Starting phenix.real_space_refine on Sun Apr 5 06:06:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ma7_63748/04_2026/9ma7_63748.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ma7_63748/04_2026/9ma7_63748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ma7_63748/04_2026/9ma7_63748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ma7_63748/04_2026/9ma7_63748.map" model { file = "/net/cci-nas-00/data/ceres_data/9ma7_63748/04_2026/9ma7_63748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ma7_63748/04_2026/9ma7_63748.cif" } resolution = 3.14 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= 0.001 sd= 0.025 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 36 5.16 5 C 5305 2.51 5 N 1414 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8435 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3158 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 27, 'TRANS': 386} Chain: "B" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 819 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "D" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 969 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Time building chain proxies: 1.96, per 1000 atoms: 0.23 Number of scatterers: 8435 At special positions: 0 Unit cell: (83.3, 122.4, 144.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1680 8.00 N 1414 7.00 C 5305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 33 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 289 " distance=2.02 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " 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: 0.72 Conformation dependent library (CDL) restraints added in 338.2 milliseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2002 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 22 sheets defined 4.7% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 78 through 81 removed outlier: 3.542A pdb=" N ASN A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.582A pdb=" N LEU A 266 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 267 " --> pdb=" O ARG A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.632A pdb=" N GLN B 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.868A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.239A pdb=" N GLY D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.645A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 32 removed outlier: 4.001A pdb=" N ASN E 32 " --> pdb=" O ILE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 32' Processing helix chain 'E' and resid 80 through 84 removed outlier: 4.033A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.991A pdb=" N GLY F 32 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.806A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.775A pdb=" N GLU G 84 " --> pdb=" O THR G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 7.084A pdb=" N GLU A 117 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N ASN A 139 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N SER A 115 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU A 116 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP A 44 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 118 " --> pdb=" O ASN A 42 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 35 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN A 58 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL A 37 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.946A pdb=" N GLY A 225 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.019A pdb=" N GLU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 166 removed outlier: 6.928A pdb=" N THR A 162 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR A 173 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 164 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 233 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 203 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 198 " --> pdb=" O GLY A 195 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 191 " --> pdb=" O CYS A 202 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 204 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL A 189 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 188 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 194 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 271 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 165 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 314 removed outlier: 6.274A pdb=" N ASN A 309 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ILE A 411 