Starting phenix.real_space_refine on Fri Sep 19 02:44:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fnq_50602/09_2025/9fnq_50602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fnq_50602/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fnq_50602/09_2025/9fnq_50602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fnq_50602/09_2025/9fnq_50602.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fnq_50602/09_2025/9fnq_50602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fnq_50602/09_2025/9fnq_50602.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F, G Time building chain proxies: 3.02, per 1000 atoms: 0.13 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 B 159 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 159 " - pdb=" SG CYS G 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: 1.90 Conformation dependent library (CDL) restraints added in 965.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.71 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: 3.80 Time building geometry restraints manager: 2.53 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 4.470 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 18.610 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.630 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (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 ARG 0.002 0.000 ARG B 194 TYR 0.014 0.001 TYR E 76 PHE 0.009 0.001 PHE G 321 TRP 0.008 0.001 TRP B 329 HIS 0.003 0.001 HIS F 186 Details of bonding type rmsd covalent geometry : bond 0.00334 (23247) covalent geometry : angle 0.55926 (31766) SS BOND : bond 0.00133 ( 7) SS BOND : angle 0.62896 ( 14) hydrogen bonds : bond 0.22699 ( 833) hydrogen bonds : angle 7.26466 ( 2394) *********************** 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 : 0.911 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: 0.6906 time to fit residues: 353.1376 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 : 0.898 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0870 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0470 chunk 111 optimal weight: 0.6980 overall best weight: 0.9660 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.164617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130754 restraints weight = 19364.834| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.53 r_work: 0.3365 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1366 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= 0.144 Angle : 0.528 4.572 31780 Z= 0.297 Chirality : 0.046 0.144 3332 Planarity : 0.004 0.031 4137 Dihedral : 4.642 32.481 3124 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.86 % Allowed : 5.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.15), residues: 2842 helix: 0.68 (0.22), residues: 504 sheet: 1.75 (0.15), residues: 1092 loop : -0.01 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 28 TYR 0.009 0.001 TYR D 357 PHE 0.012 0.001 PHE G 321 TRP 0.012 0.001 TRP F 329 HIS 0.003 0.001 HIS F 186 Details of bonding type rmsd covalent geometry : bond 0.00236 (23247) covalent geometry : angle 0.52824 (31766) SS BOND : bond 0.00258 ( 7) SS BOND : angle 0.83317 ( 14) hydrogen bonds : bond 0.05158 ( 833) hydrogen bonds : angle 4.96395 ( 2394) *********************** 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 328 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 0.944 Fit side-chains REVERT: A 84 GLU cc_start: 0.7487 (tt0) cc_final: 0.7168 (tp30) REVERT: A 138 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6514 (mm-30) REVERT: A 258 GLU cc_start: 0.7775 (tt0) cc_final: 0.7188 (tp30) REVERT: A 259 ILE cc_start: 0.8470 (mt) cc_final: 0.8226 (mm) REVERT: A 378 GLN cc_start: 0.7899 (mt0) cc_final: 0.7686 (pt0) REVERT: B 138 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: B 258 GLU cc_start: 0.7674 (tt0) cc_final: 0.7149 (tp30) REVERT: B 259 ILE cc_start: 0.8534 (mt) cc_final: 0.8215 (mm) REVERT: B 299 LYS cc_start: 0.8692 (mttt) cc_final: 0.7994 (mmmt) REVERT: B 378 GLN cc_start: 0.7886 (mt0) cc_final: 0.7513 (mm-40) REVERT: C 258 GLU cc_start: 0.7872 (tt0) cc_final: 0.7374 (tp30) REVERT: C 394 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8416 (ttt180) REVERT: D 66 LYS cc_start: 0.6406 (pttt) cc_final: 0.6185 (pttp) REVERT: D 258 GLU cc_start: 0.7736 (tt0) cc_final: 0.7169 (tp30) REVERT: D 378 GLN cc_start: 0.7929 (mt0) cc_final: 0.7594 (mm-40) REVERT: E 35 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6711 (tptt) REVERT: E 258 GLU