Starting phenix.real_space_refine on Thu May 22 06:10:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fnq_50602/05_2025/9fnq_50602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fnq_50602/05_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_50602/05_2025/9fnq_50602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fnq_50602/05_2025/9fnq_50602.map" model { file = "/net/cci-nas-00/data/ceres_data/9fnq_50602/05_2025/9fnq_50602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fnq_50602/05_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-5687/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: 8.43, per 1000 atoms: 0.37 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: 5.79 Conformation dependent library (CDL) restraints added in 2.9 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: 2.04 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: 6.15 Time building geometry restraints manager: 6.59 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: 0.18 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: 3.220 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: 0.010 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 42.570 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.910 ------------------------------------------------------------------------------- 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 : 2.897 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: 1.4086 time to fit residues: 723.6841 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 : 2.737 ------------------------------------------------------------------------------- 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 = 0.130641 restraints weight = 19280.605| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.53 r_work: 0.3364 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 2.488 Fit side-chains REVERT: A 84 GLU cc_start: 0.7482 (tt0) cc_final: 0.7161 (tp30) REVERT: A 138 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.6501 (mm-30) REVERT: A 258 GLU cc_start: 0.7774 (tt0) cc_final: 0.7190 (tp30) REVERT: A 259 ILE cc_start: 0.8485 (mt) cc_final: 0.8219 (mm) REVERT: A 378 GLN cc_start: 0.7899 (mt0) cc_final: 0.7684 (pt0) REVERT: B 138 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: B 258 GLU cc_start: 0.7671 (tt0) cc_final: 0.7149 (tp30) REVERT: B 259 ILE cc_start: 0.8530 (mt) cc_final: 0.8210 (mm) REVERT: B 299 LYS cc_start: 0.8704 (mttt) cc_final: 0.8006 (mmmt) REVERT: B 378 GLN cc_start: 0.7894 (mt0) cc_final: 0.7515 (mm-40) REVERT: C 258 GLU cc_start: 0.7847 (tt0) cc_final: 0.7360 (tp30) REVERT: D 66 LYS cc_start: 0.6412 (pttt) cc_final: 0.6188 (pttp) REVERT: D 258 GLU cc_start: 0.7732 (tt0) cc_final: 0.7168 (tp30) REVERT: D 378 GLN cc_start: 0.7933 (mt0) cc_final: 0.7598 (mm-40) REVERT: E 35 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6706 (tptt) REVERT: E 258 GLU cc_start: 0.7858 (tt0) cc_final: 0.7381 (tp30) REVERT: F 29 GLU cc_start: 0.6423 (mp0) cc_final: 0.6185 (mp0) REVERT: F 35 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6573 (tppt) REVERT: F 258 GLU cc_start: 0.7803 (tt0) cc_final: 0.7215 (tp30) REVERT: F 259 ILE cc_start: 0.8498 (mt) cc_final: 0.8231 (mm) REVERT: F 277 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7580 (tt) REVERT: G 178 ASN cc_start: 0.8235 (t0) cc_final: 0.7951 (t0) REVERT: G 258 GLU cc_start: 0.7794 (tt0) cc_final: 0.7254 (tp30) REVERT: G 277 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7855 (tp) REVERT: G 299 LYS cc_start: 0.8641 (mttt) cc_final: 0.8284 (mttm) outliers start: 44 outliers final: 17 residues processed: 312 average time/residue: 1.2564 time to fit residues: 451.1086 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 : 2.413 ------------------------------------------------------------------------------- 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: 5.9990 chunk 208 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 217 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.162253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128276 restraints weight = 19182.608| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.49 r_work: 0.3341 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 23254 Z= 0.160 Angle : 0.548 4.565 31780 Z= 0.308 Chirality : 0.046 0.144 3332 Planarity : 0.004 0.032 4137 Dihedral : 4.590 29.704 3119 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.90 % Allowed : 6.79 % 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: 1.14 (0.15), residues: 2842 helix: 0.84 (0.22), residues: 504 sheet: 1.63 (0.14), residues: 1092 loop : -0.02 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 329 HIS 0.004 0.001 HIS F 186 PHE 0.013 0.002 PHE G 321 TYR 0.009 0.001 TYR D 177 ARG 0.003 0.001 ARG F 282 Details of bonding type rmsd hydrogen bonds : bond 0.05347 ( 833) hydrogen bonds : angle 4.79538 ( 2394) SS BOND : bond 0.00256 ( 7) SS BOND : angle 0.59511 ( 14) covalent geometry : bond 0.00261 (23247) covalent geometry : angle 0.54770 (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 286 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 2.428 Fit side-chains REVERT: A 84 GLU cc_start: 0.7457 (tt0) cc_final: 0.7124 (tp30) REVERT: A 138 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6543 (mm-30) REVERT: A 258 GLU cc_start: 0.7666 (tt0) cc_final: 0.7092 (tp30) REVERT: A 259 ILE cc_start: 0.8463 (mt) cc_final: 0.8211 (mm) REVERT: A 277 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7845 (tt) REVERT: A 309 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7701 (ttmt) REVERT: A 378 GLN cc_start: 0.7886 (mt0) cc_final: 0.7680 (pt0) REVERT: B 138 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: B 207 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: B 258 GLU cc_start: 0.7747 (tt0) cc_final: 0.7209 (tp30) REVERT: B 259 ILE cc_start: 0.8538 (mt) cc_final: 0.8138 (mm) REVERT: B 299 LYS cc_start: 0.8722 (mttt) cc_final: 0.8045 (mmmt) REVERT: B 378 GLN cc_start: 0.7843 (mt0) cc_final: 0.7441 (mm-40) REVERT: C 84 GLU cc_start: 0.7600 (tt0) cc_final: 0.7249 (tp30) REVERT: C 258 GLU cc_start: 0.7750 (tt0) cc_final: 0.7264 (tp30) REVERT: D 35 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6159 (tppp) REVERT: D 258 GLU cc_start: 0.7661 (tt0) cc_final: 0.7113 (tp30) REVERT: D 378 GLN cc_start: 0.7959 (mt0) cc_final: 0.7565 (mm-40) REVERT: E 35 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6709 (tptt) REVERT: E 258 GLU cc_start: 0.7727 (tt0) cc_final: 0.7221 (tp30) REVERT: F 35 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6686 (tppt) REVERT: F 84 GLU cc_start: 0.7564 (tt0) cc_final: 0.7281 (tp30) REVERT: F 207 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8085 (t0) REVERT: F 258 GLU cc_start: 0.7691 (tt0) cc_final: 0.7138 (tp30) REVERT: F 259 ILE cc_start: 0.8459 (mt) cc_final: 0.8209 (mm) REVERT: F 277 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7710 (tt) REVERT: G 178 ASN cc_start: 0.8290 (t0) cc_final: 0.7992 (t0) REVERT: G 258 GLU cc_start: 0.7712 (tt0) cc_final: 0.7181 (tp30) REVERT: G 277 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7993 (tt) REVERT: G 299 LYS cc_start: 0.8675 (mttt) cc_final: 0.8308 (mttm) outliers start: 46 outliers final: 20 residues processed: 269 average time/residue: 1.1328 time to fit residues: 354.9022 Evaluate side-chains 263 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 2.400 ------------------------------------------------------------------------------- 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 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 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 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 47 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 166 optimal weight: 1.9990 chunk 211 optimal weight: 0.0870 chunk 35 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 234 optimal weight: 0.0370 chunk 246 optimal weight: 1.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 C 378 GLN D 174 ASN E 178 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 = 0.3853 r_free = 0.3853 target = 0.162861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131142 restraints weight = 19513.319| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.10 r_work: 0.3327 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 23254 Z= 0.139 Angle : 0.509 4.589 31780 Z= 0.284 Chirality : 0.045 0.139 3332 Planarity : 0.004 0.030 4137 Dihedral : 4.417 26.025 3119 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.61 % Allowed : 7.33 % Favored : 91.06 % 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: 