Starting phenix.real_space_refine on Sun Aug 24 06:48:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bcp_15967/08_2025/8bcp_15967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bcp_15967/08_2025/8bcp_15967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bcp_15967/08_2025/8bcp_15967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bcp_15967/08_2025/8bcp_15967.map" model { file = "/net/cci-nas-00/data/ceres_data/8bcp_15967/08_2025/8bcp_15967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bcp_15967/08_2025/8bcp_15967.cif" } resolution = 3.88 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= 0.002 sd= 0.014 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 66 5.16 5 C 11412 2.51 5 N 3021 2.21 5 O 3672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18171 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "D" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1243 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "H" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "A" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "B" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1243 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "E" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "F" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1243 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "I" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Time building chain proxies: 3.47, per 1000 atoms: 0.19 Number of scatterers: 18171 At special positions: 0 Unit cell: (154.014, 163.471, 104.027, 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 66 16.00 O 3672 8.00 N 3021 7.00 C 11412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 753.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 33 sheets defined 15.8% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 85 through 103 removed outlier: 3.656A pdb=" N GLN C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 85 through 103 Processing helix chain 'H' and resid 5 through 7 No H-bonds generated for 'chain 'H' and resid 5 through 7' Processing helix chain 'H' and resid 91 through 100 removed outlier: 3.600A pdb=" N TRP H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 190 Processing helix chain 'H' and resid 192 through 200 Processing helix chain 'H' and resid 275 through 287 Processing helix chain 'H' and resid 358 through 369 Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 85 through 103 removed outlier: 3.634A pdb=" N GLN A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 85 through 103 Processing helix chain 'G' and resid 5 through 7 No H-bonds generated for 'chain 'G' and resid 5 through 7' Processing helix chain 'G' and resid 91 through 100 removed outlier: 3.766A pdb=" N TRP G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 190 Processing helix chain 'G' and resid 192 through 200 Processing helix chain 'G' and resid 275 through 287 Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 85 through 103 removed outlier: 3.545A pdb=" N GLN E 89 " --> pdb=" O ASP E 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 18 Processing helix chain 'F' and resid 85 through 103 Processing helix chain 'I' and resid 5 through 7 No H-bonds generated for 'chain 'I' and resid 5 through 7' Processing helix chain 'I' and resid 91 through 100 removed outlier: 3.774A pdb=" N TRP I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 190 Processing helix chain 'I' and resid 192 through 200 Processing helix chain 'I' and resid 275 through 287 Processing helix chain 'I' and resid 358 through 369 Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.622A pdb=" N SER C 36 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 62 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 73 current: chain 'C' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 144 through 152 current: chain 'D' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 53 current: chain 'D' and resid 68 through 79 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 79 current: chain 'D' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 144 through 152 current: chain 'A' and resid 70 through 73 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 70 through 73 current: chain 'A' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 144 through 152 current: chain 'B' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 50 through 53 current: chain 'B' and resid 68 through 79 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 79 current: chain 'B' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 144 through 152 current: chain 'E' and resid 70 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 70 through 73 current: chain 'E' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 144 through 152 current: chain 'F' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 50 through 53 current: chain 'F' and resid 68 through 79 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 79 current: chain 'F' and resid 143 through 152 Processing sheet with id=AA3, first strand: chain 'C' and resid 108 through 112 Processing sheet with id=AA4, first strand: chain 'D' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'H' and resid 25 through 28 removed outlier: 4.362A pdb=" N ILE H 11 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE H 136 " --> pdb=" O ILE H 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 35 through 37 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 68 through 75 current: chain 'H' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 119 through 122 current: chain 'H' and resid 166 through 173 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 166 through 173 current: chain 'H' and resid 220 through 222 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 220 through 222 current: chain 'H' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 260 through 268 current: chain 'H' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 307 through 319 current: chain 'H' and resid 331 through 337 Processing sheet with id=AA7, first strand: chain 'H' and resid 43 through 46 removed outlier: 3.843A pdb=" N ILE H 45 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS H 59 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 79 through 80 Processing sheet with id=AA9, first strand: chain 'H' and resid 238 through 240 removed outlier: 3.642A pdb=" N GLY H 253 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 378 through 382 removed outlier: 3.514A pdb=" N ALA H 378 " --> pdb=" O THR H 403 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR H 403 " --> pdb=" O ALA H 378 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR H 380 " --> pdb=" O GLU H 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 389 through 390 removed outlier: 3.893A pdb=" N LEU H 390 " --> pdb=" O THR H 459 