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 311 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N SER A 413 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE A 313 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 341 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N CYS A 355 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 324 removed outlier: 3.600A pdb=" N ALA A 373 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.820A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 5 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 71 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.264A pdb=" N GLU B 10 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY B 50 " --> pdb=" O PHE B 34 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET B 48 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.634A pdb=" N ALA C 10 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.634A pdb=" N ALA C 10 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.592A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET D 18 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 83 " --> pdb=" O MET D 18 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.501A pdb=" N GLU D 10 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR D 121 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 92 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 59 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 13 removed outlier: 7.634A pdb=" N LEU E 11 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 13 removed outlier: 7.634A pdb=" N LEU E 11 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 19 through 22 removed outlier: 3.517A pdb=" N ASP E 71 " --> pdb=" O SER E 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.788A pdb=" N GLN F 5 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 23 " --> pdb=" O GLN F 5 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.958A pdb=" N TRP F 35 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP F 37 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.505A pdb=" N ALA G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA G 85 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.505A pdb=" N ALA G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA G 85 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 18 through 23 removed outlier: 4.057A pdb=" N VAL G 18 " --> pdb=" O ILE G 76 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 699 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: 1.44 Time building geometry restraints manager: 0.96 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: 2724 1.34 - 1.46: 2138 1.46 - 1.59: 3730 1.59 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 8643 Sorted by residual: bond pdb=" C ASP D 112 " pdb=" N PRO D 113 " ideal model delta sigma weight residual 1.335 1.366 -0.031 8.70e-03 1.32e+04 1.30e+01 bond pdb=" N SER E 14 " pdb=" CA SER E 14 " ideal model delta sigma weight residual 1.452 1.483 -0.031 1.11e-02 8.12e+03 7.85e+00 bond pdb=" N TYR B 108 " pdb=" CA TYR B 108 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.18e-02 7.18e+03 7.84e+00 bond pdb=" N TYR B 80 " pdb=" CA TYR B 80 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.54e+00 bond pdb=" N ASP D 99 " pdb=" CA ASP D 99 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.27e-02 6.20e+03 7.37e+00 ... (remaining 8638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 11610 2.95 - 5.89: 158 5.89 - 8.84: 16 8.84 - 11.78: 1 11.78 - 14.73: 1 Bond angle restraints: 11786 Sorted by residual: angle pdb=" C TYR B 108 " pdb=" CA TYR B 108 " pdb=" CB TYR B 108 " ideal model delta sigma weight residual 115.27 100.54 14.73 2.00e+00 2.50e-01 5.42e+01 angle pdb=" O TYR B 108 " pdb=" C TYR B 108 " pdb=" N TYR B 109 " ideal model delta sigma weight residual 120.83 124.62 -3.79 7.40e-01 1.83e+00 2.62e+01 angle pdb=" CA SER E 14 " pdb=" C SER E 14 " pdb=" N PRO E 15 " ideal model delta sigma weight residual 117.84 123.40 -5.56 1.16e+00 7.43e-01 2.30e+01 angle pdb=" CA SER E 14 " pdb=" C SER E 14 " pdb=" O SER E 14 " ideal model delta sigma weight residual 120.66 116.19 4.47 1.03e+00 9.43e-01 1.88e+01 angle pdb=" CA ARG E 78 " pdb=" CB ARG E 78 " pdb=" CG ARG E 78 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.75e+01 ... (remaining 11781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4470 17.85 - 35.71: 484 35.71 - 53.56: 116 53.56 - 71.41: 19 71.41 - 89.27: 7 Dihedral angle restraints: 5096 sinusoidal: 1935 harmonic: 3161 Sorted by residual: dihedral pdb=" C TYR B 108 " pdb=" N TYR B 108 " pdb=" CA TYR