1.31 (0.15), residues: 2842 helix: 1.07 (0.23), 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 D 370 HIS 0.003 0.001 HIS F 186 PHE 0.014 0.002 PHE G 321 TYR 0.008 0.001 TYR D 177 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 833) hydrogen bonds : angle 4.64826 ( 2394) SS BOND : bond 0.00213 ( 7) SS BOND : angle 0.49359 ( 14) covalent geometry : bond 0.00226 (23247) covalent geometry : angle 0.50896 (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 280 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 2.756 Fit side-chains REVERT: A 84 GLU cc_start: 0.7588 (tt0) cc_final: 0.7249 (tp30) REVERT: A 138 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: A 258 GLU cc_start: 0.7770 (tt0) cc_final: 0.7201 (tp30) REVERT: A 259 ILE cc_start: 0.8468 (mt) cc_final: 0.8223 (mm) REVERT: A 277 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7772 (tt) REVERT: A 309 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7744 (ttmt) REVERT: B 138 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.6836 (mm-30) REVERT: B 258 GLU cc_start: 0.7805 (tt0) cc_final: 0.7292 (tp30) REVERT: B 259 ILE cc_start: 0.8515 (mt) cc_final: 0.8137 (mm) REVERT: B 299 LYS cc_start: 0.8658 (mttt) cc_final: 0.7994 (mmmt) REVERT: B 378 GLN cc_start: 0.7847 (mt0) cc_final: 0.7472 (mm-40) REVERT: C 84 GLU cc_start: 0.7750 (tt0) cc_final: 0.7382 (tp30) REVERT: C 258 GLU cc_start: 0.7813 (tt0) cc_final: 0.7352 (tp30) REVERT: D 258 GLU cc_start: 0.7714 (tt0) cc_final: 0.7184 (tp30) REVERT: D 378 GLN cc_start: 0.8013 (mt0) cc_final: 0.7669 (mm-40) REVERT: E 35 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6778 (tptt) REVERT: E 258 GLU cc_start: 0.7794 (tt0) cc_final: 0.7265 (tp30) REVERT: F 29 GLU cc_start: 0.6593 (mp0) cc_final: 0.6383 (mp0) REVERT: F 35 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6751 (tppt) REVERT: F 84 GLU cc_start: 0.7686 (tt0) cc_final: 0.7400 (tp30) REVERT: F 207 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8191 (t0) REVERT: F 258 GLU cc_start: 0.7754 (tt0) cc_final: 0.7199 (tp30) REVERT: F 259 ILE cc_start: 0.8463 (mt) cc_final: 0.8223 (mm) REVERT: F 277 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7641 (tt) REVERT: G 178 ASN cc_start: 0.8346 (t0) cc_final: 0.8068 (t0) REVERT: G 258 GLU cc_start: 0.7789 (tt0) cc_final: 0.7268 (tp30) REVERT: G 277 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7913 (tt) REVERT: G 299 LYS cc_start: 0.8625 (mttt) cc_final: 0.8282 (mttm) outliers start: 39 outliers final: 18 residues processed: 262 average time/residue: 1.1235 time to fit residues: 344.8865 Evaluate side-chains 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 2.489 ------------------------------------------------------------------------------- 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 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 241 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 311 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 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 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: 9.9990 chunk 18 optimal weight: 0.5980 chunk 252 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 237 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 258 optimal weight: 0.0170 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 chunk 146 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- 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 C 378 GLN D 174 ASN E 195 GLN E 378 GLN F 132 HIS 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 = 0.3923 r_free = 0.3923 target = 0.169676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138814 restraints weight = 19859.728| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.07 r_work: 0.3427 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2104 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= 0.092 Angle : 0.437 4.903 31780 Z= 0.237 Chirality : 0.043 0.129 3332 Planarity : 0.003 0.029 4137 Dihedral : 3.922 21.595 3118 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.87 % Allowed : 8.24 % Favored : 90.89 % 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: 1.58 (0.15), residues: 2842 helix: 1.56 (0.24), residues: 504 sheet: 1.74 (0.14), residues: 1120 loop : 0.22 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 