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS H 456 " --> pdb=" O VAL H 442 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR H 445 " --> pdb=" O THR H 413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 395 through 396 removed outlier: 3.660A pdb=" N LEU H 430 " --> pdb=" O LEU H 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.552A pdb=" N SER A 36 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 108 through 112 Processing sheet with id=AB6, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB7, first strand: chain 'G' and resid 9 through 14 removed outlier: 4.350A pdb=" N ILE G 11 " --> pdb=" O ILE G 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 28 current: chain 'G' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 68 through 75 current: chain 'G' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 119 through 122 current: chain 'G' and resid 143 through 158 removed outlier: 5.895A pdb=" N ILE G 152 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN G 172 " --> pdb=" O ILE G 152 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN G 158 " --> pdb=" O ARG G 166 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG G 166 " --> pdb=" O ASN G 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 166 through 173 current: chain 'G' and resid 220 through 222 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 220 through 222 current: chain 'G' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 260 through 268 current: chain 'G' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 307 through 319 current: chain 'G' and resid 331 through 337 Processing sheet with id=AB8, first strand: chain 'G' and resid 43 through 46 removed outlier: 3.828A pdb=" N ILE G 45 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS G 59 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 79 through 80 Processing sheet with id=AC1, first strand: chain 'G' and resid 238 through 240 removed outlier: 3.847A pdb=" N GLY G 253 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 378 through 382 removed outlier: 3.539A pdb=" N ALA G 378 " --> pdb=" O THR G 403 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 403 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR G 380 " --> pdb=" O GLU G 401 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 389 through 390 removed outlier: 3.711A pdb=" N LEU G 390 " --> pdb=" O THR G 459 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS G 456 " --> pdb=" O VAL G 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 395 through 396 removed outlier: 3.578A pdb=" N LEU G 430 " --> pdb=" O LEU G 396 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 35 through 36 removed outlier: 7.246A pdb=" N SER E 36 " --> pdb=" O VAL E 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 108 through 112 Processing sheet with id=AC7, first strand: chain 'F' and resid 108 through 111 Processing sheet with id=AC8, first strand: chain 'I' and resid 9 through 14 removed outlier: 4.373A pdb=" N ILE I 11 " --> pdb=" O ILE I 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 25 through 28 current: chain 'I' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 68 through 75 current: chain 'I' and resid 143 through 158 removed outlier: 5.723A pdb=" N ILE I 152 " --> pdb=" O ASN I 172 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN I 172 " --> pdb=" O ILE I 152 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN I 158 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG I 166 " --> pdb=" O ASN I 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 166 through 173 current: chain 'I' and resid 220 through 222 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 220 through 222 current: chain 'I' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 260 through 268 current: chain 'I' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 307 through 319 current: chain 'I' and resid 331 through 337 Processing sheet with id=AC9, first strand: chain 'I' and resid 43 through 46 removed outlier: 3.931A pdb=" N ILE I 45 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS I 59 " --> pdb=" O ILE I 45 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 79 through 80 Processing sheet with id=AD2, first strand: chain 'I' and resid 111 through 114 Processing sheet with id=AD3, first strand: chain 'I' and resid 238 through 240 removed outlier: 3.605A pdb=" N GLY I 253 " --> pdb=" O LEU I 240 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 378 through 382 removed outlier: 3.512A pdb=" N ALA I 378 " --> pdb=" O THR I 403 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR I 380 " --> pdb=" O GLU I 401 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 389 through 390 removed outlier: 3.723A pdb=" N LEU I 390 " --> pdb=" O THR I 459 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS I 456 " --> pdb=" O VAL I 442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 395 through 396 removed outlier: 3.673A pdb=" N LEU I 430 " --> pdb=" O LEU I 396 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1083 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: 2.30 Time building geometry restraints manager: 1.37 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: 6039 1.34 - 1.46: 3176 1.46 - 1.57: 9163 1.57 - 1.69: 0 1.69 - 1.81: 123 Bond restraints: 18501 Sorted by residual: bond pdb=" CB GLU E 91 " pdb=" CG GLU E 91 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" C GLU F 47 " pdb=" N PHE F 48 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.59e-02 3.96e+03 2.26e+00 bond pdb=" CA GLU B 47 " pdb=" CB GLU B 47 " ideal model delta sigma weight residual 1.536 1.562 -0.026 2.08e-02 2.31e+03 1.59e+00 bond pdb=" CA GLU G 302 " pdb=" CB GLU G 302 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.50e-02 4.44e+03 1.41e+00 bond pdb=" CB ASN B 115 " pdb=" CG ASN B 115 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.18e+00 ... (remaining 18496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 24559 1.41 - 2.83: 468 2.83 - 4.24: 106 4.24 - 5.65: 25 5.65 - 7.06: 3 Bond angle restraints: 25161 Sorted by residual: angle pdb=" CA GLU B 44 " pdb=" CB GLU B 44 " pdb=" CG GLU B 44 " ideal model delta sigma weight residual 114.10 120.42 -6.32 2.00e+00 2.50e-01 1.00e+01 angle pdb=" N GLY D 60 " pdb=" CA GLY D 60 " pdb=" C GLY D 60 " ideal model delta sigma weight residual 110.87 115.35 -4.48 1.54e+00 4.22e-01 8.45e+00 angle pdb=" CB GLU E 91 " pdb=" CG GLU E 91 " pdb=" CD GLU E 91 " ideal model delta sigma weight residual 112.60 117.51 -4.91 1.70e+00 3.46e-01 8.34e+00 angle pdb=" CA GLU E 91 " pdb=" CB GLU E 91 " pdb=" CG GLU E 91 " ideal model delta sigma weight residual 114.10 119.84 -5.74 2.00e+00 2.50e-01 8.23e+00 angle pdb=" CA GLU A 58 " pdb=" CB GLU A 58 " pdb=" CG GLU A 58 " ideal model delta sigma weight residual 