B 108 " pdb=" CB TYR B 108 " ideal model delta harmonic sigma weight residual -122.60 -109.60 -13.00 0 2.50e+00 1.60e-01 2.71e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 50.12 42.88 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CA TYR D 102 " pdb=" C TYR D 102 " pdb=" N SER D 103 " pdb=" CA SER D 103 " ideal model delta harmonic sigma weight residual 180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1120 0.074 - 0.148: 176 0.148 - 0.222: 7 0.222 - 0.296: 4 0.296 - 0.370: 2 Chirality restraints: 1309 Sorted by residual: chirality pdb=" CA TYR B 108 " pdb=" N TYR B 108 " pdb=" C TYR B 108 " pdb=" CB TYR B 108 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA ASN B 106 " pdb=" N ASN B 106 " pdb=" C ASN B 106 " pdb=" CB ASN B 106 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA CYS A 367 " pdb=" N CYS A 367 " pdb=" C CYS A 367 " pdb=" CB CYS A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1306 not shown) Planarity restraints: 1527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 279 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C ASN A 279 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN A 279 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY A 280 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 100 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO E 101 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 101 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 101 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 44 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO E 45 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 45 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 45 " 0.034 5.00e-02 4.00e+02 ... (remaining 1524 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2520 2.82 - 3.34: 6625 3.34 - 3.86: 13735 3.86 - 4.38: 14876 4.38 - 4.90: 27216 Nonbonded interactions: 64972 Sorted by model distance: nonbonded pdb=" OG SER C 25 " pdb=" OD1 ASN C 28 " model vdw 2.300 3.040 nonbonded pdb=" NE2 GLN D 6 " pdb=" OG1 THR D 118 " model vdw 2.304 3.120 nonbonded pdb=" OG1 THR A 180 " pdb=" OG SER A 185 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR E 37 " pdb=" OE1 GLN E 90 " model vdw 2.338 3.040 nonbonded pdb=" N ASP B 112 " pdb=" OD1 ASP B 112 " model vdw 2.353 3.120 ... (remaining 64967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8653 Z= 0.227 Angle : 0.804 14.729 11806 Z= 0.446 Chirality : 0.053 0.370 1309 Planarity : 0.006 0.064 1527 Dihedral : 15.661 89.265 3064 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.10 % Favored : 94.71 % Rotamer: Outliers : 1.07 % Allowed : 23.50 % Favored : 75.43 % Cbeta Deviations : 0.10 % 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 are not related in a simple way. whole: -0.29 (0.26), residues: 1097 helix: -4.46 (0.40), residues: 6 sheet: 0.72 (0.24), residues: 466 loop : -0.88 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 17 TYR 0.032 0.002 TYR C 33 PHE 0.015 0.001 PHE A 17 TRP 0.031 0.002 TRP B 36 HIS 0.008 0.002 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8643) covalent geometry : angle 0.80250 (11786) SS BOND : bond 0.00508 ( 10) SS BOND : angle 1.53186 ( 20) hydrogen bonds : bond 0.27543 ( 267) hydrogen bonds : angle 10.15078 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.304 Fit side-chains REVERT: A 66 VAL cc_start: 0.8677 (p) cc_final: 0.8325 (t) REVERT: A 99 SER cc_start: 0.7949 (p) cc_final: 0.7167 (p) REVERT: A 137 MET cc_start: 0.7490 (mmt) cc_final: 0.7173 (mmp) REVERT: A 193 MET cc_start: 0.6540 (mtt) cc_final: 0.6285 (mtt) REVERT: A 273 TYR cc_start: 0.6245 (m-80) cc_final: 0.4958 (m-80) REVERT: A 275 PHE cc_start: 0.7310 (m-80) cc_final: 0.7047 (m-80) REVERT: A 368 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7231 (pp20) REVERT: A 394 LEU cc_start: 0.8107 (tp) cc_final: 0.7901 (tp) REVERT: A 410 VAL cc_start: 0.8307 (t) cc_final: 0.8095 (p) REVERT: B 4 LEU cc_start: 0.8193 (mp) cc_final: 0.7829 (tt) REVERT: B 20 VAL cc_start: 0.6982 (t) cc_final: 0.6677 (t) REVERT: C 95 SER cc_start: 0.7860 (m) cc_final: 0.7562 (p) REVERT: E 7 SER cc_start: 0.6213 (OUTLIER) cc_final: 0.5926 (p) REVERT: E 13 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7343 (tt) REVERT: E 14 SER cc_start: 0.5351 (OUTLIER) cc_final: 0.4863 (p) REVERT: E 31 SER cc_start: 0.8455 (m) cc_final: 0.8026 (t) REVERT: E 82 GLU cc_start: 0.7975 (mp0) cc_final: 0.7772 (mp0) outliers start: 10 outliers final: 1 residues processed: 190 average time/residue: 0.0804 time to fit residues: 21.7899 Evaluate side-chains 165 