103 HIS 0.002 0.001 HIS F 341 PHE 0.013 0.001 PHE G 321 TYR 0.006 0.001 TYR E 304 ARG 0.001 0.000 ARG C 220 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 833) hydrogen bonds : angle 4.34833 ( 2394) SS BOND : bond 0.00102 ( 7) SS BOND : angle 0.38986 ( 14) covalent geometry : bond 0.00159 (23247) covalent geometry : angle 0.43691 (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 289 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 268 time to evaluate : 2.494 Fit side-chains REVERT: A 84 GLU cc_start: 0.7548 (tt0) cc_final: 0.7224 (tp30) REVERT: A 258 GLU cc_start: 0.7574 (tt0) cc_final: 0.7061 (tp30) REVERT: A 259 ILE cc_start: 0.8277 (mt) cc_final: 0.7970 (mm) REVERT: B 258 GLU cc_start: 0.7589 (tt0) cc_final: 0.7089 (tp30) REVERT: B 299 LYS cc_start: 0.8437 (mttt) cc_final: 0.8037 (mtpt) REVERT: B 378 GLN cc_start: 0.7728 (mt0) cc_final: 0.7403 (mm-40) REVERT: C 84 GLU cc_start: 0.7685 (tt0) cc_final: 0.7344 (tp30) REVERT: C 258 GLU cc_start: 0.7710 (tt0) cc_final: 0.7207 (tp30) REVERT: D 35 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6094 (tppp) REVERT: D 258 GLU cc_start: 0.7607 (tt0) cc_final: 0.7133 (tp30) REVERT: E 258 GLU cc_start: 0.7618 (tt0) cc_final: 0.7083 (tp30) REVERT: E 299 LYS cc_start: 0.8366 (mttt) cc_final: 0.8120 (mttm) REVERT: F 35 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6528 (tppt) REVERT: F 84 GLU cc_start: 0.7661 (tt0) cc_final: 0.7362 (tp30) REVERT: F 258 GLU cc_start: 0.7615 (tt0) cc_final: 0.7070 (tp30) REVERT: F 259 ILE cc_start: 0.8194 (mt) cc_final: 0.7882 (mm) REVERT: G 258 GLU cc_start: 0.7701 (tt0) cc_final: 0.7164 (tp30) REVERT: G 277 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7718 (tp) REVERT: G 299 LYS cc_start: 0.8400 (mttt) cc_final: 0.8045 (mttm) outliers start: 21 outliers final: 5 residues processed: 280 average time/residue: 1.0356 time to fit residues: 342.3363 Evaluate side-chains 257 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 249 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 27 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 285 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 167 optimal weight: 0.2980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 379 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126971 restraints weight = 19339.547| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.10 r_work: 0.3287 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2062 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 : 0.607 5.075 31780 Z= 0.342 Chirality : 0.048 0.150 3332 Planarity : 0.005 0.032 4137 Dihedral : 4.611 18.492 3117 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.86 % Allowed : 7.62 % Favored : 90.52 % 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: 1.27 (0.15), residues: 2842 helix: 0.89 (0.22), residues: 504 sheet: 1.78 (0.14), residues: 1078 loop : 0.03 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 329 HIS 0.005 0.002 HIS D 186 PHE 0.010 0.002 PHE G 343 TYR 0.011 0.002 TYR D 177 ARG 0.005 0.001 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.05835 ( 833) hydrogen bonds : angle 4.74051 ( 2394) SS BOND : bond 0.00360 ( 7) SS BOND : angle 0.38854 ( 14) covalent geometry : bond 0.00340 (23247) covalent geometry : angle 0.60681 (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 289 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 2.533 Fit side-chains REVERT: A 84 GLU cc_start: 0.7491 (tt0) cc_final: 0.7101 (tp30) REVERT: A 138 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.6562 (mm-30) REVERT: A 258 GLU cc_start: 0.7853 (tt0) cc_final: 0.7183 (tp30) REVERT: A 259 ILE cc_start: 0.8539 (mt) cc_final: 0.8324 (mm) REVERT: A 309 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7750 (ttmt) REVERT: B 138 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.6816 (mm-30) REVERT: B 258 GLU cc_start: 0.7790 (tt0) cc_final: 0.7241 (tp30) REVERT: B 299 LYS cc_start: 0.8743 (mttt) cc_final: 0.8095 (mmmt) REVERT: B 378 GLN cc_start: 0.7913 (mt0) cc_final: 0.7507 (mm-40) REVERT: C 84 GLU cc_start: 0.7599 (tt0) cc_final: 0.7233 (tp30) REVERT: C 138 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.6836 (mm-30) REVERT: C 258 GLU cc_start: 0.7907 (tt0) cc_final: 0.7377 (tp30) REVERT: D 35 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6444 (tppp) REVERT: D 258 GLU cc_start: 0.7793 (tt0) cc_final: 0.7174 (tp30) REVERT: E 258 GLU cc_start: 0.7861 (tt0) cc_final: 0.7205 (tp30) REVERT: E 299 LYS cc_start: 0.8699 (mttt) cc_final: 0.8385 (mtpm) REVERT: F 35 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6794 (tppt) REVERT: F 84 GLU cc_start: 0.7611 (tt0) cc_final: 0.7277 (tp30) REVERT: F 207 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8173 (t0) REVERT: F 258 GLU cc_start: 0.7793 (tt0) cc_final: 0.7144 (tp30) REVERT: F 259 ILE cc_start: 0.8488 (mt) cc_final: 0.8251 (mm) REVERT: G 138 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: G 178 ASN cc_start: 0.8393 (t0) cc_final: 0.8087 (t0) REVERT: G 258 GLU cc_start: 0.7753 (tt0) cc_final: 0.7167 (tp30) REVERT: G 277 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8135 (tt) outliers start: 45 outliers final: 17 residues processed: 267 average time/residue: 1.1143 time to fit residues: 347.5938 Evaluate side-chains 257 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 2.747 ------------------------------------------------------------------------------- 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 309 LYS 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 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 241 THR 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 350 ASP Chi-restraints excluded: chain G residue 89 SER 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: 9.9990 chunk 92 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 244 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 217 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 379 GLN D 174 ASN E 195 GLN E 378 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 = 0.3799 r_free = 0.3799 target = 0.157769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125300 restraints weight = 19297.053| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.06 r_work: 0.3266 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 23254 Z= 0.223 Angle : 0.658 5.443 31780 Z= 0.373 Chirality : 0.050 0.168 3332 Planarity : 0.005 0.033 4137 Dihedral : 4.891 17.912 3115 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.95 % Allowed : 7.37 % 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: 0.91 (0.15), residues: 2842 helix: 0.53 (0.22), residues: 504 sheet: 1.68 (0.14), residues: 1043 loop : -0.23 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 370 HIS 0.006 0.002 HIS F 186 PHE 0.013 0.002 PHE G 321 TYR 0.013 0.002 TYR A 76 ARG 0.006 0.001 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.06355 ( 833) hydrogen bonds : angle 4.95464 ( 2394) SS BOND : bond 0.00394 ( 7) SS BOND : angle 0.51065 ( 14) covalent geometry : bond 0.00385 (23247) covalent geometry : angle 0.65756 (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 283 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 2.592 Fit side-chains REVERT: A 84 GLU cc_start: 0.7557 (tt0) cc_final: 0.7219 (tp30) REVERT: A 138 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.6668 (mm-30) REVERT: A 258 GLU cc_start: 0.8016 (tt0) cc_final: 0.7330 (tp30) REVERT: A 277 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7941 (tt) REVERT: A 309 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7774 (ttmt) REVERT: B 138 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: B 258 GLU cc_start: 0.7944 (tt0) cc_final: 0.7379 (tp30) REVERT: B 277 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7754 (tt) REVERT: B 378 GLN cc_start: 0.7981 (mt0) cc_final: 0.7595 (mm-40) REVERT: C 84 GLU cc_start: 0.7688 (tt0) cc_final: 0.7354 (tp30) REVERT: C 138 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.6899 (mm-30) REVERT: C 258 GLU cc_start: 0.8033 (tt0) cc_final: 0.7539 (tp30) REVERT: C 311 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: D 35 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6650 (tppp) REVERT: D 258 GLU cc_start: 0.7855 (tt0) cc_final: 0.7307 (tp30) REVERT: E 258 GLU cc_start: 0.8027 (tt0) cc_final: 0.7389 (tp30) REVERT: F 35 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6981 (tppt) REVERT: F 84 GLU cc_start: 0.7684 (tt0) cc_final: 0.7369 (tp30) REVERT: F 207 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8205 (t0) REVERT: F 258 GLU cc_start: 0.7921 (tt0) cc_final: 0.7288 (tp30) REVERT: F 259 ILE cc_start: 0.8568 (mt) cc_final: 0.8339 (mm) REVERT: F 277 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8072 (tt) REVERT: G 138 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: G 207 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: G 258 GLU cc_start: 0.7920 (tt0) cc_final: 0.7365 (tp30) REVERT: G 277 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8144 (tt) outliers start: 47 outliers final: 21 residues processed: 258 average time/residue: 1.1837 time to fit residues: 356.1636 Evaluate side-chains 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 2.568 ------------------------------------------------------------------------------- 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 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 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 311 ASP 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 89 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 39 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 379 GLN D 174 ASN E 174 ASN E 195 GLN E 263 GLN E 378 GLN F 174 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124697 restraints weight = 19198.412| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.09 r_work: 0.3263 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23254 Z= 0.228 Angle : 0.665 5.458 31780 Z= 0.377 Chirality : 0.050 0.175 3332 Planarity : 0.005 0.040 4137 Dihedral : 4.948 17.657 3115 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.82 % Allowed : 7.66 % Favored : 90.52 % 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: 0.85 (0.15), residues: 2842 helix: 0.48 (0.21), residues: 504 sheet: 1.56 (0.14), residues: 1113 loop : -0.30 (0.17), 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 0.015 0.003 PHE E 321 TYR 0.013 0.002 TYR G 76 ARG 0.006 0.001 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.06423 ( 833) hydrogen bonds : angle 5.01208 ( 2394) SS BOND : bond 0.00407 ( 7) SS BOND : angle 0.48837 ( 14) covalent geometry : bond 0.00395 (23247) covalent geometry : angle 0.66512 (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 271 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 2.481 Fit side-chains REVERT: A 84 GLU cc_start: 0.7490 (tt0) cc_final: 0.7127 (tp30) REVERT: A 138 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.6588 (mm-30) REVERT: A 258 GLU cc_start: 0.7965 (tt0) cc_final: 0.7253 (tp30) REVERT: A 277 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7926 (tt) REVERT: A 309 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7754 (ttmt) REVERT: B 258 GLU cc_start: 0.7870 (tt0) cc_final: 0.7282 (tp30) REVERT: B 277 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7775 (tt) REVERT: B 378 GLN cc_start: 0.7855 (mt0) cc_final: 0.7429 (mm-40) REVERT: C 84 GLU cc_start: 0.7612 (tt0) cc_final: 0.7252 (tp30) REVERT: C 138 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: C 258 GLU cc_start: 0.7972 (tt0) cc_final: 0.7458 (tp30) REVERT: C 311 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: D 35 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6584 (tppp) REVERT: D 258 GLU cc_start: 0.7832 (tt0) cc_final: 0.7273 (tp30) REVERT: E 258 GLU cc_start: 0.7938 (tt0) cc_final: 0.7289 (tp30) REVERT: E 277 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8091 (tt) REVERT: F 35 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6908 (tppt) REVERT: F 84 GLU cc_start: 0.7597 (tt0) cc_final: 0.7265 (tp30) REVERT: F 207 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8189 (t0) REVERT: F 258 GLU cc_start: 0.7817 (tt0) cc_final: 0.7163 (tp30) REVERT: F 259 ILE cc_start: 0.8495 (mt) cc_final: 0.8240 (mm) REVERT: F 277 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8056 (tt) REVERT: G 138 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.6976 (mm-30) REVERT: G 207 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8282 (m-30) REVERT: G 258 GLU cc_start: 0.7839 (tt0) cc_final: 0.7290 (tp30) REVERT: G 277 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8190 (tt) outliers start: 44 outliers final: 21 residues processed: 248 average time/residue: 1.1230 time to fit residues: 325.1404 Evaluate side-chains 258 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 2.596 ------------------------------------------------------------------------------- 