114.10 119.66 -5.56 2.00e+00 2.50e-01 7.73e+00 ... (remaining 25156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 9566 17.89 - 35.79: 1198 35.79 - 53.68: 291 53.68 - 71.57: 59 71.57 - 89.47: 22 Dihedral angle restraints: 11136 sinusoidal: 4365 harmonic: 6771 Sorted by residual: dihedral pdb=" CA ASP I 141 " pdb=" CB ASP I 141 " pdb=" CG ASP I 141 " pdb=" OD1 ASP I 141 " ideal model delta sinusoidal sigma weight residual -30.00 -88.83 58.83 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ILE B 45 " pdb=" C ILE B 45 " pdb=" N ARG B 46 " pdb=" CA ARG B 46 " ideal model delta harmonic sigma weight residual 180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU G 107 " pdb=" CG GLU G 107 " pdb=" CD GLU G 107 " pdb=" OE1 GLU G 107 " ideal model delta sinusoidal sigma weight residual 0.00 89.47 -89.47 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 11133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1832 0.031 - 0.061: 658 0.061 - 0.092: 220 0.092 - 0.122: 193 0.122 - 0.153: 16 Chirality restraints: 2919 Sorted by residual: chirality pdb=" CA ASN B 115 " pdb=" N ASN B 115 " pdb=" C ASN B 115 " pdb=" CB ASN B 115 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA PRO F 64 " pdb=" N PRO F 64 " pdb=" C PRO F 64 " pdb=" CB PRO F 64 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA PRO B 64 " pdb=" N PRO B 64 " pdb=" C PRO B 64 " pdb=" CB PRO B 64 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 2916 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 115 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C ASN B 115 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN B 115 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY B 116 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 58 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" CD GLU B 58 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU B 58 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 58 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 63 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO F 64 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 64 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 64 " 0.026 5.00e-02 4.00e+02 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 692 2.70 - 3.25: 17681 3.25 - 3.80: 27836 3.80 - 4.35: 34983 4.35 - 4.90: 60889 Nonbonded interactions: 142081 Sorted by model distance: nonbonded pdb=" OG SER E 36 " pdb=" OH TYR E 50 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASN B 115 " pdb=" OG SER B 117 " model vdw 2.180 3.040 nonbonded pdb=" OD1 ASN F 115 " pdb=" OG SER F 117 " model vdw 2.200 3.040 nonbonded pdb=" O THR D 99 " pdb=" OG1 THR D 103 " model vdw 2.214 3.040 nonbonded pdb=" O THR B 99 " pdb=" OG1 THR B 103 " model vdw 2.215 3.040 ... (remaining 142076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 156) selection = chain 'B' selection = (chain 'C' and resid 1 through 156) selection = chain 'D' selection = (chain 'E' and resid 1 through 156) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.130 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.060 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18501 Z= 0.121 Angle : 0.528 7.063 25161 Z= 0.286 Chirality : 0.043 0.153 2919 Planarity : 0.004 0.057 3264 Dihedral : 17.057 89.469 6792 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Rotamer: Outliers : 0.30 % Allowed : 28.00 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2319 helix: 1.70 (0.29), residues: 318 sheet: -0.11 (0.20), residues: 780 loop : -1.27 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 157 TYR 0.019 0.001 TYR H 303 PHE 0.032 0.001 PHE I 231 TRP 0.008 0.001 TRP I 144 HIS 0.004 0.001 HIS H 318 Details of bonding type rmsd covalent geometry : bond 0.00266 (18501) covalent geometry : angle 0.52824 (25161) hydrogen bonds : bond 0.19370 ( 386) hydrogen bonds : angle 7.48216 ( 1083) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 571 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: C 103 THR cc_start: 0.4594 (p) cc_final: 0.4344 (p) REVERT: D 41 LYS cc_start: 0.6069 (mttm) cc_final: 0.5631 (tptp) REVERT: D 122 GLU cc_start: 0.6353 (pt0) cc_final: 0.6046 (pm20) REVERT: D 156 ARG cc_start: 0.4413 (pmt-80) cc_final: 0.3206 (tpm170) REVERT: H 1 MET cc_start: 0.6133 (ttp) cc_final: 0.5853 (ttp) REVERT: H 139 LEU cc_start: 0.7109 (tt) cc_final: 0.6729 (tt) REVERT: H 347 ASP cc_start: 0.5862 (p0) cc_final: 0.5443 (t0) REVERT: A 1 MET cc_start: 0.5695 (mpp) cc_final: 0.5107 (mmt) REVERT: A 29 ASN cc_start: 0.7357 (m110) cc_final: 0.6873 (m110) REVERT: B 1 MET cc_start: 0.2613 (pmm) cc_final: 0.0662 (mmm) REVERT: B 86 ILE cc_start: 0.6285 (tt) cc_final: 0.5620 (tt) REVERT: B 132 SER cc_start: 0.4907 (t) cc_final: 0.4284 (m) REVERT: G 189 ILE cc_start: 0.5985 (mm) cc_final: 0.5686 (mm) REVERT: F 83 LYS cc_start: 0.6358 (mtmm) cc_final: 0.6059 (mttt) REVERT: F 101 ILE cc_start: 0.7851 (mm) cc_final: 0.7555 (mm) REVERT: I 129 HIS cc_start: 0.4165 (m-70) cc_final: 0.3680 (m-70) outliers start: 6 outliers final: 1 residues processed: 574 average time/residue: 0.1211 time to fit residues: 104.5752 Evaluate side-chains 368 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 0.0270 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 87 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 ASN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 GLN A 106 ASN B 54 HIS B 67 GLN B 89 GLN G 38 GLN G 122 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS F 23 GLN F 68 GLN I 153 ASN I 219 ASN I 243 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122498 restraints weight = 27790.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122365 restraints weight = 23312.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122291 restraints weight = 22274.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122686 restraints weight = 20025.