cc_start: 0.7853 (tt0) cc_final: 0.7389 (tp30) REVERT: E 385 MET cc_start: 0.8790 (mmm) cc_final: 0.8570 (mmm) REVERT: F 29 GLU cc_start: 0.6423 (mp0) cc_final: 0.6218 (mp0) REVERT: F 35 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6576 (tppt) REVERT: F 258 GLU cc_start: 0.7793 (tt0) cc_final: 0.7197 (tp30) REVERT: F 259 ILE cc_start: 0.8500 (mt) cc_final: 0.8238 (mm) REVERT: F 277 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7574 (tt) REVERT: G 178 ASN cc_start: 0.8230 (t0) cc_final: 0.7943 (t0) REVERT: G 258 GLU cc_start: 0.7797 (tt0) cc_final: 0.7256 (tp30) REVERT: G 277 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7846 (tp) REVERT: G 299 LYS cc_start: 0.8627 (mttt) cc_final: 0.8264 (mttm) outliers start: 45 outliers final: 18 residues processed: 309 average time/residue: 0.6430 time to fit residues: 227.1838 Evaluate side-chains 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 250 VAL 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 206 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 170 optimal weight: 0.0970 chunk 165 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 195 GLN C 174 ASN C 378 GLN D 195 GLN E 195 GLN E 378 GLN F 378 GLN G 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.163388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130165 restraints weight = 19420.115| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.43 r_work: 0.3353 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1705 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= 0.147 Angle : 0.525 4.616 31780 Z= 0.294 Chirality : 0.045 0.141 3332 Planarity : 0.004 0.030 4137 Dihedral : 4.520 29.719 3120 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.99 % Allowed : 6.54 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.15), residues: 2842 helix: 0.96 (0.22), residues: 504 sheet: 1.67 (0.14), residues: 1092 loop : -0.00 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 362 TYR 0.008 0.001 TYR D 177 PHE 0.013 0.002 PHE G 321 TRP 0.010 0.001 TRP G 329 HIS 0.003 0.001 HIS F 186 Details of bonding type rmsd covalent geometry : bond 0.00238 (23247) covalent geometry : angle 0.52481 (31766) SS BOND : bond 0.00236 ( 7) SS BOND : angle 0.59634 ( 14) hydrogen bonds : bond 0.04966 ( 833) hydrogen bonds : angle 4.75151 ( 2394) *********************** 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 291 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 0.904 Fit side-chains REVERT: A 84 GLU cc_start: 0.7499 (tt0) cc_final: 0.7169 (tp30) REVERT: A 138 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.6597 (mm-30) REVERT: A 207 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8053 (t0) REVERT: A 258 GLU cc_start: 0.7709 (tt0) cc_final: 0.7148 (tp30) REVERT: A 259 ILE cc_start: 0.8455 (mt) cc_final: 0.8206 (mm) REVERT: A 277 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7779 (tt) REVERT: A 309 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7702 (ttmt) REVERT: B 138 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.6742 (mm-30) REVERT: B 258 GLU cc_start: 0.7719 (tt0) cc_final: 0.7208 (tp30) REVERT: B 259 ILE cc_start: 0.8536 (mt) cc_final: 0.8149 (mm) REVERT: B 299 LYS cc_start: 0.8684 (mttt) cc_final: 0.8003 (mmmt) REVERT: B 378 GLN cc_start: 0.7878 (mt0) cc_final: 0.7504 (mm-40) REVERT: C 258 GLU cc_start: 0.7766 (tt0) cc_final: 0.7304 (tp30) REVERT: C 394 ARG cc_start: 0.8591 (ttt180) cc_final: 0.8386 (ttt180) REVERT: D 35 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6098 (tppp) REVERT: D 258 GLU cc_start: 0.7675 (tt0) cc_final: 0.7140 (tp30) REVERT: D 378 GLN cc_start: 0.7945 (mt0) cc_final: 0.7597 (mm-40) REVERT: E 35 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6673 (tptt) REVERT: E 258 GLU cc_start: 0.7787 (tt0) cc_final: 0.7300 (tp30) REVERT: E 277 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8096 (tp) REVERT: E 309 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8185 (tptt) REVERT: F 29 GLU cc_start: 0.6469 (mp0) cc_final: 0.6248 (mp0) REVERT: F 35 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6619 (tppt) REVERT: F 84 GLU cc_start: 0.7600 (tt0) cc_final: 0.7337 (tp30) REVERT: F 207 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8079 (t0) REVERT: F 258 GLU cc_start: 0.7748 (tt0) cc_final: 0.7197 (tp30) REVERT: F 259 ILE cc_start: 0.8488 (mt) cc_final: 0.8235 (mm) REVERT: F 277 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7628 (tt) REVERT: G 178 ASN cc_start: 0.8271 (t0) cc_final: 0.7994 (t0) REVERT: G 258 GLU cc_start: 0.7733 (tt0) cc_final: 0.7217 (tp30) REVERT: G 277 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7901 (tt) REVERT: G 299 LYS cc_start: 0.8625 (mttt) cc_final: 0.8279 (mttm) outliers start: 48 outliers final: 21 residues processed: 272 average time/residue: 0.5363 time to fit residues: 169.9998 Evaluate side-chains 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 250 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 86 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 263 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 C 378 GLN D 174 ASN E 195 GLN E 378 GLN F 174 ASN F 378 GLN G 174 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122364 restraints weight = 19196.143| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.10 r_work: 0.3213 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.006 0.044 23254 Z= 0.332 Angle : 0.857 7.362 31780 Z= 0.487 Chirality : 0.059 0.319 3332 Planarity : 0.007 0.056 4137 Dihedral : 5.515 26.464 3120 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.44 % Allowed : 6.71 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.14), residues: 2842 helix: 0.17 (0.21), residues: 497 sheet: 1.63 (0.14), residues: 1120 loop : -0.56 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG D 362 TYR 0.024 0.003 TYR G 76 PHE 0.016 0.004 PHE C 245 TRP 0.019 0.003 TRP G 54 HIS 0.009 0.003 HIS F 186 Details of bonding type rmsd covalent geometry : bond 0.00626 (23247) covalent geometry : angle 0.85729 (31766) SS BOND : bond 0.00751 ( 7) SS BOND : angle 0.96952 ( 14) hydrogen bonds : bond 0.08260 ( 833) hydrogen bonds : angle 5.35824 ( 2394) *********************** 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 302 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 243 time to evaluate : 0.867 Fit side-chains REVERT: A 84 GLU cc_start: 0.7587 (tt0) cc_final: 0.7239 (tp30) REVERT: A 138 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: A 207 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: A 258 GLU cc_start: 0.8124 (tt0) cc_final: 0.7436 (tp30) REVERT: A 277 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8136 (tt) REVERT: A 309 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7922 (ttmt) REVERT: B 138 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6866 (mm-30) REVERT: B 207 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8298 (m-30) REVERT: B 277 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.7850 (tt) REVERT: B 378 GLN cc_start: 0.8034 (mt0) cc_final: 0.7625 (mm-40) REVERT: C 84 GLU cc_start: 0.7669 (tt0) cc_final: 0.7339 (tp30) REVERT: C 138 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6944 (mm-30) REVERT: C 258 GLU cc_start: 0.8086 (tt0) cc_final: 0.7508 (tp30) REVERT: D 35 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.6763 (tppp) REVERT: D 258 GLU cc_start: 0.7971 (tt0) cc_final: 0.7357 (tp30) REVERT: D 378 GLN cc_start: 0.8145 (mt0) cc_final: 0.7763 (mm-40) REVERT: E 258 GLU cc_start: 0.8060 (tt0) cc_final: 0.7359 (tp30) REVERT: E 309 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8367 (tptt) REVERT: F 35 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7181 (tppt) REVERT: F 84 GLU cc_start: 0.7740 (tt0) cc_final: 0.7423 (tp30) REVERT: F 243 ASN cc_start: 0.7283 (m-40) cc_final: 0.7063 (m110) REVERT: F 258 GLU cc_start: 0.8022 (tt0) cc_final: 0.7332 (tp30) REVERT: F 277 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8072 (tt) REVERT: F 311 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8428 (m-30) REVERT: G 138 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7072 (mm-30) REVERT: G 207 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8380 (m-30) REVERT: G 277 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8322 (tp) REVERT: G 309 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8384 (ttmt) outliers start: 59 outliers final: 21 residues processed: 277 average time/residue: 0.6056 time to fit residues: 193.1720 Evaluate side-chains 263 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 311 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 250 VAL Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 309 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 121 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 279 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 D 195 GLN E 195 GLN E 263 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 = 0.3800 r_free = 0.3800 target = 0.157919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127002 restraints weight = 19261.779| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.15 r_work: 0.3260 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 23254 Z= 0.197 Angle : 0.612 4.706 31780 Z= 0.347 Chirality : 0.048 0.149 3332 Planarity : 0.005 0.034 4137 Dihedral : 4.952 24.993 3117 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.15 % Allowed : 6.