Starting phenix.real_space_refine on Mon Nov 18 23:06:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/11_2024/8bcp_15967.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/11_2024/8bcp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/11_2024/8bcp_15967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/11_2024/8bcp_15967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/11_2024/8bcp_15967.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/11_2024/8bcp_15967.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 10.88, per 1000 atoms: 0.60 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: 4.93 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.27 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: 5.67 Time building geometry restraints manager: 5.68 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 42.520 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.780 ------------------------------------------------------------------------------- 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= 0.176 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 : 10.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (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 TRP 0.008 0.001 TRP I 144 HIS 0.004 0.001 HIS H 318 PHE 0.032 0.001 PHE I 231 TYR 0.019 0.001 TYR H 303 ARG 0.003 0.000 ARG E 157 *********************** 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 : 1.959 Fit side-chains revert: symmetry clash REVERT: C 103 THR cc_start: 0.4594 (p) cc_final: 0.4340 (p) REVERT: D 41 LYS cc_start: 0.6069 (mttm) cc_final: 0.5628 (tptp) REVERT: D 122 GLU cc_start: 0.6353 (pt0) cc_final: 0.6045 (pm20) REVERT: D 156 ARG cc_start: 0.4413 (pmt-80) cc_final: 0.3203 (tpm170) REVERT: H 1 MET cc_start: 0.6133 (ttp) cc_final: 0.5834 (ttp) REVERT: H 139 LEU cc_start: 0.7109 (tt) cc_final: 0.6725 (tt) REVERT: H 347 ASP cc_start: 0.5862 (p0) cc_final: 0.5446 (t0) REVERT: A 1 MET cc_start: 0.5695 (mpp) cc_final: 0.5099 (mmt) REVERT: A 29 ASN cc_start: 0.7357 (m110) cc_final: 0.6861 (m110) REVERT: A 79 TYR cc_start: 0.5359 (m-80) cc_final: 0.5121 (m-10) REVERT: A 114 PRO cc_start: 0.8092 (Cg_exo) cc_final: 0.7888 (Cg_endo) REVERT: B 1 MET cc_start: 0.2613 (pmm) cc_final: 0.0679 (mmm) REVERT: B 86 ILE cc_start: 0.6285 (tt) cc_final: 0.5630 (tt) REVERT: B 132 SER cc_start: 0.4907 (t) cc_final: 0.4283 (m) REVERT: G 189 ILE cc_start: 0.5985 (mm) cc_final: 0.5693 (mm) REVERT: F 83 LYS cc_start: 0.6358 (mtmm) cc_final: 0.6058 (mttt) REVERT: F 101 ILE cc_start: 0.7851 (mm) cc_final: 0.7549 (mm) REVERT: I 129 HIS cc_start: 0.4165 (m-70) cc_final: 0.3686 (m-70) outliers start: 6 outliers final: 1 residues processed: 574 average time/residue: 0.3209 time to fit residues: 276.4613 Evaluate side-chains 366 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 2.173 ------------------------------------------------------------------------------- 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 192 optimal weight: 0.8980 chunk 172 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 40.0000 chunk 69 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 0.0030 chunk 207 optimal weight: 4.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 ASN D 87 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 ASN H 122 ASN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 GLN A 54 HIS A 106 ASN B 54 HIS B 67 GLN B 89 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 23 GLN F 68 GLN I 219 ASN I 243 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 18501 Z= 0.352 Angle : 0.700 11.948 25161 Z= 0.374 Chirality : 0.051 0.535 2919 Planarity : 0.005 0.065 3264 Dihedral : 4.452 30.946 2513 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 6.17 % Allowed : 24.59 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2319 helix: 1.03 (0.26), residues: 342 sheet: -0.30 (0.19), residues: 774 loop : -1.34 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 144 HIS 0.008 0.002 HIS H 318 PHE 0.028 0.003 PHE I 12 TYR 0.033 0.003 TYR I 239 ARG 0.010 0.001 ARG I 292 *********************** 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 542 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 417 time to evaluate : 2.182 Fit side-chains revert: symmetry clash REVERT: C 91 GLU cc_start: 0.6315 (tm-30) cc_final: 0.5683 (tm-30) REVERT: D 122 GLU cc_start: 0.6613 (pt0) cc_final: 0.6286 (pm20) REVERT: D 156 ARG cc_start: 0.4917 (pmt-80) cc_final: 0.3404 (tpm170) REVERT: H 197 MET cc_start: 0.7670 (mmm) cc_final: 0.7433 (ttm) REVERT: H 209 THR cc_start: 0.8259 (m) cc_final: 0.7999 (m) REVERT: H 239 TYR cc_start: 0.7059 (m-80) cc_final: 0.6410 (m-80) REVERT: H 347 ASP cc_start: 0.6487 (p0) cc_final: 0.5961 (t0) REVERT: A 29 ASN cc_start: 0.7744 (m110) cc_final: 0.7532 (m110) REVERT: A 67 GLN cc_start: 0.6626 (mt0) cc_final: 0.6294 (mt0) REVERT: B 1 MET cc_start: 0.3349 (pmm) cc_final: 0.1298 (mmm) REVERT: B 34 ASN cc_start: 0.5900 (t0) cc_final: 0.5566 (t0) REVERT: B 122 GLU cc_start: 0.6862 (pm20) cc_final: 0.6542 (mp0) REVERT: G 220 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7659 (tttt) REVERT: G 222 TYR cc_start: 0.8223 (m-10) cc_final: 0.7924 (m-10) REVERT: G 373 THR cc_start: 0.6560 (p) cc_final: 0.6198 (p) REVERT: E 2 ASP cc_start: 0.7389 (t0) cc_final: 0.7163 (t0) REVERT: E 26 GLU cc_start: 0.5836 (OUTLIER) cc_final: 0.5385 (mm-30) REVERT: E 37 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7237 (ttp80) REVERT: E 119 PHE cc_start: 0.6495 (m-10) cc_final: 0.6173 (m-10) REVERT: E 158 SER cc_start: 0.5895 (OUTLIER) cc_final: 0.5669 (p) REVERT: F 23 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.6041 (mp10) REVERT: F 58 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5410 (tm-30) REVERT: F 70 MET cc_start: 0.7266 (tpp) cc_final: 0.6891 (tpp) REVERT: I 27 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8183 (tm-30) REVERT: I 120 MET cc_start: 0.4623 (ptm) cc_final: 0.4335 (ptt) REVERT: I 121 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.6928 (t) REVERT: I 180 ASP cc_start: 0.5602 (OUTLIER) cc_final: 0.5364 (t0) REVERT: I 357 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7480 (t80) outliers start: 125 outliers final: 58 residues processed: 515 average time/residue: 0.2952 time to fit residues: 234.0715 Evaluate side-chains 406 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 341 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 100 VAL 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 127 ILE Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 122 ASN 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 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 334 VAL 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 99 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 VAL 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 B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 334 VAL 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 55 ILE 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 158 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 23 GLN 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 30 VAL Chi-restraints excluded: chain I residue 34 ILE 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 230 THR Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 357 TYR 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 115 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 224 optimal weight: 0.0670 chunk 184 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN H 122 ASN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 89 GLN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4492 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= 0.171 Angle : 0.542 6.984 25161 Z= 0.280 Chirality : 0.044 0.186 2919 Planarity : 0.003 0.046 3264 Dihedral : 4.088 29.996 2513 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.59 % Rotamer: Outliers : 4.00 % Allowed : 26.32 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.17), residues: 2319 helix: 1.51 (0.27), residues: 333 sheet: -0.63 (0.19), residues: 828 loop : -1.10 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 69 HIS 0.006 0.001 HIS I 318 PHE 0.016 0.001 PHE H 119 TYR 0.029 0.001 TYR G 196 ARG 0.004 0.000 ARG E 4 *********************** 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 447 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 366 