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 14 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN D 3 GLN D 6 GLN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN G 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.159739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.138805 restraints weight = 13234.335| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.81 r_work: 0.3805 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8653 Z= 0.198 Angle : 0.691 7.346 11806 Z= 0.365 Chirality : 0.048 0.149 1309 Planarity : 0.006 0.062 1527 Dihedral : 6.094 58.415 1208 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.56 % Favored : 95.26 % Rotamer: Outliers : 4.06 % Allowed : 22.86 % Favored : 73.08 % 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 are not related in a simple way. whole: -0.18 (0.26), residues: 1097 helix: -4.30 (0.48), residues: 6 sheet: 0.81 (0.24), residues: 473 loop : -0.84 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 62 TYR 0.030 0.002 TYR C 33 PHE 0.025 0.003 PHE B 34 TRP 0.020 0.002 TRP A 153 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8643) covalent geometry : angle 0.68977 (11786) SS BOND : bond 0.00354 ( 10) SS BOND : angle 1.05662 ( 20) hydrogen bonds : bond 0.05007 ( 267) hydrogen bonds : angle 7.07335 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7452 (mmp) cc_final: 0.7104 (mmp) REVERT: A 193 MET cc_start: 0.7159 (mtt) cc_final: 0.6886 (mtt) REVERT: A 385 SER cc_start: 0.7865 (t) cc_final: 0.7434 (p) REVERT: B 20 VAL cc_start: 0.6906 (t) cc_final: 0.6692 (t) REVERT: B 46 GLU cc_start: 0.6490 (mp0) cc_final: 0.6139 (mp0) REVERT: C 95 SER cc_start: 0.8401 (m) cc_final: 0.8118 (p) REVERT: D 74 MET cc_start: 0.6998 (mmm) cc_final: 0.6210 (mmm) REVERT: E 46 ARG cc_start: 0.8285 (mtm110) cc_final: 0.8001 (mtp-110) REVERT: F 33 TYR cc_start: 0.5522 (OUTLIER) cc_final: 0.5103 (m-80) REVERT: F 98 ARG cc_start: 0.5682 (ttm170) cc_final: 0.5150 (ttt-90) outliers start: 38 outliers final: 25 residues processed: 198 average time/residue: 0.0754 time to fit residues: 21.6935 Evaluate side-chains 195 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN D 3 GLN D 6 GLN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.154450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.134040 restraints weight = 12928.405| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.71 r_work: 0.3737 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8653 Z= 0.283 Angle : 0.751 11.653 11806 Z= 0.394 Chirality : 0.050 0.216 1309 Planarity : 0.006 0.059 1527 Dihedral : 5.467 19.726 1199 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.02 % Favored : 93.80 % Rotamer: Outliers : 5.77 % Allowed : 23.50 % Favored : 70.73 % 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 are not related in a simple way. whole: -0.33 (0.26), residues: 1097 helix: -4.20 (0.51), residues: 6 sheet: 0.83 (0.25), residues: 475 loop : -1.08 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 62 TYR 0.020 0.003 TYR G 99 PHE 0.035 0.003 PHE D 111 TRP 0.027 0.003 TRP C 36 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00650 ( 8643) covalent geometry : angle 0.74923 (11786) SS BOND : bond 0.00551 ( 10) SS BOND : angle 1.44790 ( 20) hydrogen bonds : bond 0.05517 ( 267) hydrogen bonds : angle 6.66695 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 0.302 Fit side-chains REVERT: A 53 ASP cc_start: 0.7204 (t70) cc_final: 0.6907 (t70) REVERT: A 70 ARG cc_start: 0.7889 (mmt180) cc_final: 0.6533 (mmm160) REVERT: A 100 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8190 (mtmm) REVERT: A 274 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.8013 (t) REVERT: A 385 SER cc_start: 0.8249 (t) cc_final: 0.7937 (p) REVERT: B 43 GLN cc_start: 0.8447 (mp10) cc_final: 0.7898 (mp10) REVERT: C 95 SER cc_start: 0.8542 (m) cc_final: 0.8269 (p) REVERT: D 74 MET cc_start: 0.7054 (mmm) cc_final: 0.6264 (mmm) REVERT: F 98 ARG cc_start: 0.6005 (ttm170) cc_final: 0.5573 (mtp85) REVERT: F 99 ASP cc_start: 0.0093 (OUTLIER) cc_final: -0.0272 (t70) REVERT: F 105 TYR cc_start: 0.2398 (OUTLIER) cc_final: 0.1278 (t80) outliers start: 54 outliers final: 33 residues processed: 202 average time/residue: 0.0790 time to fit residues: 22.7038 Evaluate side-chains 199 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 54 HIS Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 96 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 108 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.156720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.135825 restraints weight = 