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122829 restraints weight = 17739.912| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 18501 Z= 0.256 Angle : 0.776 11.032 25161 Z= 0.412 Chirality : 0.052 0.296 2919 Planarity : 0.006 0.079 3264 Dihedral : 4.749 33.628 2513 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.67 % Favored : 96.21 % Rotamer: Outliers : 7.01 % Allowed : 24.54 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.17), residues: 2319 helix: 0.85 (0.26), residues: 324 sheet: -0.40 (0.19), residues: 762 loop : -1.40 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 56 TYR 0.026 0.003 TYR F 62 PHE 0.037 0.003 PHE I 12 TRP 0.030 0.004 TRP H 144 HIS 0.006 0.002 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00583 (18501) covalent geometry : angle 0.77639 (25161) hydrogen bonds : bond 0.04877 ( 386) hydrogen bonds : angle 5.33801 ( 1083) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 410 time to evaluate : 0.592 Fit side-chains REVERT: C 72 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7671 (tp) REVERT: C 91 GLU cc_start: 0.6492 (tm-30) cc_final: 0.6073 (tm-30) REVERT: D 122 GLU cc_start: 0.7018 (pt0) cc_final: 0.6751 (pm20) REVERT: D 156 ARG cc_start: 0.5292 (pmt-80) cc_final: 0.3554 (tpm170) REVERT: H 63 ASP cc_start: 0.6067 (p0) cc_final: 0.5776 (m-30) REVERT: H 120 MET cc_start: 0.6309 (pmm) cc_final: 0.5315 (pmm) REVERT: H 197 MET cc_start: 0.7551 (mmm) cc_final: 0.7271 (ttm) REVERT: H 278 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.6026 (mm-30) REVERT: H 347 ASP cc_start: 0.6474 (p0) cc_final: 0.6051 (t0) REVERT: A 72 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7998 (tp) REVERT: B 1 MET cc_start: 0.3692 (pmm) cc_final: 0.1591 (mmm) REVERT: B 34 ASN cc_start: 0.6796 (t0) cc_final: 0.6544 (t0) REVERT: B 69 TRP cc_start: 0.8039 (m100) cc_final: 0.6935 (m100) REVERT: G 63 ASP cc_start: 0.5082 (OUTLIER) cc_final: 0.4332 (m-30) REVERT: G 172 ASN cc_start: 0.8315 (m-40) cc_final: 0.8104 (m-40) REVERT: G 373 THR cc_start: 0.6838 (p) cc_final: 0.6477 (p) REVERT: E 2 ASP cc_start: 0.7643 (t0) cc_final: 0.7382 (t0) REVERT: E 26 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5601 (mm-30) REVERT: F 11 MET cc_start: 0.7339 (tpp) cc_final: 0.7110 (tpp) REVERT: F 58 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5733 (tm-30) REVERT: F 62 TYR cc_start: 0.8155 (m-10) cc_final: 0.7699 (m-80) REVERT: I 120 MET cc_start: 0.6516 (ptm) cc_final: 0.6179 (ptt) REVERT: I 180 ASP cc_start: 0.6147 (OUTLIER) cc_final: 0.5896 (t0) outliers start: 142 outliers final: 68 residues processed: 521 average time/residue: 0.1055 time to fit residues: 86.1362 Evaluate side-chains 400 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 325 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 149 SER Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 156 optimal weight: 0.3980 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 69 optimal weight: 40.0000 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 223 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN A 153 GLN B 89 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN G 200 GLN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN I 62 ASN I 151 GLN I 219 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.117693 restraints weight = 27827.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117126 restraints weight = 28715.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118041 restraints weight = 25992.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118571 restraints weight = 20508.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118721 restraints weight = 17284.812| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18501 Z= 0.186 Angle : 0.611 9.377 25161 Z= 0.323 Chirality : 0.048 0.567 2919 Planarity : 0.004 0.048 3264 Dihedral : 4.466 34.752 2513 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.20 % Rotamer: Outliers : 5.48 % Allowed : 25.63 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.17), residues: 2319 helix: 1.15 (0.28), residues: 330 sheet: -0.88 (0.18), residues: 876 loop : -1.21 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 56 TYR 0.027 0.002 TYR I 222 PHE 0.018 0.002 PHE H 72 TRP 0.027 0.002 TRP D 69 HIS 0.010 0.001 HIS I 318 Details of bonding type rmsd covalent geometry : bond 0.00420 (18501) covalent geometry : angle 0.61146 (25161) hydrogen bonds : bond 0.04453 ( 386) hydrogen bonds : angle 5.12747 ( 1083) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 349 time to evaluate : 0.550 Fit side-chains REVERT: C 72 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8054 (tp) REVERT: D 18 GLN cc_start: 0.7465 (mt0) cc_final: 0.7256 (mt0) REVERT: D 122 GLU cc_start: 0.7241 (pt0) cc_final: 0.7002 (pm20) REVERT: D 156 ARG cc_start: 0.6229 (pmt-80) cc_final: 0.3808 (tpp-160) REVERT: H 23 THR cc_start: 0.8627 (p) cc_final: 0.8312 (t) REVERT: H 63 ASP cc_start: 0.6962 (p0) cc_final: 0.6261 (m-30) REVERT: H 142 LYS cc_start: 0.7673 (mmmt) cc_final: 0.6944 (mttt) REVERT: B 18 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6110 (mp10) REVERT: B 69 TRP cc_start: 0.8680 (m100) cc_final: 0.7733 (m100) REVERT: B 80 ASP cc_start: 0.7065 (t0) cc_final: 0.6520 (t0) REVERT: B 91 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5451 (tm-30) REVERT: G 63 ASP cc_start: 0.5778 (OUTLIER) cc_final: 0.4714 (m-30) REVERT: G 191 ILE cc_start: 0.7571 (pt) cc_final: 0.7319 (pt) REVERT: G 370 ASP cc_start: 0.7848 (t70) cc_final: 0.7460 (t70) REVERT: E 18 GLN cc_start: 0.7069 (mt0) cc_final: 0.6869 (mt0) REVERT: F 73 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7874 (tm-30) REVERT: F 101 ILE cc_start: 0.8291 (mm) cc_final: 0.8060 (mm) REVERT: I 34 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8249 (mt) REVERT: I 76 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8495 (mp) REVERT: I 139 LEU cc_start: 0.8412 (tt) cc_final: 0.8139 (tp) REVERT: I 180 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.7069 (t0) REVERT: I 200 GLN cc_start: 0.8018 (tp40) cc_final: 0.7817 (tp-100) outliers start: 111 outliers final: 55 residues processed: 436 average time/residue: 0.1102 time to fit residues: 75.7608 Evaluate side-chains 348 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 286 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 4 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 0 optimal weight: 10.0000 chunk 208 optimal weight: 0.6980 chunk 222 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 200 optimal weight: 0.0050 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120347 restraints weight = 27737.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119316 restraints weight = 27600.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119658 restraints weight = 25113.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120254 restraints weight = 21755.