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.6305 (tm-30) cc_final: 0.5711 (tm-30) REVERT: C 158 SER cc_start: 0.7479 (t) cc_final: 0.7137 (t) REVERT: D 4 ARG cc_start: 0.6624 (ptm-80) cc_final: 0.6139 (ttp-110) REVERT: D 19 MET cc_start: 0.6366 (ttm) cc_final: 0.6153 (ttm) REVERT: D 122 GLU cc_start: 0.6659 (pt0) cc_final: 0.6441 (pm20) REVERT: D 156 ARG cc_start: 0.5268 (pmt-80) cc_final: 0.3503 (tpm170) REVERT: H 197 MET cc_start: 0.7750 (mmm) cc_final: 0.7366 (ttm) REVERT: H 209 THR cc_start: 0.8383 (m) cc_final: 0.6860 (t) REVERT: H 239 TYR cc_start: 0.7005 (m-80) cc_final: 0.6323 (m-80) REVERT: H 347 ASP cc_start: 0.6657 (p0) cc_final: 0.6172 (t0) REVERT: A 1 MET cc_start: 0.6937 (mpp) cc_final: 0.6710 (mpp) REVERT: A 113 LYS cc_start: 0.7778 (tttt) cc_final: 0.7016 (mmtt) REVERT: B 1 MET cc_start: 0.3245 (pmm) cc_final: 0.1456 (mmm) REVERT: B 34 ASN cc_start: 0.5944 (t0) cc_final: 0.5736 (t0) REVERT: B 91 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.4586 (tm-30) REVERT: B 126 MET cc_start: 0.7186 (mmm) cc_final: 0.6560 (mmt) REVERT: B 132 SER cc_start: 0.7534 (t) cc_final: 0.6813 (m) REVERT: G 170 SER cc_start: 0.7163 (m) cc_final: 0.6917 (p) REVERT: G 241 THR cc_start: 0.6124 (OUTLIER) cc_final: 0.5559 (p) REVERT: G 373 THR cc_start: 0.6544 (p) cc_final: 0.6143 (p) REVERT: E 4 ARG cc_start: 0.5157 (tpp80) cc_final: 0.4889 (tpp80) REVERT: E 37 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7134 (ttp80) REVERT: E 119 PHE cc_start: 0.6613 (m-10) cc_final: 0.6237 (m-10) REVERT: F 23 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.6479 (pm20) REVERT: I 121 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7112 (t) outliers start: 81 outliers final: 45 residues processed: 424 average time/residue: 0.2941 time to fit residues: 192.6880 Evaluate side-chains 383 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 334 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 119 PHE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 121 VAL 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 334 VAL Chi-restraints excluded: chain H residue 455 THR 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 131 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 4 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain E residue 7 ILE 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 F residue 7 ILE Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 85 ASP 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 34 ILE 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 164 ILE Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 380 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 HIS B 89 GLN G 62 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN ** I 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN I 153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.8396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 18501 Z= 0.404 Angle : 0.769 10.521 25161 Z= 0.406 Chirality : 0.052 0.321 2919 Planarity : 0.005 0.061 3264 Dihedral : 5.277 42.360 2513 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 7.41 % Allowed : 25.53 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2319 helix: 0.59 (0.27), residues: 333 sheet: -0.60 (0.19), residues: 735 loop : -1.64 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 69 HIS 0.009 0.002 HIS G 113 PHE 0.019 0.003 PHE H 119 TYR 0.035 0.003 TYR I 357 ARG 0.011 0.001 ARG G 53 *********************** 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 500 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 350 time to evaluate : 2.345 Fit side-chains REVERT: D 23 GLN cc_start: 0.6599 (pt0) cc_final: 0.6115 (pm20) REVERT: D 91 GLU cc_start: 0.7624 (tp30) cc_final: 0.7406 (tm-30) REVERT: D 156 ARG cc_start: 0.6718 (pmt-80) cc_final: 0.4040 (tpm170) REVERT: H 2 SER cc_start: 0.7129 (p) cc_final: 0.6795 (m) REVERT: H 23 THR cc_start: 0.9065 (p) cc_final: 0.8775 (t) REVERT: H 142 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7254 (mttp) REVERT: A 1 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7244 (pmm) REVERT: A 29 ASN cc_start: 0.7941 (m110) cc_final: 0.7737 (m110) REVERT: A 77 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7696 (pp) REVERT: A 91 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6837 (tm-30) REVERT: B 3 HIS cc_start: 0.6153 (OUTLIER) cc_final: 0.5854 (m90) REVERT: B 18 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: B 26 GLU cc_start: 0.7502 (tp30) cc_final: 0.7297 (tp30) REVERT: B 45 ILE cc_start: 0.6726 (mm) cc_final: 0.6270 (mm) REVERT: B 69 TRP cc_start: 0.9012 (m100) cc_final: 0.8253 (m100) REVERT: B 70 MET cc_start: 0.7700 (tpp) cc_final: 0.7307 (mmt) REVERT: B 80 ASP cc_start: 0.7209 (t0) cc_final: 0.6665 (t0) REVERT: B 89 GLN cc_start: 0.6865 (mt0) cc_final: 0.6421 (mt0) REVERT: G 4 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: G 191 ILE cc_start: 0.7735 (pt) cc_final: 0.7420 (pt) REVERT: G 247 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7103 (mtm180) REVERT: G 284 ILE cc_start: 0.8223 (pt) cc_final: 0.8007 (mt) REVERT: G 370 ASP cc_start: 0.8043 (t70) cc_final: 0.7633 (t70) REVERT: E 18 GLN cc_start: 0.7304 (mt0) cc_final: 0.7092 (mt0) REVERT: E 127 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7901 (pt) REVERT: E 135 GLU cc_start: 0.5974 (pt0) cc_final: 0.5698 (pt0) REVERT: F 58 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: F 91 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6558 (tm-30) REVERT: I 153 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7763 (t0) REVERT: I 237 ILE cc_start: 0.8681 (mm) cc_final: 0.8283 (mm) REVERT: I 238 THR cc_start: 0.8340 (m) cc_final: 0.7608 (p) REVERT: I 269 LEU cc_start: 0.7766 (mp) cc_final: 0.7370 (mp) outliers start: 150 outliers final: 76 residues processed: 476 average time/residue: 0.2826 time to fit residues: 210.7779 Evaluate side-chains 367 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 283 time to evaluate : 2.146 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 237 ILE 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 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 461 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 36 SER 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 3 HIS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 107 LEU 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 88 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 342 ASP 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 86 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 6 SER 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 90 LEU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 18 THR 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 149 SER Chi-restraints excluded: chain I residue 153 ASN Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 211 LEU 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 380 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 430 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 GLN ** H 206 ASN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.8685 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= 0.241 Angle : 0.587 7.626 25161 Z= 0.306 Chirality : 0.046 0.217 2919 Planarity : 0.004 0.049 3264 Dihedral : 4.634 41.722 2513 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 4.69 % Allowed : 28.49 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.17), residues: 2319 helix: 1.27 (0.27), residues: 333 sheet: -0.67 (0.18), residues: 792 loop : -1.40 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 144 HIS 0.006 0.001 HIS I 318 PHE 0.021 0.002 PHE I 231 TYR 0.017 0.002 TYR G 196 ARG 0.009 0.000 ARG H 292 *********************** 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 403 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 308 time to evaluate : 1.942 Fit side-chains REVERT: D 91 GLU cc_start: 0.7699 (tp30) cc_final: 0.7144 (tm-30) REVERT: D 156 ARG cc_start: 0.6627 (pmt-80) cc_final: 0.3909 (tpm170) REVERT: H 2 SER cc_start: 0.6938 (p) cc_final: 0.6594 (m) REVERT: H 23 THR cc_start: 0.8969 (p) cc_final: 0.8701 (t) REVERT: H 142 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7278 (mttp) REVERT: H 306 GLU cc_start: 0.7928 (mp0) cc_final: 0.7463 (mm-30) REVERT: A 70 MET cc_start: 0.7589 (ttm) cc_final: 0.7160 (ttt) REVERT: A 77 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7592 (pp) REVERT: A 91 