13181.781| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.81 r_work: 0.3755 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8653 Z= 0.171 Angle : 0.656 7.930 11806 Z= 0.339 Chirality : 0.046 0.141 1309 Planarity : 0.006 0.059 1527 Dihedral : 5.179 25.007 1199 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.47 % Favored : 94.35 % Rotamer: Outliers : 5.13 % Allowed : 24.15 % Favored : 70.73 % 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 are not related in a simple way. whole: -0.24 (0.26), residues: 1097 helix: -4.00 (0.61), residues: 6 sheet: 0.88 (0.25), residues: 474 loop : -1.01 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 46 TYR 0.031 0.002 TYR D 27 PHE 0.022 0.002 PHE A 275 TRP 0.022 0.002 TRP A 153 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8643) covalent geometry : angle 0.65566 (11786) SS BOND : bond 0.00328 ( 10) SS BOND : angle 0.94992 ( 20) hydrogen bonds : bond 0.04238 ( 267) hydrogen bonds : angle 6.35571 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7282 (t70) cc_final: 0.6953 (t70) REVERT: A 70 ARG cc_start: 0.7701 (mmt180) cc_final: 0.6486 (mmm160) REVERT: A 100 LYS cc_start: 0.8578 (mtmm) cc_final: 0.8177 (mtmm) REVERT: A 159 THR cc_start: 0.8308 (m) cc_final: 0.7111 (p) REVERT: A 349 THR cc_start: 0.7537 (t) cc_final: 0.7282 (m) REVERT: A 381 ASP cc_start: 0.7757 (t70) cc_final: 0.7395 (t0) REVERT: A 385 SER cc_start: 0.8328 (t) cc_final: 0.7986 (p) REVERT: B 43 GLN cc_start: 0.8413 (mp10) cc_final: 0.7852 (mp10) REVERT: B 111 MET cc_start: 0.7155 (mpp) cc_final: 0.6446 (mtt) REVERT: C 95 SER cc_start: 0.8542 (m) cc_final: 0.8242 (p) REVERT: D 74 MET cc_start: 0.6950 (mmm) cc_final: 0.6400 (mtm) REVERT: E 28 SER cc_start: 0.5914 (OUTLIER) cc_final: 0.5597 (p) REVERT: E 46 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.8123 (mtp-110) REVERT: E 82 GLU cc_start: 0.8076 (mp0) cc_final: 0.7774 (mp0) REVERT: F 98 ARG cc_start: 0.5782 (ttm170) cc_final: 0.5362 (mtp85) REVERT: F 99 ASP cc_start: 0.0592 (OUTLIER) cc_final: 0.0185 (t70) outliers start: 48 outliers final: 32 residues processed: 202 average time/residue: 0.0740 time to fit residues: 21.5199 Evaluate side-chains 201 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN G 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.156320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.135751 restraints weight = 12986.625| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.76 r_work: 0.3755 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8653 Z= 0.173 Angle : 0.647 7.099 11806 Z= 0.336 Chirality : 0.046 0.145 1309 Planarity : 0.005 0.061 1527 Dihedral : 5.131 24.169 1199 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.93 % Favored : 93.89 % Rotamer: Outliers : 5.88 % Allowed : 23.29 % Favored : 70.83 % 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 are not related in a simple way. whole: -0.24 (0.26), residues: 1097 helix: -4.11 (0.55), residues: 6 sheet: 0.91 (0.25), residues: 472 loop : -1.03 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 46 TYR 0.022 0.002 TYR A 288 PHE 0.022 0.002 PHE A 275 TRP 0.020 0.002 TRP C 36 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8643) covalent geometry : angle 0.64660 (11786) SS BOND : bond 0.00311 ( 10) SS BOND : angle 1.04398 ( 20) hydrogen bonds : bond 0.04228 ( 267) hydrogen bonds : angle 6.10094 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7202 (t70) cc_final: 0.6871 (t70) REVERT: A 70 ARG cc_start: 0.7682 (mmt180) cc_final: 0.6521 (mmm160) REVERT: A 100 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8167 (mtmm) REVERT: A 349 THR cc_start: 0.7483 (t) cc_final: 0.7234 (m) REVERT: A 381 ASP cc_start: 0.7729 (t70) cc_final: 0.7395 (t0) REVERT: A 385 SER cc_start: 0.8340 (t) cc_final: 0.8066 (p) REVERT: B 43 GLN cc_start: 0.8410 (mp10) cc_final: 0.7931 (mp10) REVERT: B 111 MET cc_start: 0.7120 (mpp) cc_final: 0.6628 (mtt) REVERT: C 95 SER cc_start: 0.8550 (m) cc_final: 0.8267 (p) REVERT: D 72 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6525 (pmt170) REVERT: E 28 SER cc_start: 0.5854 (OUTLIER) cc_final: 0.5567 (p) REVERT: E 46 ARG cc_start: 0.8442 (mtp-110) cc_final: 0.8205 (mtp-110) REVERT: E 82 GLU cc_start: 0.8085 (mp0) cc_final: 0.7803 (mp0) REVERT: F 98 ARG cc_start: 0.5844 (ttm170) cc_final: 0.5410 (mtp85) REVERT: F 99 ASP cc_start: 0.0937 (OUTLIER) cc_final: 0.0594 (t70) outliers start: 55 outliers final: 39 residues processed: 198 average time/residue: 0.0796 time to fit residues: 22.5533 Evaluate side-chains 208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 