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120616 restraints weight = 17977.574| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18501 Z= 0.113 Angle : 0.537 7.246 25161 Z= 0.278 Chirality : 0.044 0.220 2919 Planarity : 0.004 0.043 3264 Dihedral : 4.168 34.580 2513 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.20 % Rotamer: Outliers : 4.35 % Allowed : 27.31 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.17), residues: 2319 helix: 1.47 (0.28), residues: 336 sheet: -0.55 (0.18), residues: 825 loop : -1.15 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 292 TYR 0.021 0.001 TYR H 303 PHE 0.020 0.001 PHE C 119 TRP 0.017 0.001 TRP I 70 HIS 0.007 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00256 (18501) covalent geometry : angle 0.53689 (25161) hydrogen bonds : bond 0.03141 ( 386) hydrogen bonds : angle 4.77388 ( 1083) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 307 time to evaluate : 0.507 Fit side-chains REVERT: C 30 ASN cc_start: 0.7427 (t0) cc_final: 0.7169 (t0) REVERT: C 91 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6368 (tm-30) REVERT: D 122 GLU cc_start: 0.7460 (pt0) cc_final: 0.7125 (pm20) REVERT: D 156 ARG cc_start: 0.6191 (pmt-80) cc_final: 0.3685 (tpm170) REVERT: H 23 THR cc_start: 0.8843 (p) cc_final: 0.8456 (t) REVERT: H 63 ASP cc_start: 0.6890 (p0) cc_final: 0.6282 (m-30) REVERT: H 142 LYS cc_start: 0.7759 (mmmt) cc_final: 0.7114 (mttt) REVERT: A 113 LYS cc_start: 0.7464 (tttt) cc_final: 0.6760 (mmtt) REVERT: B 69 TRP cc_start: 0.8620 (m100) cc_final: 0.7817 (m100) REVERT: B 80 ASP cc_start: 0.7112 (t0) cc_final: 0.6587 (t0) REVERT: B 91 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5435 (tm-30) REVERT: B 96 ASP cc_start: 0.7262 (t0) cc_final: 0.6672 (m-30) REVERT: G 191 ILE cc_start: 0.7227 (pt) cc_final: 0.6939 (pt) REVERT: G 200 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6483 (pt0) REVERT: G 261 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8845 (tt) REVERT: E 4 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.5664 (ttp80) REVERT: F 58 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: I 180 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7090 (t0) REVERT: I 200 GLN cc_start: 0.7812 (tp40) cc_final: 0.7606 (tp40) outliers start: 88 outliers final: 52 residues processed: 371 average time/residue: 0.1015 time to fit residues: 60.1647 Evaluate side-chains 347 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 289 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 403 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 108 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 144 optimal weight: 0.6980 chunk 147 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 150 optimal weight: 0.0870 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN I 153 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119025 restraints weight = 27754.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117869 restraints weight = 27080.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118498 restraints weight = 26689.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119029 restraints weight = 21928.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119147 restraints weight = 17992.864| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.7711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18501 Z= 0.115 Angle : 0.523 7.408 25161 Z= 0.270 Chirality : 0.044 0.207 2919 Planarity : 0.004 0.042 3264 Dihedral : 4.036 32.399 2513 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.77 % Rotamer: Outliers : 4.74 % Allowed : 26.62 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.17), residues: 2319 helix: 1.63 (0.28), residues: 333 sheet: -0.57 (0.18), residues: 834 loop : -1.14 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 247 TYR 0.012 0.001 TYR G 222 PHE 0.027 0.001 PHE C 119 TRP 0.013 0.001 TRP I 70 HIS 0.006 0.001 HIS I 318 Details of bonding type rmsd covalent geometry : bond 0.00263 (18501) covalent geometry : angle 0.52337 (25161) hydrogen bonds : bond 0.03075 ( 386) hydrogen bonds : angle 4.57357 ( 1083) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 306 time to evaluate : 0.670 Fit side-chains REVERT: C 91 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6730 (tm-30) REVERT: D 122 GLU cc_start: 0.7409 (pt0) cc_final: 0.7148 (pm20) REVERT: D 156 ARG cc_start: 0.6220 (pmt-80) cc_final: 0.3710 (tpm170) REVERT: H 2 SER cc_start: 0.7442 (p) cc_final: 0.7116 (m) REVERT: H 23 THR cc_start: 0.8809 (p) cc_final: 0.8463 (t) REVERT: H 63 ASP cc_start: 0.6986 (p0) cc_final: 0.6438 (m-30) REVERT: H 69 GLU cc_start: 0.7591 (tt0) cc_final: 0.7319 (tm-30) REVERT: H 142 LYS cc_start: 0.7788 (mmmt) cc_final: 0.7361 (mttt) REVERT: A 79 TYR cc_start: 0.7628 (m-80) cc_final: 0.6641 (m-80) REVERT: A 113 LYS cc_start: 0.7330 (tttt) cc_final: 0.6751 (mmtt) REVERT: B 18 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6615 (mp10) REVERT: B 45 ILE cc_start: 0.6888 (mm) cc_final: 0.6471 (mm) REVERT: B 69 TRP cc_start: 0.8626 (m100) cc_final: 0.7840 (m100) REVERT: B 70 MET cc_start: 0.7277 (tpp) cc_final: 0.6985 (mmt) REVERT: B 80 ASP cc_start: 0.7404 (t0) cc_final: 0.6714 (t0) REVERT: B 89 GLN cc_start: 0.6839 (mt0) cc_final: 0.6629 (mt0) REVERT: B 91 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5317 (tm-30) REVERT: B 96 ASP cc_start: 0.7245 (t0) cc_final: 0.6830 (m-30) REVERT: G 63 ASP cc_start: 0.5842 (OUTLIER) cc_final: 0.4982 (m-30) REVERT: G 191 ILE cc_start: 0.7349 (pt) cc_final: 0.7037 (pt) REVERT: G 247 ARG cc_start: 0.8024 (ttm110) cc_final: 0.7109 (mtm180) REVERT: G 261 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8955 (tt) REVERT: E 4 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6500 (ttp80) REVERT: E 11 MET cc_start: 0.7483 (ttm) cc_final: 0.6823 (tpt) REVERT: F 58 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6618 (tm-30) REVERT: F 70 MET cc_start: 0.7378 (tpp) cc_final: 0.7141 (tpp) REVERT: F 73 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7766 (tm-30) REVERT: I 210 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8922 (pt) outliers start: 96 outliers final: 60 residues processed: 380 average time/residue: 0.1064 time to fit residues: 64.6243 Evaluate side-chains 360 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 293 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 403 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 162 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN H 126 ASN H 318 HIS A 115 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN I 4 GLN I 235 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116266 restraints weight = 27643.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115568 restraints weight = 24969.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115913 restraints weight = 22270.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116140 restraints weight = 20758.