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 18 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: B 45 ILE cc_start: 0.6776 (mm) cc_final: 0.6255 (mm) REVERT: B 69 TRP cc_start: 0.8956 (m100) cc_final: 0.8255 (m100) REVERT: B 80 ASP cc_start: 0.7382 (t0) cc_final: 0.6771 (t0) REVERT: B 89 GLN cc_start: 0.7073 (mt0) cc_final: 0.6773 (mt0) REVERT: B 96 ASP cc_start: 0.7621 (t0) cc_final: 0.7078 (m-30) REVERT: B 113 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5668 (mttm) REVERT: G 4 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7774 (mp10) REVERT: G 38 GLN cc_start: 0.8364 (tt0) cc_final: 0.7560 (tt0) REVERT: G 191 ILE cc_start: 0.7630 (pt) cc_final: 0.7402 (pt) REVERT: G 255 PHE cc_start: 0.7761 (m-10) cc_final: 0.7538 (m-80) REVERT: G 370 ASP cc_start: 0.7944 (t70) cc_final: 0.7466 (t70) REVERT: E 91 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6907 (tm-30) REVERT: F 1 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.4805 (tpt) REVERT: F 58 GLU cc_start: 0.7660 (tm-30) cc_final: 0.6989 (tm-30) REVERT: F 70 MET cc_start: 0.7445 (tpp) cc_final: 0.6891 (tpp) REVERT: I 237 ILE cc_start: 0.8515 (mm) cc_final: 0.8311 (mm) outliers start: 95 outliers final: 67 residues processed: 379 average time/residue: 0.2762 time to fit residues: 165.1169 Evaluate side-chains 355 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 283 time to evaluate : 2.285 ------------------------------------------------------------------------------- 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 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 91 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 326 THR 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 101 ILE Chi-restraints excluded: chain A residue 115 ASN 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 16 SER Chi-restraints excluded: chain B residue 18 GLN 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 55 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 55 ILE 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 46 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 266 THR 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 450 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.8940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18501 Z= 0.205 Angle : 0.554 7.458 25161 Z= 0.289 Chirality : 0.045 0.208 2919 Planarity : 0.004 0.045 3264 Dihedral : 4.383 40.292 2513 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 4.79 % Allowed : 28.15 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2319 helix: 1.41 (0.27), residues: 336 sheet: -0.75 (0.18), residues: 828 loop : -1.26 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 144 HIS 0.005 0.001 HIS I 318 PHE 0.018 0.001 PHE I 231 TYR 0.014 0.001 TYR G 196 ARG 0.005 0.000 ARG G 247 *********************** 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 412 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 315 time to evaluate : 2.068 Fit side-chains REVERT: H 23 THR cc_start: 0.9031 (p) cc_final: 0.8771 (t) REVERT: H 120 MET cc_start: 0.8556 (pmm) cc_final: 0.8052 (ptp) REVERT: H 141 ASP cc_start: 0.6446 (t70) cc_final: 0.6168 (t70) REVERT: H 142 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7310 (mttp) REVERT: A 1 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7470 (mpp) REVERT: A 77 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7595 (pp) REVERT: A 113 LYS cc_start: 0.7388 (tttt) cc_final: 0.6743 (mmtt) REVERT: B 18 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: B 45 ILE cc_start: 0.6830 (mm) cc_final: 0.6338 (mm) REVERT: B 69 TRP cc_start: 0.8956 (m100) cc_final: 0.8093 (m100) REVERT: B 70 MET cc_start: 0.7824 (tpp) cc_final: 0.7140 (mmt) REVERT: B 80 ASP cc_start: 0.7430 (t0) cc_final: 0.6752 (t0) REVERT: B 89 GLN cc_start: 0.7066 (mt0) cc_final: 0.6819 (mt0) REVERT: B 96 ASP cc_start: 0.7278 (t0) cc_final: 0.6930 (m-30) REVERT: B 113 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5779 (mttm) REVERT: B 122 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7059 (mt-10) REVERT: G 4 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: G 38 GLN cc_start: 0.8261 (tt0) cc_final: 0.7438 (tt0) REVERT: G 191 ILE cc_start: 