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.15), residues: 2842 helix: 0.47 (0.22), residues: 504 sheet: 1.48 (0.14), residues: 1106 loop : -0.18 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 362 TYR 0.014 0.002 TYR G 76 PHE 0.019 0.002 PHE G 321 TRP 0.013 0.002 TRP D 370 HIS 0.005 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00326 (23247) covalent geometry : angle 0.61186 (31766) SS BOND : bond 0.00313 ( 7) SS BOND : angle 0.57894 ( 14) hydrogen bonds : bond 0.05772 ( 833) hydrogen bonds : angle 5.01759 ( 2394) *********************** 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 277 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 0.876 Fit side-chains REVERT: A 84 GLU cc_start: 0.7556 (tt0) cc_final: 0.7174 (tp30) REVERT: A 138 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6636 (mm-30) REVERT: A 258 GLU cc_start: 0.8009 (tt0) cc_final: 0.7302 (tp30) REVERT: A 277 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7971 (tt) REVERT: A 309 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7781 (ttmt) REVERT: B 132 HIS cc_start: 0.8100 (m90) cc_final: 0.7898 (m-70) REVERT: B 138 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.6889 (mm-30) REVERT: B 258 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: B 378 GLN cc_start: 0.7852 (mt0) cc_final: 0.7475 (mm-40) REVERT: C 138 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.6853 (mm-30) REVERT: C 258 GLU cc_start: 0.7983 (tt0) cc_final: 0.7474 (tp30) REVERT: C 311 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: D 35 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6527 (tppp) REVERT: D 258 GLU cc_start: 0.7820 (tt0) cc_final: 0.7284 (tp30) REVERT: D 378 GLN cc_start: 0.8015 (mt0) cc_final: 0.7619 (mm-40) REVERT: E 35 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6970 (tptt) REVERT: E 258 GLU cc_start: 0.7981 (tt0) cc_final: 0.7329 (tp30) REVERT: E 277 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8068 (tt) REVERT: F 35 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6861 (tppt) REVERT: F 84 GLU cc_start: 0.7676 (tt0) cc_final: 0.7327 (tp30) REVERT: F 207 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8249 (t0) REVERT: F 258 GLU cc_start: 0.7880 (tt0) cc_final: 0.7227 (tp30) REVERT: F 277 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7875 (tt) REVERT: G 138 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.6948 (mm-30) REVERT: G 277 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8142 (tt) outliers start: 52 outliers final: 22 residues processed: 255 average time/residue: 0.5395 time to fit residues: 159.6892 Evaluate side-chains 259 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 258 GLU 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 250 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 227 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 130 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 281 optimal weight: 0.0040 chunk 250 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 overall best weight: 2.8798 ------------------------------------------------------------------------------- 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 D 195 GLN E 195 GLN F 132 HIS F 174 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124045 restraints weight = 19360.920| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.12 r_work: 0.3237 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2253 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= 0.243 Angle : 0.695 5.482 31780 Z= 0.395 Chirality : 0.051 0.202 3332 Planarity : 0.005 0.036 4137 Dihedral : 5.166 25.547 3117 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.65 % Allowed : 6.63 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.14), residues: 2842 helix: 0.32 (0.21), residues: 504 sheet: 1.53 (0.14), residues: 1113 loop : -0.45 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 362 TYR 0.015 0.002 TYR G 76 PHE 0.018 0.003 PHE G 321 TRP 0.015 0.002 TRP C 370 HIS 0.007 0.002 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00424 (23247) covalent geometry : angle 0.69538 (31766) SS BOND : bond 0.00462 ( 7) SS BOND : angle 0.63810 ( 14) hydrogen bonds : bond 0.06871 ( 833) hydrogen bonds : angle 5.12269 ( 2394) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 220 time to evaluate : 0.926 Fit side-chains REVERT: A 84 GLU cc_start: 0.7585 (tt0) cc_final: 0.7229 (tp30) REVERT: A 138 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.6753 (mm-30) REVERT: A 258 GLU cc_start: 0.7988 (tt0) cc_final: 0.7287 (tp30) REVERT: A 277 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8061 (tt) REVERT: A 309 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7850 (ttmt) REVERT: B 138 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: B 207 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8412 (m-30) REVERT: B 277 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 378 GLN cc_start: 0.7931 (mt0) cc_final: 0.7554 (mm-40) REVERT: C 84 GLU cc_start: 0.7672 (tt0) cc_final: 0.7326 (tp30) REVERT: C 138 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.6920 (mm-30) REVERT: C 258 GLU cc_start: 0.8060 (tt0) cc_final: 0.7537 (tp30) REVERT: D 35 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.6631 (tppp) REVERT: D 47 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5862 (mp) REVERT: D 258 GLU cc_start: 0.7939 (tt0) cc_final: 0.7382 (tp30) REVERT: D 378 GLN cc_start: 0.8035 (mt0) cc_final: 0.7675 (mm-40) REVERT: E 35 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7184 (tppt) REVERT: E 258 GLU cc_start: 0.8015 (tt0) cc_final: 0.7372 (tp30) REVERT: E 277 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8150 (tt) REVERT: F 35 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.6949 (tppt) REVERT: F 84 GLU cc_start: 0.7733 (tt0) cc_final: 0.7394 (tp30) REVERT: F 207 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8272 (t0) REVERT: F 258 GLU cc_start: 0.7990 (tt0) cc_final: 0.7339 (tp30) REVERT: F 277 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.7984 (tt) REVERT: F 311 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8399 (m-30) REVERT: G 138 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: G 207 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8319 (m-30) REVERT: G 277 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8229 (tt) outliers start: 64 outliers final: 25 residues processed: 260 average time/residue: 0.5547 time to fit residues: 168.1870 Evaluate side-chains 263 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain 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 47 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 47 ILE 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 159 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 D 195 GLN 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 = 0.3779 r_free = 0.3779 target = 0.155823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122599 restraints weight = 19020.103| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.07 r_work: 0.3261 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23254 Z= 0.275 Angle : 0.749 5.942 31780 Z= 0.426 Chirality : 0.054 0.249 3332 Planarity : 0.006 0.043 4137 Dihedral : 5.323 25.810 3117 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.57 % Allowed : 7.04 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.14), residues: 2842 helix: 0.19 (0.21), residues: 504 sheet: 1.50 (0.14), residues: 1113 loop : -0.55 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 362 TYR 0.017 0.002 TYR G 76 PHE 0.019 0.003 PHE G 321 TRP 0.016 0.002 TRP C 370 HIS 0.009 0.002 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00492 (23247) covalent geometry : angle 0.74916 (31766) SS BOND : bond 0.00551 ( 7) SS BOND : angle 0.70611 ( 14) hydrogen bonds : bond 0.07363 ( 833) hydrogen bonds : angle 5.20805 ( 2394) *********************** 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: 62 poor density : 221 time to evaluate : 0.927 Fit side-chains REVERT: A 76 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.6106 (t80) REVERT: A 84 GLU cc_start: 0.7476 (tt0) cc_final: 0.7133 (tp30) REVERT: A 138 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6668 (mm-30) REVERT: A 258 GLU cc_start: 0.7876 (tt0) cc_final: 0.7162 (tp30) REVERT: A 277 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 309 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8316 (tptt) REVERT: B 62 ASN cc_start: 0.7304 (m-40) cc_final: 0.7079 (m-40) REVERT: B 138 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.6853 (mm-30) REVERT: B 207 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: B 277 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7810 (tt) REVERT: B 378 GLN cc_start: 0.7894 (mt0) cc_final: 0.7519 (mm-40) REVERT: C 84 GLU cc_start: 0.7552 (tt0) cc_final: 0.7228 (tp30) REVERT: C 138 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: C 258 GLU cc_start: 0.7889 (tt0) cc_final: 0.7318 (tp30) REVERT: D 35 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6604 (tppp) REVERT: D 47 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.6054 (mp) REVERT: D 258 GLU cc_start: 0.7882 (tt0) cc_final: 0.7277 (tp30) REVERT: D 378 GLN cc_start: 0.7943 (mt0) cc_final: 0.7581 (mm-40) REVERT: E 258 GLU cc_start: 0.7916 (tt0) cc_final: 0.7248 (tp30) REVERT: E 277 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8086 (tt) REVERT: F 35 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7011 (tppt) REVERT: F 84 GLU cc_start: 0.7642 (tt0) cc_final: 0.7312 (tp30) REVERT: F 258 GLU cc_start: 0.7952 (tt0) cc_final: 0.7269 (tp30) REVERT: F 277 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8018 (tt) REVERT: F 311 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: G 138 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: G 207 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: G 277 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8207 (tp) outliers start: 62 outliers final: 28 residues processed: 261 average time/residue: 0.5742 time to fit residues: 174.3658 Evaluate side-chains 263 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 218 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 48 SER 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 48 SER Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 158 optimal weight: 4.9990 chunk 125 optimal weight: 0.0470 chunk 266 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- 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 D 195 GLN E 174 ASN E 195 GLN F 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126019 restraints weight = 19071.411| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.09 r_work: 0.3298 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 23254 Z= 0.182 Angle : 0.585 4.448 31780 Z= 0.331 Chirality : 0.047 0.147 3332 Planarity : 0.004 0.034 4137 Dihedral : 4.882 25.038 3117 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.11 % Allowed : 7.58 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.15), residues: 2842 helix: 0.56 (0.22), residues: 504 sheet: 1.43 (0.14), residues: 1106 loop : -0.23 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.011 0.002 TYR D 357 PHE 0.021 0.002 PHE G 321 TRP 0.012 0.001 TRP D 370 HIS 0.005 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00298 (23247) covalent geometry : angle 0.58461 (31766) SS BOND : bond 0.00255 ( 7) SS BOND : angle 0.49438 ( 14) hydrogen bonds : bond 0.05412 ( 833) hydrogen bonds : angle 4.92518 ( 2394) *********************** 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 273 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 1.067 Fit side-chains REVERT: A 84 GLU cc_start: 0.7573 (tt0) cc_final: 0.7243 (tp30) REVERT: A 138 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.6659 (mm-30) REVERT: A 258 GLU cc_start: 0.7870 (tt0) cc_final: 0.7244 (tp30) REVERT: A 277 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7918 (tt) REVERT: A 309 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7724 (ttmt) REVERT: B 62 ASN cc_start: 0.7104 (m-40) cc_final: 0.6898 (m-40) REVERT: B 138 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.6900 (mm-30) REVERT: B 207 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: B 277 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7713 (tt) REVERT: B 378 GLN cc_start: 0.7878 (mt0) cc_final: 0.7495 (mm-40) REVERT: C 42 MET cc_start: 0.4133 (ptp) cc_final: 0.3861 (mtt) REVERT: C 138 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.6885 (mm-30) REVERT: C 258 GLU cc_start: 0.7932 (tt0) cc_final: 0.7473 (tp30) REVERT: D 35 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6529 (tppp) REVERT: D 258 GLU cc_start: 0.7828 (tt0) cc_final: 0.7333 (tp30) REVERT: D 378 GLN cc_start: 0.7916 (mt0) cc_final: 0.7588 (mm-40) REVERT: E 35 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6956 (tptt) REVERT: E 258 GLU cc_start: 0.7892 (tt0) cc_final: 0.7315 (tp30) REVERT: E 277 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8021 (tt) REVERT: F 35 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6881 (tppt) REVERT: F 84 GLU cc_start: 0.7641 (tt0) cc_final: 0.7346 (tp30) REVERT: F 207 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8183 (t0) REVERT: F 258 GLU cc_start: 0.7876 (tt0) cc_final: 0.7290 (tp30) REVERT: F 277 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7818 (tt) REVERT: G 138 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.6961 (mm-30) REVERT: G 277 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8103 (tt) outliers start: 51 outliers final: 27 residues processed: 252 average time/residue: 0.5545 time to fit residues: 163.1832 Evaluate side-chains 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER 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 350 ASP Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL 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 250 VAL 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 48 SER 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 48 SER Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 10 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 221 optimal weight: 0.0670 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- 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 D 195 GLN E 174 ASN E 195 GLN F 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121766 restraints weight = 19038.254| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.09 r_work: 0.3241 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23254 Z= 0.298 Angle : 0.788 6.313 31780 Z= 0.448 Chirality : 0.055 0.268 3332 Planarity : 0.006 0.042 4137 Dihedral : 5.378 26.462 3117 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.07 % Allowed : 7.95 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.14), residues: 2842 helix: 0.14 (0.21), residues: 504 sheet: 1.56 (0.14), residues: 1106 loop : -0.62 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 362 TYR 0.018 0.003 TYR G 76 PHE 0.018 0.003 PHE F 321 TRP 0.017 0.003 TRP C 370 HIS 0.009 0.002 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00546 (23247) covalent geometry : angle 0.78785 (31766) SS BOND : bond 0.00635 ( 7) SS BOND : angle 0.72698 ( 14) hydrogen bonds : bond 0.07750 ( 833) hydrogen bonds : angle 5.25345 ( 2394) *********************** 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 271 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.853 Fit side-chains REVERT: A 84 GLU cc_start: 0.7553 (tt0) cc_final: 0.7213 (tp30) REVERT: A 138 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.6773 (mm-30) REVERT: A 258 GLU cc_start: 0.7949 (tt0) cc_final: 0.7239 (tp30) REVERT: A 277 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8126 (tt) REVERT: B 62 ASN cc_start: 0.7211 (m-40) cc_final: 0.7004 (m-40) REVERT: B 138 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: B 277 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7827 (tt) REVERT: B 378 GLN cc_start: 0.7986 (mt0) cc_final: 0.7626 (mm-40) REVERT: C 84 GLU cc_start: 0.7642 (tt0) cc_final: 0.7308 (tp30) REVERT: C 138 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: C 258 GLU cc_start: 0.7975 (tt0) cc_final: 0.7414 (tp30) REVERT: D 35 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.6768 (tppp) REVERT: D 258 GLU cc_start: 0.7956 (tt0) cc_final: 0.7376 (tp30) REVERT: D 378 GLN cc_start: 0.8039 (mt0) cc_final: 0.7698 (mm-40) REVERT: E 258 GLU cc_start: 0.7990 (tt0) cc_final: 0.7329 (tp30) REVERT: E 277 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8145 (tt) REVERT: F 35 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7110 (tppt) REVERT: F 84 GLU cc_start: 0.7718 (tt0) cc_final: 0.7394 (tp30) REVERT: F 258 GLU cc_start: 0.8054 (tt0) cc_final: 0.7389 (tp30) REVERT: F 277 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8073 (tt) REVERT: F 311 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8393 (m-30) REVERT: G 138 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7056 (mm-30) REVERT: G 207 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8341 (m-30) REVERT: G 277 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8252 (tp) outliers start: 50 outliers final: 26 residues processed: 251 average time/residue: 0.5703 time to fit residues: 165.7913 Evaluate side-chains 258 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 48 SER 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 48 SER Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 309 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 15 optimal weight: 5.9990 chunk 264 