0.0030 chunk 62 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.158705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.138195 restraints weight = 12966.193| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.75 r_work: 0.3789 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8653 Z= 0.114 Angle : 0.606 7.522 11806 Z= 0.311 Chirality : 0.045 0.159 1309 Planarity : 0.005 0.056 1527 Dihedral : 4.800 21.557 1199 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.56 % Favored : 95.26 % Rotamer: Outliers : 4.70 % Allowed : 24.25 % Favored : 71.05 % 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 are not related in a simple way. whole: -0.12 (0.26), residues: 1097 helix: -4.11 (0.54), residues: 6 sheet: 0.97 (0.25), residues: 464 loop : -0.90 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.019 0.001 TYR A 288 PHE 0.020 0.002 PHE A 275 TRP 0.016 0.001 TRP A 153 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8643) covalent geometry : angle 0.60551 (11786) SS BOND : bond 0.00465 ( 10) SS BOND : angle 0.78924 ( 20) hydrogen bonds : bond 0.03452 ( 267) hydrogen bonds : angle 5.86133 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7234 (t70) cc_final: 0.6886 (t70) REVERT: A 100 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8138 (mtmm) REVERT: A 117 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7266 (mt-10) REVERT: A 349 THR cc_start: 0.7455 (t) cc_final: 0.7212 (m) REVERT: A 381 ASP cc_start: 0.7689 (t70) cc_final: 0.7364 (t0) REVERT: A 385 SER cc_start: 0.8332 (t) cc_final: 0.8023 (p) REVERT: B 43 GLN cc_start: 0.8378 (mp10) cc_final: 0.7916 (mp10) REVERT: B 67 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7563 (ttt180) REVERT: B 111 MET cc_start: 0.7001 (mpp) cc_final: 0.6531 (mtt) REVERT: C 95 SER cc_start: 0.8559 (m) cc_final: 0.8286 (p) REVERT: E 28 SER cc_start: 0.5780 (OUTLIER) cc_final: 0.5518 (p) REVERT: E 46 ARG cc_start: 0.8396 (mtp-110) cc_final: 0.8186 (mtp-110) REVERT: E 82 GLU cc_start: 0.8089 (mp0) cc_final: 0.7819 (mp0) REVERT: F 98 ARG cc_start: 0.5604 (ttm170) cc_final: 0.5214 (mmm160) REVERT: F 99 ASP cc_start: 0.0915 (OUTLIER) cc_final: 0.0553 (t70) outliers start: 44 outliers final: 32 residues processed: 194 average time/residue: 0.0727 time to fit residues: 20.5578 Evaluate side-chains 198 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.0670 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.157107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.136555 restraints weight = 13033.718| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.78 r_work: 0.3767 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8653 Z= 0.148 Angle : 0.619 7.415 11806 Z= 0.321 Chirality : 0.045 0.171 1309 Planarity : 0.005 0.059 1527 Dihedral : 4.835 23.075 1199 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.83 % Favored : 93.98 % Rotamer: Outliers : 5.13 % Allowed : 24.68 % Favored : 70.19 % 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 are not related in a simple way. whole: -0.12 (0.26), residues: 1097 helix: -4.08 (0.56), residues: 6 sheet: 0.93 (0.25), residues: 467 loop : -0.86 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.020 0.002 TYR A 288 PHE 0.018 0.002 PHE A 275 TRP 0.018 0.002 TRP A 153 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8643) covalent geometry : angle 0.61785 (11786) SS BOND : bond 0.00302 ( 10) SS BOND : angle 1.11136 ( 20) hydrogen bonds : bond 0.03799 ( 267) hydrogen bonds : angle 5.76506 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7162 (t70) cc_final: 0.6850 (t70) REVERT: A 70 ARG cc_start: 0.7665 (mmt180) cc_final: 0.6535 (mmm160) REVERT: A 100 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8173 (mtmm) REVERT: A 199 ASP cc_start: 0.7074 (t0) cc_final: 0.6798 (t0) REVERT: A 273 TYR cc_start: 0.7187 (m-80) cc_final: 0.6748 (m-10) REVERT: A 291 GLN cc_start: 0.7815 (mt0) cc_final: 0.7476 (mm-40) REVERT: A 349 THR cc_start: 0.7455 (t) cc_final: 0.7208 (m) REVERT: A 385 SER cc_start: 0.8369 (t) cc_final: 0.8065 (p) REVERT: B 6 GLN cc_start: 0.6546 (pm20) cc_final: 0.6115 (pm20) REVERT: B 43 GLN cc_start: 0.8384 (mp10) cc_final: 0.7957 (mp10) REVERT: B 67 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7577 (ttt180) REVERT: B 98 ARG cc_start: 0.7802 (tmm-80) cc_final: 0.6160 (tpt170) REVERT: B 111 MET cc_start: 0.6922 (mpp) cc_final: 0.6568 (mtt) REVERT: C 95 SER cc_start: 0.8564 (m) cc_final: 0.8300 (p) REVERT: D 6 GLN cc_start: 0.8139 (mt0) cc_final: 0.7657 (tt0) REVERT: E 28 SER cc_start: 0.5789 (OUTLIER) cc_final: 0.5520 (p) REVERT: E 46 ARG cc_start: 