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116398 restraints weight = 18580.837| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.8735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18501 Z= 0.155 Angle : 0.577 10.655 25161 Z= 0.297 Chirality : 0.045 0.202 2919 Planarity : 0.004 0.044 3264 Dihedral : 4.223 32.611 2513 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 5.23 % Allowed : 26.86 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.17), residues: 2319 helix: 1.46 (0.27), residues: 333 sheet: -0.64 (0.18), residues: 849 loop : -1.06 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 157 TYR 0.016 0.002 TYR I 280 PHE 0.014 0.001 PHE H 231 TRP 0.016 0.001 TRP I 144 HIS 0.006 0.001 HIS I 318 Details of bonding type rmsd covalent geometry : bond 0.00360 (18501) covalent geometry : angle 0.57689 (25161) hydrogen bonds : bond 0.03355 ( 386) hydrogen bonds : angle 4.59782 ( 1083) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 312 time to evaluate : 0.563 Fit side-chains REVERT: D 18 GLN cc_start: 0.7658 (mt0) cc_final: 0.7352 (mt0) REVERT: D 45 ILE cc_start: 0.6494 (mm) cc_final: 0.6246 (mm) REVERT: D 156 ARG cc_start: 0.6513 (pmt-80) cc_final: 0.3898 (tpm170) REVERT: H 2 SER cc_start: 0.6944 (p) cc_final: 0.6626 (m) REVERT: H 23 THR cc_start: 0.8811 (p) cc_final: 0.8510 (t) REVERT: H 63 ASP cc_start: 0.6988 (p0) cc_final: 0.6329 (m-30) REVERT: H 142 LYS cc_start: 0.7800 (mmmt) cc_final: 0.7443 (mttt) REVERT: H 283 LEU cc_start: 0.7042 (mt) cc_final: 0.6373 (mt) REVERT: H 327 ASP cc_start: 0.6857 (t0) cc_final: 0.6560 (t0) REVERT: H 370 ASP cc_start: 0.6184 (t70) cc_final: 0.5901 (t70) REVERT: A 1 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7337 (pmm) REVERT: A 79 TYR cc_start: 0.7921 (m-80) cc_final: 0.7524 (m-80) REVERT: A 91 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6757 (tm-30) REVERT: A 113 LYS cc_start: 0.7297 (tttt) cc_final: 0.6824 (mmtt) REVERT: B 18 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6830 (mp10) REVERT: B 45 ILE cc_start: 0.7134 (mm) cc_final: 0.6635 (mm) REVERT: B 69 TRP cc_start: 0.8785 (m100) cc_final: 0.7953 (m100) REVERT: B 70 MET cc_start: 0.7581 (tpp) cc_final: 0.7299 (mmt) REVERT: B 78 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9115 (m) REVERT: B 80 ASP cc_start: 0.7364 (t0) cc_final: 0.6690 (t0) REVERT: B 89 GLN cc_start: 0.7040 (mt0) cc_final: 0.6694 (mt0) REVERT: B 91 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5319 (tm-30) REVERT: B 96 ASP cc_start: 0.7334 (t0) cc_final: 0.6831 (m-30) REVERT: B 122 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7090 (mt-10) REVERT: G 4 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: G 63 ASP cc_start: 0.6064 (OUTLIER) cc_final: 0.5674 (m-30) REVERT: G 191 ILE cc_start: 0.7606 (pt) cc_final: 0.7278 (pt) REVERT: G 283 LEU cc_start: 0.8150 (mt) cc_final: 0.7832 (mt) REVERT: G 306 GLU cc_start: 0.6967 (mp0) cc_final: 0.6595 (pt0) REVERT: E 11 MET cc_start: 0.7554 (ttm) cc_final: 0.6960 (tpt) REVERT: E 135 GLU cc_start: 0.5876 (pt0) cc_final: 0.5643 (pt0) REVERT: F 13 ASP cc_start: 0.8159 (t0) cc_final: 0.7807 (t0) REVERT: F 17 LYS cc_start: 0.8019 (mttt) cc_final: 0.7637 (mttt) REVERT: F 58 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: F 91 GLU cc_start: 0.7836 (tp30) cc_final: 0.7496 (tp30) REVERT: I 197 MET cc_start: 0.7199 (tpp) cc_final: 0.6918 (tpp) REVERT: I 261 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8627 (tt) outliers start: 106 outliers final: 63 residues processed: 391 average time/residue: 0.1045 time to fit residues: 65.4819 Evaluate side-chains 346 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 275 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 4 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 224 ILE Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 212 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.137565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115470 restraints weight = 27824.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.114470 restraints weight = 25518.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.114515 restraints weight = 24184.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114896 restraints weight = 22796.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115068 restraints weight = 19676.927| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.9101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18501 Z= 0.144 Angle : 0.555 6.833 25161 Z= 0.285 Chirality : 0.045 0.198 2919 Planarity : 0.004 0.044 3264 Dihedral : 4.202 32.504 2513 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.36 % Favored : 96.51 % Rotamer: Outliers : 4.69 % Allowed : 27.31 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.17), residues: 2319 helix: 1.66 (0.27), residues: 330 sheet: -0.58 (0.18), residues: 852 loop : -1.17 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 247 TYR 0.011 0.001 TYR G 280 PHE 0.016 0.001 PHE I 231 TRP 0.011 0.001 TRP I 144 HIS 0.006 0.001 HIS I 318 Details of bonding type rmsd covalent geometry : bond 0.00337 (18501) covalent geometry : angle 0.55511 (25161) hydrogen bonds : bond 0.03182 ( 386) hydrogen bonds : angle 4.52303 ( 1083) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 306 time to evaluate : 0.675 Fit side-chains REVERT: C 62 TYR cc_start: 0.8566 (m-80) cc_final: 0.8364 (m-10) REVERT: D 18 GLN cc_start: 0.7860 (mt0) cc_final: 0.7578 (mt0) REVERT: D 91 GLU cc_start: 0.8010 (tp30) cc_final: 0.7512 (tm-30) REVERT: H 23 THR cc_start: 0.8869 (p) cc_final: 0.8593 (t) REVERT: H 63 ASP cc_start: 0.6932 (p0) cc_final: 0.6275 (m-30) REVERT: H 142 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7557 (mttt) REVERT: A 1 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7331 (pmm) REVERT: A 3 HIS cc_start: 0.7542 (m-70) cc_final: 0.7331 (m-70) REVERT: A 79 TYR cc_start: 0.7942 (m-80) cc_final: 0.7568 (m-80) REVERT: A 91 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6785 (tm-30) REVERT: A 113 LYS cc_start: 0.7162 (tttt) cc_final: 0.6929 (mmtt) REVERT: B 18 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: B 69 TRP cc_start: 0.8823 (m100) cc_final: 0.7969 (m100) REVERT: B 70 MET cc_start: 0.7704 (tpp) cc_final: 0.7375 (mmt) REVERT: B 78 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9151 (m) REVERT: B 80 ASP cc_start: 0.7532 (t0) cc_final: 0.6809 (t0) REVERT: B 89 GLN cc_start: 0.7244 (mt0) cc_final: 0.6889 (mt0) REVERT: B 91 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5746 (tm-30) REVERT: B 96 ASP cc_start: 0.7263 (t0) cc_final: 0.6997 (m-30) REVERT: G 4 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: G 63 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.5960 (m-30) REVERT: G 191 ILE cc_start: 0.7656 (pt) cc_final: 0.7318 (pt) REVERT: G 247 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7166 (mtm180) REVERT: G 283 LEU cc_start: 0.8041 (mt) cc_final: 0.7814 (mt) REVERT: G 370 ASP cc_start: 0.7984 (t70) cc_final: 0.7634 (t70) REVERT: E 11 MET cc_start: 0.7593 (ttm) cc_final: 0.7025 (tpt) REVERT: E 16 SER cc_start: 0.7640 (m) cc_final: 0.7388 (t) REVERT: E 70 MET cc_start: 0.8363 (tpp) cc_final: 0.8141 (tpp) REVERT: F 58 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: F 70 MET cc_start: 0.7200 (tpp) cc_final: 0.6996 (tpp) REVERT: F 91 GLU cc_start: 0.7807 (tp30) cc_final: 0.7401 (tm-30) REVERT: I 200 GLN cc_start: 0.7640 (tp-100) cc_final: 0.7061 (tt0) REVERT: I 210 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8855 (pt) outliers start: 95 outliers final: 63 residues processed: 376 average time/residue: 0.1017 time to fit residues: 61.9575 Evaluate side-chains 361 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 290 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 4 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 445 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 127 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 191 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN A 29 ASN A 115 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111791 restraints weight = 27795.