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 143 THR 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 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 311 ASP Chi-restraints excluded: chain D residue 378 GLN 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 89 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 18 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.157923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125364 restraints weight = 19176.115| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.09 r_work: 0.3275 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2258 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= 0.209 Angle : 0.630 4.888 31780 Z= 0.357 Chirality : 0.049 0.155 3332 Planarity : 0.005 0.033 4137 Dihedral : 4.865 17.230 3115 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.57 % Allowed : 7.99 % 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: 0.89 (0.15), residues: 2842 helix: 0.52 (0.22), residues: 504 sheet: 1.56 (0.14), residues: 1078 loop : -0.20 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 370 HIS 0.005 0.002 HIS B 186 PHE 0.016 0.002 PHE G 321 TYR 0.011 0.002 TYR D 177 ARG 0.005 0.001 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.06004 ( 833) hydrogen bonds : angle 4.95102 ( 2394) SS BOND : bond 0.00342 ( 7) SS BOND : angle 0.47712 ( 14) covalent geometry : bond 0.00356 (23247) covalent geometry : angle 0.63024 (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 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 2.550 Fit side-chains REVERT: A 84 GLU cc_start: 0.7519 (tt0) cc_final: 0.7150 (tp30) REVERT: A 138 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.6607 (mm-30) REVERT: A 258 GLU cc_start: 0.7951 (tt0) cc_final: 0.7241 (tp30) REVERT: A 277 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7919 (tt) REVERT: A 309 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7720 (ttmt) REVERT: B 258 GLU cc_start: 0.7843 (tt0) cc_final: 0.7257 (tp30) REVERT: B 277 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7769 (tt) REVERT: B 378 GLN cc_start: 0.7833 (mt0) cc_final: 0.7403 (mm-40) REVERT: C 84 GLU cc_start: 0.7602 (tt0) cc_final: 0.7243 (tp30) REVERT: C 258 GLU cc_start: 0.7966 (tt0) cc_final: 0.7446 (tp30) REVERT: C 311 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: D 35 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6551 (tppp) REVERT: D 258 GLU cc_start: 0.7812 (tt0) cc_final: 0.7257 (tp30) REVERT: E 258 GLU cc_start: 0.7896 (tt0) cc_final: 0.7244 (tp30) REVERT: E 277 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8047 (tt) REVERT: F 35 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6864 (tppt) REVERT: F 84 GLU cc_start: 0.7597 (tt0) cc_final: 0.7264 (tp30) REVERT: F 207 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8184 (t0) REVERT: F 258 GLU cc_start: 0.7795 (tt0) cc_final: 0.7145 (tp30) REVERT: F 259 ILE cc_start: 0.8471 (mt) cc_final: 0.8203 (mm) REVERT: F 277 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8042 (tt) REVERT: G 138 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: G 258 GLU cc_start: 0.7825 (tt0) cc_final: 0.7273 (tp30) REVERT: G 277 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8174 (tt) outliers start: 38 outliers final: 23 residues processed: 244 average time/residue: 1.1884 time to fit residues: 346.0541 Evaluate side-chains 259 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 2.623 ------------------------------------------------------------------------------- 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 311 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 143 THR 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 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 241 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 378 GLN 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 89 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 26 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 196 optimal weight: 0.0030 chunk 230 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.162704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130620 restraints weight = 19446.375| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.09 r_work: 0.3340 