D 378 GLN cc_start: 0.8004 (mt0) cc_final: 0.7604 (mm-40) REVERT: E 35 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7013 (tptt) REVERT: E 258 GLU cc_start: 0.7928 (tt0) cc_final: 0.7269 (tp30) REVERT: E 277 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7972 (tt) REVERT: F 35 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6839 (tppt) REVERT: F 84 GLU cc_start: 0.7606 (tt0) cc_final: 0.7267 (tp30) REVERT: F 207 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8195 (t0) REVERT: F 258 GLU cc_start: 0.7813 (tt0) cc_final: 0.7155 (tp30) REVERT: F 259 ILE cc_start: 0.8446 (mt) cc_final: 0.8171 (mm) REVERT: F 277 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7884 (tt) REVERT: G 138 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.6962 (mm-30) REVERT: G 277 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8160 (tt) outliers start: 40 outliers final: 22 residues processed: 241 average time/residue: 1.1994 time to fit residues: 336.6333 Evaluate side-chains 255 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 5 optimal weight: 0.0870 chunk 229 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 178 optimal weight: 0.0060 chunk 179 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 276 optimal weight: 0.9990 overall best weight: 1.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 195 GLN B 174 ASN C 174 ASN D 174 ASN E 195 GLN F 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.160145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127128 restraints weight = 19214.569| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.11 r_work: 0.3307 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 23254 Z= 0.173 Angle : 0.567 4.474 31780 Z= 0.320 Chirality : 0.047 0.145 3332 Planarity : 0.004 0.034 4137 Dihedral : 4.693 17.768 3115 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.53 % Allowed : 8.03 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 2842 helix: 0.69 (0.22), residues: 504 sheet: 1.45 (0.14), residues: 1106 loop : -0.10 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 370 HIS 0.005 0.001 HIS A 132 PHE 0.019 0.002 PHE G 321 TYR 0.009 0.001 TYR D 357 ARG 0.002 0.000 ARG B 144 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 833) hydrogen bonds : angle 4.82287 ( 2394) SS BOND : bond 0.00228 ( 7) SS BOND : angle 0.45972 ( 14) covalent geometry : bond 0.00283 (23247) covalent geometry : angle 0.56696 (31766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23223.50 seconds wall clock time: 398 minutes 24.55 seconds (23904.55 seconds total)