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 D 195 GLN E 174 ASN E 195 GLN F 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.158602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125450 restraints weight = 19217.502| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.11 r_work: 0.3287 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 23254 Z= 0.192 Angle : 0.606 4.974 31780 Z= 0.343 Chirality : 0.048 0.148 3332 Planarity : 0.005 0.034 4137 Dihedral : 4.956 25.130 3117 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.70 % Allowed : 8.41 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.15), residues: 2842 helix: 0.49 (0.22), residues: 504 sheet: 1.40 (0.14), residues: 1141 loop : -0.40 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 362 TYR 0.011 0.002 TYR D 357 PHE 0.021 0.002 PHE F 321 TRP 0.013 0.002 TRP C 370 HIS 0.006 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00317 (23247) covalent geometry : angle 0.60603 (31766) SS BOND : bond 0.00275 ( 7) SS BOND : angle 0.50722 ( 14) hydrogen bonds : bond 0.05667 ( 833) hydrogen bonds : angle 4.96852 ( 2394) ********************** 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 256 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.922 Fit side-chains REVERT: A 84 GLU cc_start: 0.7581 (tt0) cc_final: 0.7241 (tp30) REVERT: A 138 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.6685 (mm-30) REVERT: A 258 GLU cc_start: 0.7876 (tt0) cc_final: 0.7227 (tp30) REVERT: A 277 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7952 (tt) REVERT: B 138 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.6908 (mm-30) REVERT: B 258 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: B 277 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7727 (tt) REVERT: B 378 GLN cc_start: 0.7905 (mt0) cc_final: 0.7558 (mm-40) REVERT: C 138 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.6893 (mm-30) REVERT: C 258 GLU cc_start: 0.7895 (tt0) cc_final: 0.7409 (tp30) REVERT: D 35 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6560 (tppp) REVERT: D 258 GLU cc_start: 0.7875 (tt0) cc_final: 0.7359 (tp30) REVERT: D 378 GLN cc_start: 0.7964 (mt0) cc_final: 0.7609 (mm-40) REVERT: E 35 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7015 (tptt) REVERT: E 258 GLU cc_start: 0.7919 (tt0) cc_final: 0.7306 (tp30) REVERT: E 277 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8046 (tt) REVERT: F 35 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6926 (tppt) REVERT: F 84 GLU cc_start: 0.7650 (tt0) cc_final: 0.7349 (tp30) REVERT: F 207 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8194 (t0) REVERT: F 258 GLU cc_start: 0.7908 (tt0) cc_final: 0.7293 (tp30) REVERT: F 277 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7858 (tt) REVERT: G 138 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.6975 (mm-30) REVERT: G 277 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8139 (tt) outliers start: 41 outliers final: 24 residues processed: 239 average time/residue: 0.5648 time to fit residues: 156.9829 Evaluate side-chains 251 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 138 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 38 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 242 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 D 195 GLN E 174 ASN E 195 GLN F 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123950 restraints weight = 19136.635| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.07 r_work: 0.3269 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2394 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= 0.225 Angle : 0.662 5.047 31780 Z= 0.376 Chirality : 0.050 0.174 3332 Planarity : 0.005 0.034 4137 Dihedral : 5.087 25.792 3117 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.74 % Allowed : 8.32 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.14), residues: 2842 helix: 0.40 (0.21), residues: 504 sheet: 1.52 (0.14), residues: 1113 loop : -0.48 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 362 TYR 0.012 0.002 TYR D 357 PHE 0.021 0.002 PHE G 321 TRP 0.015 0.002 TRP C 370 HIS 0.007 0.002 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00385 (23247) covalent geometry : angle 0.66227 (31766) SS BOND : bond 0.00384 ( 7) SS BOND : angle 0.54847 ( 14) hydrogen bonds : bond 0.06484 ( 833) hydrogen bonds : angle 5.04007 ( 2394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11798.35 seconds wall clock time: 200 minutes 19.48 seconds (12019.48 seconds total)