0.8467 (mtp-110) cc_final: 0.8251 (mtp-110) REVERT: E 82 GLU cc_start: 0.8088 (mp0) cc_final: 0.7817 (mp0) REVERT: F 98 ARG cc_start: 0.5721 (ttm170) cc_final: 0.5341 (mmm160) REVERT: F 99 ASP cc_start: 0.0900 (OUTLIER) cc_final: 0.0539 (t70) outliers start: 48 outliers final: 41 residues processed: 201 average time/residue: 0.0760 time to fit residues: 21.9041 Evaluate side-chains 215 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 104 optimal weight: 0.0470 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.156393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.136048 restraints weight = 12938.117| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.75 r_work: 0.3758 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8653 Z= 0.170 Angle : 0.638 9.074 11806 Z= 0.329 Chirality : 0.046 0.170 1309 Planarity : 0.005 0.059 1527 Dihedral : 4.934 24.097 1199 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.02 % Favored : 93.80 % Rotamer: Outliers : 5.34 % Allowed : 24.04 % Favored : 70.62 % 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 are not related in a simple way. whole: -0.19 (0.26), residues: 1097 helix: -4.08 (0.56), residues: 6 sheet: 0.89 (0.25), residues: 466 loop : -0.92 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 109 TYR 0.022 0.002 TYR A 288 PHE 0.018 0.002 PHE D 111 TRP 0.018 0.002 TRP A 153 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8643) covalent geometry : angle 0.63710 (11786) SS BOND : bond 0.00353 ( 10) SS BOND : angle 1.09911 ( 20) hydrogen bonds : bond 0.03970 ( 267) hydrogen bonds : angle 5.73350 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7157 (t70) cc_final: 0.6850 (t70) REVERT: A 70 ARG cc_start: 0.7691 (mmt180) cc_final: 0.6551 (mmm160) REVERT: A 114 VAL cc_start: 0.8243 (t) cc_final: 0.8040 (m) REVERT: A 199 ASP cc_start: 0.7074 (t0) cc_final: 0.6815 (t0) REVERT: A 385 SER cc_start: 0.8365 (t) cc_final: 0.8075 (p) REVERT: B 43 GLN cc_start: 0.8416 (mp10) cc_final: 0.7929 (mp10) REVERT: B 45 PRO cc_start: 0.6998 (Cg_endo) cc_final: 0.6729 (Cg_exo) REVERT: B 67 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7605 (ttt180) REVERT: B 98 ARG cc_start: 0.7797 (tmm-80) cc_final: 0.6186 (tpt170) REVERT: B 111 MET cc_start: 0.6900 (mpp) cc_final: 0.6564 (mtt) REVERT: C 95 SER cc_start: 0.8572 (m) cc_final: 0.8314 (p) REVERT: D 6 GLN cc_start: 0.8197 (mt0) cc_final: 0.7718 (tt0) REVERT: E 28 SER cc_start: 0.5775 (OUTLIER) cc_final: 0.5516 (p) REVERT: E 46 ARG cc_start: 0.8499 (mtp-110) cc_final: 0.8278 (mtp-110) REVERT: F 98 ARG cc_start: 0.5729 (ttm170) cc_final: 0.5329 (mmm160) REVERT: F 99 ASP cc_start: 0.1185 (OUTLIER) cc_final: 0.0826 (t70) outliers start: 50 outliers final: 40 residues processed: 200 average time/residue: 0.0788 time to fit residues: 22.4628 Evaluate side-chains 212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.156645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136147 restraints weight = 12936.248| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.76 r_work: 0.3764 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8653 Z= 0.153 Angle : 0.629 7.819 11806 Z= 0.324 Chirality : 0.045 0.165 1309 Planarity : 0.005 0.059 1527 Dihedral : 4.906 23.340 1199 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.83 % Favored : 93.98 % Rotamer: Outliers : 5.13 % Allowed : 24.57 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.26), residues: 1097 helix: -4.09 (0.55), residues: 6 sheet: 0.83 (0.24), residues: 476 loop : -0.91 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 109 TYR 0.024 0.002 TYR A 273 PHE 0.017 0.002 PHE A 275 TRP 0.015 0.002 TRP C 36 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8643) covalent geometry : angle 0.62839 (11786) SS BOND : bond 0.00302 ( 10) SS BOND : angle 1.04733 ( 20) hydrogen bonds : bond 0.03820 ( 267) hydrogen bonds : angle 5.69362 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7152 (t70) cc_final: 0.6844 (t70) REVERT: A 70 ARG cc_start: 0.7669 (mmt180) cc_final: 0.6538 (mmm160) REVERT: A 159 THR cc_start: 0.8312 (m) cc_final: 0.7035 (p) REVERT: A 199 ASP cc_start: 0.7087 (t0) cc_final: 0.6835 (t0) REVERT: A 352 ASP cc_start: 0.7251 (m-30) cc_final: 0.7048 (m-30) REVERT: A 385 SER cc_start: 0.8360 (t) cc_final: 0.8099 (p) REVERT: B 43 GLN cc_start: 0.8436 (mp10) cc_final: 0.7933 (mp10) REVERT: B 45 PRO cc_start: 0.7008 (Cg_endo) cc_final: 0.6730 (Cg_exo) REVERT: B 67 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7604 (ttt180) REVERT: B 98 ARG cc_start: 0.7798 (tmm-80) cc_final: 0.6206 (tpt170) REVERT: B 111 MET cc_start: 