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2244 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= 0.133 Angle : 0.503 4.516 31780 Z= 0.280 Chirality : 0.044 0.138 3332 Planarity : 0.004 0.032 4137 Dihedral : 4.386 16.795 3115 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.04 % Allowed : 8.49 % Favored : 90.48 % 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: 1.01 (0.23), residues: 504 sheet: 1.52 (0.14), residues: 1106 loop : 0.05 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 370 HIS 0.003 0.001 HIS A 132 PHE 0.017 0.002 PHE A 321 TYR 0.008 0.001 TYR F 304 ARG 0.001 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 833) hydrogen bonds : angle 4.63736 ( 2394) SS BOND : bond 0.00137 ( 7) SS BOND : angle 0.41942 ( 14) covalent geometry : bond 0.00216 (23247) covalent geometry : angle 0.50268 (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 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 2.465 Fit side-chains REVERT: A 84 GLU cc_start: 0.7490 (tt0) cc_final: 0.7111 (tp30) REVERT: A 138 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.6585 (mm-30) REVERT: A 258 GLU cc_start: 0.7784 (tt0) cc_final: 0.7156 (tp30) REVERT: B 258 GLU cc_start: 0.7764 (tt0) cc_final: 0.7202 (tp30) REVERT: B 299 LYS cc_start: 0.8629 (mttt) cc_final: 0.7957 (mmmt) REVERT: B 378 GLN cc_start: 0.7706 (mt0) cc_final: 0.7320 (mm-40) REVERT: C 84 GLU cc_start: 0.7611 (tt0) cc_final: 0.7236 (tp30) REVERT: C 258 GLU cc_start: 0.7758 (tt0) cc_final: 0.7258 (tp30) REVERT: D 35 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6345 (tppp) REVERT: D 258 GLU cc_start: 0.7690 (tt0) cc_final: 0.7139 (tp30) REVERT: E 258 GLU cc_start: 0.7802 (tt0) cc_final: 0.7224 (tp30) REVERT: E 299 LYS cc_start: 0.8622 (mttt) cc_final: 0.8332 (mttm) REVERT: F 35 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6753 (tppt) REVERT: F 84 GLU cc_start: 0.7601 (tt0) cc_final: 0.7264 (tp30) REVERT: F 207 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8141 (t0) REVERT: F 258 GLU cc_start: 0.7656 (tt0) cc_final: 0.7077 (tp30) REVERT: F 259 ILE cc_start: 0.8351 (mt) cc_final: 0.8085 (mm) REVERT: F 277 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7900 (tp) REVERT: G 138 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.6897 (mm-30) REVERT: G 178 ASN cc_start: 0.8386 (t0) cc_final: 0.8083 (t0) REVERT: G 258 GLU cc_start: 0.7729 (tt0) cc_final: 0.7173 (tp30) REVERT: G 277 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7916 (tt) outliers start: 25 outliers final: 10 residues processed: 245 average time/residue: 1.1030 time to fit residues: 316.7489 Evaluate side-chains 246 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 229 time to evaluate : 2.518 ------------------------------------------------------------------------------- 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 350 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 35 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 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 277 LEU 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: 0.6980 chunk 229 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.157165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124241 restraints weight = 19161.010| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.10 r_work: 0.3268 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23254 Z= 0.230 Angle : 0.668 5.237 31780 Z= 0.378 Chirality : 0.051 0.156 3332 Planarity : 0.005 0.035 4137 Dihedral : 4.919 19.641 3115 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.16 % Allowed : 8.57 % Favored : 90.27 % 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: 0.88 (0.15), residues: 2842 helix: 0.51 (0.22), residues: 504 sheet: 1.56 (0.14), residues: 1113 loop : -0.28 (0.17), residues: 1225 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 0.015 0.003 PHE G 321 TYR 0.012 0.002 TYR G 76 ARG 0.006 0.001 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.06510 ( 833) hydrogen bonds : angle 4.97238 ( 2394) SS BOND : bond 0.00400 ( 7) SS BOND : angle 0.46784 ( 14) covalent geometry : bond 0.00401 (23247) covalent geometry : angle 0.66776 (31766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22096.40 seconds wall clock time: 381 minutes 43.88 seconds (22903.88 seconds total)