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110880 restraints weight = 30012.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112742 restraints weight = 28342.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112777 restraints weight = 20393.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112939 restraints weight = 17713.065| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.9512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18501 Z= 0.175 Angle : 0.577 7.286 25161 Z= 0.299 Chirality : 0.046 0.221 2919 Planarity : 0.004 0.045 3264 Dihedral : 4.328 33.403 2513 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.62 % Favored : 96.25 % Rotamer: Outliers : 4.84 % Allowed : 27.11 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.17), residues: 2319 helix: 1.51 (0.27), residues: 333 sheet: -0.67 (0.18), residues: 840 loop : -1.22 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 247 TYR 0.014 0.002 TYR I 196 PHE 0.016 0.001 PHE I 231 TRP 0.013 0.001 TRP I 144 HIS 0.006 0.001 HIS I 318 Details of bonding type rmsd covalent geometry : bond 0.00411 (18501) covalent geometry : angle 0.57668 (25161) hydrogen bonds : bond 0.03377 ( 386) hydrogen bonds : angle 4.59347 ( 1083) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 289 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: C 62 TYR cc_start: 0.8697 (m-80) cc_final: 0.8448 (m-80) REVERT: D 25 ASP cc_start: 0.8600 (m-30) cc_final: 0.8287 (m-30) REVERT: D 45 ILE cc_start: 0.6445 (mm) cc_final: 0.6117 (mm) REVERT: H 23 THR cc_start: 0.9007 (p) cc_final: 0.8761 (t) REVERT: H 63 ASP cc_start: 0.7080 (p0) cc_final: 0.6403 (m-30) REVERT: H 136 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8492 (mt) REVERT: H 142 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7469 (mttp) REVERT: H 327 ASP cc_start: 0.6666 (t0) cc_final: 0.5077 (p0) REVERT: A 1 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7395 (pmm) REVERT: A 3 HIS cc_start: 0.7378 (m-70) cc_final: 0.7147 (m-70) REVERT: A 79 TYR cc_start: 0.8039 (m-80) cc_final: 0.7747 (m-80) REVERT: A 91 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6401 (tm-30) REVERT: A 113 LYS cc_start: 0.7253 (tttt) cc_final: 0.7011 (mmtt) REVERT: B 18 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6971 (mp10) REVERT: B 70 MET cc_start: 0.7793 (tpp) cc_final: 0.7432 (mmt) REVERT: B 80 ASP cc_start: 0.7567 (t0) cc_final: 0.6804 (t0) REVERT: B 89 GLN cc_start: 0.7319 (mt0) cc_final: 0.6671 (mt0) REVERT: B 91 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5861 (tm-30) REVERT: B 96 ASP cc_start: 0.7229 (t0) cc_final: 0.6963 (m-30) REVERT: G 4 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: G 191 ILE cc_start: 0.7825 (pt) cc_final: 0.7474 (pt) REVERT: G 306 GLU cc_start: 0.7082 (mp0) cc_final: 0.6801 (pt0) REVERT: G 370 ASP cc_start: 0.8021 (t70) cc_final: 0.7691 (t70) REVERT: E 11 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7190 (tpt) REVERT: E 16 SER cc_start: 0.7956 (m) cc_final: 0.7535 (t) REVERT: E 91 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6432 (tm-30) REVERT: F 58 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: F 91 GLU cc_start: 0.7799 (tp30) cc_final: 0.7482 (tm-30) REVERT: I 200 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7249 (tt0) REVERT: I 210 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8843 (pt) outliers start: 98 outliers final: 75 residues processed: 362 average time/residue: 0.1014 time to fit residues: 59.1311 Evaluate side-chains 365 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 282 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 4 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain I residue 445 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 223 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 93 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS F 23 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 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 = 0.3521 r_free = 0.3521 target = 0.135509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112499 restraints weight = 27632.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111736 restraints weight = 31548.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113175 restraints weight = 29677.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113506 restraints weight = 20925.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.113986 restraints weight = 19395.068| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.9701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18501 Z= 0.138 Angle : 0.554 7.869 25161 Z= 0.286 Chirality : 0.045 0.195 2919 Planarity : 0.003 0.045 3264 Dihedral : 4.248 32.933 2513 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.45 % Favored : 96.42 % Rotamer: Outliers : 4.40 % Allowed : 27.21 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.17), residues: 2319 helix: 1.56 (0.27), residues: 333 sheet: -0.56 (0.18), residues: 843 loop : -1.24 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 37 TYR 0.013 0.001 TYR I 196 PHE 0.018 0.001 PHE I 231 TRP 0.010 0.001 TRP I 144 HIS 0.006 0.001 HIS I 318 Details of bonding type rmsd covalent geometry : bond 0.00324 (18501) covalent geometry : angle 0.55398 (25161) hydrogen bonds : bond 0.03159 ( 386) hydrogen bonds : angle 4.53655 ( 1083) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 306 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.7017 (pmm) REVERT: C 62 TYR cc_start: 0.8700 (m-80) cc_final: 0.8366 (m-10) REVERT: D 25 ASP cc_start: 0.8634 (m-30) cc_final: 0.8310 (m-30) REVERT: D 45 ILE cc_start: 0.6532 (mm) cc_final: 0.6225 (mm) REVERT: H 23 THR cc_start: 0.8999 (p) cc_final: 0.8776 (t) REVERT: H 63 ASP cc_start: 0.7084 (p0) cc_final: 0.6269 (m-30) REVERT: H 84 THR cc_start: 0.8051 (p) cc_final: 0.7748 (t) REVERT: H 142 LYS cc_start: 0.7843 (mmmt) cc_final: 0.7561 (mttt) REVERT: H 327 ASP cc_start: 0.6693 (t0) cc_final: 0.5151 (p0) REVERT: A 1 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7450 (pmm) REVERT: A 79 TYR cc_start: 0.8011 (m-80) cc_final: 0.7751 (m-80) REVERT: A 91 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6384 (tm-30) REVERT: A 113 LYS cc_start: 0.7162 (tttt) cc_final: 0.6955 (mmtt) REVERT: B 18 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6958 (mp10) REVERT: B 70 MET cc_start: 0.7883 (tpp) cc_final: 0.7657 (mmt) REVERT: B 80 ASP cc_start: 0.7517 (t0) cc_final: 0.6791 (t0) REVERT: B 89 GLN cc_start: 0.7328 (mt0) cc_final: 0.6655 (mt0) REVERT: B 91 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.5858 (tm-30) REVERT: B 96 ASP cc_start: 0.7162 (t0) cc_final: 0.6946 (m-30) REVERT: B 113 LYS cc_start: 0.6361 (OUTLIER) cc_final: 0.6077 (mmtt) REVERT: G 4 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: G 63 ASP cc_start: 0.6854 (p0) cc_final: 0.6583 (m-30) REVERT: G 191 ILE cc_start: 0.7817 (pt) cc_final: 0.7457 (pt) REVERT: G 306 GLU cc_start: 0.7130 (mp0) cc_final: 0.6806 (pt0) REVERT: G 370 ASP cc_start: 0.7986 (t70) cc_final: 0.7661 (t70) REVERT: E 11 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7227 (tpt) REVERT: E 16 SER cc_start: 0.8437 (m) cc_final: 0.7866 (t) REVERT: E 91 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6425 (tm-30) REVERT: F 91 GLU cc_start: 0.7780 (tp30) cc_final: 0.7425 (tm-30) REVERT: I 63 ASP cc_start: 0.7282 (p0) cc_final: 0.6573 (m-30) REVERT: I 200 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7163 (tt0) REVERT: I 210 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8799 (pt) outliers start: 89 outliers final: 72 residues processed: 372 average time/residue: 0.0988 time to fit residues: 60.1462 Evaluate side-chains 373 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 4 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 445 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 157 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN D 18 GLN A 115 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111795 restraints weight = 27821.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110936 restraints weight = 29440.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111364 restraints weight = 31369.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112391 restraints weight = 24308.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112481 restraints weight = 19227.224| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 1.0023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18501 Z= 0.190 Angle : 0.608 11.716 25161 Z= 0.315 Chirality : 0.046 0.205 2919 Planarity : 0.004 0.046 3264 Dihedral : 4.443 34.661 2513 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.52 % Rotamer: Outliers : 4.54 % Allowed : 27.26 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.17), residues: 2319 helix: 1.45 (0.28), residues: 333 sheet: -0.74 (0.18), residues: 846 loop : -1.26 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 37 TYR 0.027 0.002 TYR G 303 PHE 0.017 0.002 PHE I 231 TRP 0.014 0.002 TRP I 144 HIS 0.006 0.001 HIS I 318 Details of bonding type rmsd covalent geometry : bond 0.00451 (18501) covalent geometry : angle 0.60814 (25161) hydrogen bonds : bond 0.03528 ( 386) hydrogen bonds : angle 4.60709 ( 1083) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 296 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6906 (pmm) REVERT: C 62 TYR cc_start: 0.8765 (m-80) cc_final: 0.8496 (m-80) REVERT: D 18 GLN cc_start: 0.8018 (mt0) cc_final: 0.7786 (mt0) REVERT: D 25 ASP cc_start: 0.8712 (m-30) cc_final: 0.8405 (m-30) REVERT: D 45 ILE cc_start: 0.6361 (mm) cc_final: 0.6051 (mm) REVERT: H 23 THR cc_start: 0.9001 (p) cc_final: 0.8777 (t) REVERT: H 63 ASP cc_start: 0.7079 (p0) cc_final: 0.6497 (m-30) REVERT: H 84 THR cc_start: 0.8081 (p) cc_final: 0.7801 (t) REVERT: H 142 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7532 (mttp) REVERT: H 327 ASP cc_start: 0.6907 (t0) cc_final: 0.5486 (p0) REVERT: A 91 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6435 (tm-30) REVERT: B 18 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6994 (mp10) REVERT: B 70 MET cc_start: 0.7956 (tpp) cc_final: 0.7736 (mmt) REVERT: B 80 ASP cc_start: 0.7745 (t0) cc_final: 0.6880 (t0) REVERT: B 89 GLN cc_start: 0.7428 (mt0) cc_final: 0.6757 (mt0) REVERT: B 91 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6550 (tp30) REVERT: B 96 ASP cc_start: 0.7293 (t0) cc_final: 0.7004 (m-30) REVERT: B 113 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.6115 (mmtt) REVERT: G 4 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: G 63 ASP cc_start: 0.6688 (p0) cc_final: 0.6342 (m-30) REVERT: G 191 ILE cc_start: 0.7969 (pt) cc_final: 0.7633 (pt) REVERT: G 280 TYR cc_start: 0.8492 (t80) cc_final: 0.8204 (t80) REVERT: G 370 ASP cc_start: 0.8020 (t70) cc_final: 0.7668 (t70) REVERT: E 11 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7294 (tpt) REVERT: E 16 SER cc_start: 0.8809 (m) cc_final: 0.8010 (t) REVERT: E 91 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6588 (tm-30) REVERT: F 70 MET cc_start: 0.7830 (tpp) cc_final: 0.7565 (mmt) REVERT: F 91 GLU cc_start: 0.7828 (tp30) cc_final: 0.7609 (tp30) REVERT: I 210 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8847 (pt) outliers start: 92 outliers final: 71 residues processed: 362 average time/residue: 0.1248 time to fit residues: 72.8973 Evaluate side-chains 366 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 288 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 4 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 245 MET Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain I residue 450 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 5 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 173 optimal weight: 6.9990 chunk 219 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114302 restraints weight = 27492.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113529 restraints weight = 29864.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114705 restraints weight = 28296.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115117 restraints weight = 21794.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115363 restraints weight = 20216.955| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 1.0062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18501 Z= 0.115 Angle : 0.561 11.274 25161 Z= 0.287 Chirality : 0.044 0.187 2919 Planarity : 0.003 0.045 3264 Dihedral : 4.242 34.352 2513 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.10 % Favored : 96.77 % Rotamer: Outliers : 3.70 % Allowed : 28.44 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.17), residues: 2319 helix: 1.60 (0.28), residues: 333 sheet: -0.51 (0.18), residues: 837 loop : -1.25 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 359 TYR 0.021 0.001 TYR G 303 PHE 0.020 0.001 PHE I 231 TRP 0.009 0.001 TRP I 144 HIS 0.006 0.001 HIS I 318 Details of bonding type rmsd covalent geometry : bond 0.00267 (18501) covalent geometry : angle 0.56075 (25161) hydrogen bonds : bond 0.03148 ( 386) hydrogen bonds : angle 4.49326 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2420.38 seconds wall clock time: 42 minutes 58.57 seconds (2578.57 seconds total)