0.6866 (mpp) cc_final: 0.6599 (mtt) REVERT: C 95 SER cc_start: 0.8583 (m) cc_final: 0.8328 (p) REVERT: E 28 SER cc_start: 0.5736 (OUTLIER) cc_final: 0.5496 (p) REVERT: E 46 ARG cc_start: 0.8492 (mtp-110) cc_final: 0.8278 (mtp-110) REVERT: E 62 ARG cc_start: 0.7195 (mpp80) cc_final: 0.6466 (mtm180) REVERT: F 98 ARG cc_start: 0.5690 (ttm170) cc_final: 0.5297 (mmm160) REVERT: F 99 ASP cc_start: 0.1177 (OUTLIER) cc_final: 0.0823 (t70) outliers start: 48 outliers final: 41 residues processed: 204 average time/residue: 0.0766 time to fit residues: 22.4565 Evaluate side-chains 214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.0000 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN F 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.157866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.137295 restraints weight = 12936.422| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.78 r_work: 0.3775 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8653 Z= 0.124 Angle : 0.611 8.018 11806 Z= 0.314 Chirality : 0.045 0.161 1309 Planarity : 0.005 0.058 1527 Dihedral : 4.815 22.106 1199 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.29 % Favored : 94.53 % Rotamer: Outliers : 4.59 % Allowed : 24.89 % Favored : 70.51 % 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 are not related in a simple way. whole: -0.19 (0.26), residues: 1097 helix: -4.09 (0.55), residues: 6 sheet: 0.84 (0.24), residues: 468 loop : -0.87 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 109 TYR 0.028 0.002 TYR A 273 PHE 0.016 0.001 PHE A 275 TRP 0.015 0.002 TRP C 36 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8643) covalent geometry : angle 0.61031 (11786) SS BOND : bond 0.00258 ( 10) SS BOND : angle 0.85108 ( 20) hydrogen bonds : bond 0.03526 ( 267) hydrogen bonds : angle 5.65400 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7170 (t70) cc_final: 0.6859 (t70) REVERT: A 70 ARG cc_start: 0.7582 (mmt180) cc_final: 0.6449 (mmm160) REVERT: A 93 LEU cc_start: 0.8249 (mp) cc_final: 0.8043 (mt) REVERT: A 159 THR cc_start: 0.8269 (m) cc_final: 0.7017 (p) REVERT: A 199 ASP cc_start: 0.7103 (t0) cc_final: 0.6867 (t0) REVERT: A 381 ASP cc_start: 0.7707 (t70) cc_final: 0.7217 (t0) REVERT: A 385 SER cc_start: 0.8355 (t) cc_final: 0.8081 (p) REVERT: B 43 GLN cc_start: 0.8433 (mp10) cc_final: 0.7919 (mp10) REVERT: B 67 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7602 (ttt180) REVERT: B 98 ARG cc_start: 0.7791 (tmm-80) cc_final: 0.6171 (tpt170) REVERT: B 111 MET cc_start: 0.6818 (mpp) cc_final: 0.6598 (mtt) REVERT: C 95 SER cc_start: 0.8577 (m) cc_final: 0.8304 (p) REVERT: D 6 GLN cc_start: 0.8167 (mt0) cc_final: 0.7650 (tt0) REVERT: E 28 SER cc_start: 0.5706 (OUTLIER) cc_final: 0.5485 (p) REVERT: E 46 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.8196 (mtp-110) REVERT: E 62 ARG cc_start: 0.7223 (mpp80) cc_final: 0.6504 (mtm180) REVERT: F 98 ARG cc_start: 0.5602 (ttm170) cc_final: 0.5183 (mmm160) REVERT: F 99 ASP cc_start: 0.1126 (OUTLIER) cc_final: 0.0772 (t70) outliers start: 43 outliers final: 40 residues processed: 195 average time/residue: 0.0756 time to fit residues: 21.3185 Evaluate side-chains 211 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 104 optimal weight: 0.0980 chunk 106 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN F 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.158710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.138335 restraints weight = 12895.297| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.75 r_work: 0.3788 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8653 Z= 0.113 Angle : 0.598 8.070 11806 Z= 0.307 Chirality : 0.045 0.156 1309 Planarity : 0.005 0.058 1527 Dihedral : 4.703 22.720 1199 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.10 % Favored : 94.71 % Rotamer: Outliers : 4.49 % Allowed : 24.89 % Favored : 70.62 % 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 are not related in a simple way. whole: -0.11 (0.26), residues: 1097 helix: -4.09 (0.55), residues: 6 sheet: 0.90 (0.24), residues: 467 loop : -0.82 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 109 TYR 0.025 0.002 TYR A 273 PHE 0.016 0.001 PHE A 275 TRP 0.014 0.001 TRP C 36 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8643) covalent geometry : angle 0.59701 (11786) SS BOND : bond 0.00232 ( 10) SS BOND : angle 0.93051 ( 20) hydrogen bonds : bond 0.03348 ( 267) hydrogen bonds : angle 5.53734 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1937.57 seconds wall clock time: 33 minutes 54.95 seconds (2034.95 seconds total)