0.7632 (pt) cc_final: 0.7338 (pt) REVERT: G 247 ARG cc_start: 0.8197 (ttm110) cc_final: 0.7143 (mtm180) REVERT: G 255 PHE cc_start: 0.7815 (m-10) cc_final: 0.7465 (m-80) REVERT: G 370 ASP cc_start: 0.7791 (t70) cc_final: 0.7354 (t70) REVERT: F 35 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7654 (m) REVERT: F 58 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7079 (tm-30) REVERT: F 70 MET cc_start: 0.7413 (tpp) cc_final: 0.6994 (mmt) REVERT: F 73 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7684 (tm-30) REVERT: F 82 GLU cc_start: 0.7370 (tt0) cc_final: 0.7105 (tt0) REVERT: I 277 MET cc_start: 0.8336 (mmm) cc_final: 0.8044 (mmm) outliers start: 97 outliers final: 72 residues processed: 385 average time/residue: 0.2650 time to fit residues: 161.3540 Evaluate side-chains 368 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 290 time to evaluate : 2.163 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 133 THR 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 38 GLN Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 121 VAL 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 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 347 ASP 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 18 GLN 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 74 THR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 249 THR 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 326 THR Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 51 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 E residue 158 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 230 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 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 450 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 124 optimal weight: 0.1980 chunk 185 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN C 67 GLN H 206 ASN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.9400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18501 Z= 0.245 Angle : 0.578 8.709 25161 Z= 0.300 Chirality : 0.045 0.210 2919 Planarity : 0.004 0.045 3264 Dihedral : 4.426 39.448 2513 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 5.23 % Allowed : 28.49 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2319 helix: 1.39 (0.27), residues: 336 sheet: -0.87 (0.18), residues: 819 loop : -1.33 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 144 HIS 0.005 0.001 HIS I 318 PHE 0.018 0.001 PHE C 119 TYR 0.013 0.002 TYR I 280 ARG 0.005 0.000 ARG G 247 *********************** 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 425 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 319 time to evaluate : 2.264 Fit side-chains revert: symmetry clash REVERT: D 14 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8206 (ttt180) REVERT: D 91 GLU cc_start: 0.7936 (tp30) cc_final: 0.7415 (tm-30) REVERT: H 23 THR cc_start: 0.9043 (p) cc_final: 0.8819 (t) REVERT: H 120 MET cc_start: 0.8708 (pmm) cc_final: 0.8169 (ptp) REVERT: H 141 ASP cc_start: 0.6387 (t70) cc_final: 0.6054 (t0) REVERT: H 142 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7362 (mttp) REVERT: H 306 GLU cc_start: 0.7794 (mp0) cc_final: 0.7293 (mm-30) REVERT: H 370 ASP cc_start: 0.6801 (t0) cc_final: 0.6517 (t0) REVERT: A 77 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7539 (pp) REVERT: A 91 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6484 (tm-30) REVERT: A 113 LYS cc_start: 0.7294 (tttt) cc_final: 0.6764 (mmtt) REVERT: A 134 ASP cc_start: 0.5723 (t70) cc_final: 0.5489 (t70) REVERT: B 3 HIS cc_start: 0.5637 (OUTLIER) cc_final: 0.5146 (m90) REVERT: B 13 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7407 (t0) REVERT: B 18 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: B 69 TRP cc_start: 0.9042 (m100) cc_final: 0.8176 (m100) REVERT: B 70 MET cc_start: 0.7932 (tpp) cc_final: 0.7251 (mmt) REVERT: B 80 ASP cc_start: 0.7454 (t0) cc_final: 0.6778 (t0) REVERT: B 89 GLN cc_start: 0.7271 (mt0) cc_final: 0.6987 (mt0) REVERT: B 96 ASP cc_start: 0.7607 (t0) cc_final: 0.6996 (m-30) REVERT: B 113 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5762 (mttm) REVERT: G 4 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: G 191 ILE cc_start: 0.7758 (pt) cc_final: 0.7466 (pt) REVERT: G 216 MET cc_start: 0.7973 (mpp) cc_final: 0.7733 (mpp) REVERT: G 255 PHE cc_start: 0.7984 (m-10) cc_final: 0.7617 (m-80) REVERT: G 277 MET cc_start: 0.7515 (mmm) cc_final: 0.7222 (mmp) REVERT: G 284 ILE cc_start: 0.8409 (pt) cc_final: 0.8074 (mt) REVERT: G 370 ASP cc_start: 0.7922 (t70) cc_final: 0.7533 (t70) REVERT: E 11 MET cc_start: 0.7574 (ttm) cc_final: 0.7040 (tpt) REVERT: E 16 SER cc_start: 0.7784 (m) cc_final: 0.7375 (t) REVERT: E 91 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6943 (tm-30) REVERT: F 13 ASP cc_start: 0.8181 (t0) cc_final: 0.7837 (t0) REVERT: F 17 LYS cc_start: 0.8089 (mttt) cc_final: 0.7782 (mttt) REVERT: F 58 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: F 70 MET cc_start: 0.7443 (tpp) cc_final: 0.7093 (mmt) REVERT: F 73 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7590 (tm-30) REVERT: I 269 LEU cc_start: 0.7778 (mp) cc_final: 0.7568 (mp) outliers start: 106 outliers final: 81 residues processed: 400 average time/residue: 0.2853 time to fit residues: 182.1123 Evaluate side-chains 387 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 299 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 146 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 38 GLN Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 164 ILE 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 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 347 ASP 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 133 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 93 LEU 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 88 ILE Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 249 THR 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 327 ASP Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 182 GLN 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 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 450 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 6.9990 chunk 87 optimal weight: 0.2980 chunk 131 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 149 optimal weight: 30.0000 chunk 108 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 ASN H 126 ASN ** H 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.9930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18501 Z= 0.288 Angle : 0.597 7.800 25161 Z= 0.310 Chirality : 0.046 0.206 2919 Planarity : 0.004 0.047 3264 Dihedral : 4.547 40.538 2513 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 4.94 % Allowed : 28.35 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2319 helix: 1.39 (0.28), residues: 333 sheet: -0.82 (0.18), residues: 813 loop : -1.36 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 144 HIS 0.005 0.001 HIS G 135 PHE 0.021 0.002 PHE C 119 TYR 0.022 0.002 TYR G 303 ARG 0.006 0.001 ARG G 247 *********************** 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 408 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 308 time to evaluate : 2.164 Fit side-chains REVERT: C 91 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7111 (tm-30) REVERT: D 14 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8143 (ttt180) REVERT: D 70 MET cc_start: 0.8103 (mpp) cc_final: 0.7719 (mmm) REVERT: D 91 GLU cc_start: 0.7980 (tp30) cc_final: 0.7652 (tm-30) REVERT: H 84 THR cc_start: 0.8213 (p) cc_final: 0.7887 (t) REVERT: H 120 MET cc_start: 0.8682 (pmm) cc_final: 0.8218 (ptp) REVERT: H 141 ASP cc_start: 0.6259 (t70) cc_final: 0.6004 (t0) REVERT: H 142 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7367 (mttp) REVERT: H 283 LEU cc_start: 0.7769 (mt) cc_final: 0.7556 (tp) REVERT: H 306 GLU cc_start: 0.7780 (mp0) cc_final: 0.7283 (mm-30) REVERT: H 370 ASP cc_start: 0.7242 (t0) cc_final: 0.7000 (t70) REVERT: A 77 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7675 (pp) REVERT: A 86 ILE cc_start: 0.8118 (mm) cc_final: 0.7690 (mt) REVERT: A 91 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6574 (tm-30) REVERT: A 113 LYS cc_start: 0.7229 (tttt) cc_final: 0.6712 (mmtt) REVERT: B 13 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7437 (t0) REVERT: B 18 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: B 69 TRP cc_start: 0.9078 (m100) cc_final: 0.8153 (m100) REVERT: B 70 MET cc_start: 0.7996 (tpp) cc_final: 0.7337 (mmt) REVERT: B 80 ASP cc_start: 0.7648 (t0) cc_final: 0.6940 (t0) REVERT: B 89 GLN cc_start: 0.7271 (mt0) cc_final: 0.6934 (mt0) REVERT: B 96 ASP cc_start: 0.7597 (t0) cc_final: 0.7033 (m-30) REVERT: B 113 LYS cc_start: 0.6203 (OUTLIER) cc_final: 0.5838 (mttm) REVERT: G 4 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7051 (mp10) REVERT: G 38 GLN cc_start: 0.8338 (tt0) cc_final: 0.8083 (tt0) REVERT: G 191 ILE cc_start: 0.7951 (pt) cc_final: 0.7630 (pt) REVERT: G 216 MET cc_start: 0.7954 (mpp) cc_final: 0.7187 (mtt) REVERT: G 247 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7204 (mtm180) REVERT: G 255 PHE cc_start: 0.8142 (m-10) cc_final: 0.7896 (m-80) REVERT: G 284 ILE cc_start: 0.8499 (pt) cc_final: 0.8241 (mt) REVERT: G 306 GLU cc_start: 0.7373 (mp0) cc_final: 0.6785 (mm-30) REVERT: G 348 GLU cc_start: 0.7336 (mp0) cc_final: 0.6976 (mp0) REVERT: G 370 ASP cc_start: 0.8037 (t70) cc_final: 0.7728 (t70) REVERT: E 1 MET cc_start: 0.8037 (ptp) cc_final: 0.6594 (mmm) REVERT: E 11 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7167 (tpt) REVERT: E 16 SER cc_start: 0.8769 (m) cc_final: 0.7983 (t) REVERT: F 58 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: F 70 MET cc_start: 0.7310 (tpp) cc_final: 0.6963 (mmt) REVERT: F 91 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6973 (tm-30) REVERT: I 44 ASP cc_start: 0.7800 (m-30) cc_final: 0.7258 (t0) REVERT: I 49 GLU cc_start: 0.6428 (tp30) cc_final: 0.6108 (tt0) REVERT: I 139 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8359 (tp) REVERT: I 148 ASP cc_start: 0.8163 (t70) cc_final: 0.7818 (t0) REVERT: I 200 GLN cc_start: 0.8014 (tp40) cc_final: 0.7439 (tt0) outliers start: 100 outliers final: 80 residues processed: 383 average time/residue: 0.2707 time to fit residues: 165.6851 Evaluate side-chains 377 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 289 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 THR 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 38 GLN Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 147 ILE 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 295 ILE 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 133 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 93 LEU 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 121 VAL 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 249 THR 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 327 ASP Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 51 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 E residue 158 SER Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 130 SER 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 46 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 211 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 204 optimal weight: 0.0000 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 160 optimal weight: 0.1980 chunk 62 optimal weight: 20.0000 chunk 185 optimal weight: 0.0770 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.9972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18501 Z= 0.152 Angle : 0.540 7.634 25161 Z= 0.279 Chirality : 0.044 0.192 2919 Planarity : 0.003 0.045 3264 Dihedral : 4.200 38.290 2513 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 3.21 % Allowed : 30.32 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2319 helix: 1.56 (0.28), residues: 333 sheet: -0.66 (0.18), residues: 807 loop : -1.30 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 36 HIS 0.006 0.001 HIS I 318 PHE 0.020 0.001 PHE I 231 TYR 0.021 0.001 TYR G 303 ARG 0.006 0.000 ARG G 247 *********************** 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 401 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 336 time to evaluate : 2.219 Fit side-chains REVERT: C 58 GLU cc_start: 0.7697 (tt0) cc_final: 0.7308 (tt0) REVERT: C 91 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6866 (tm-30) REVERT: D 14 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8163 (ttt180) REVERT: D 70 MET cc_start: 0.8025 (mpp) cc_final: 0.7783 (mmm) REVERT: D 115 ASN cc_start: 0.6616 (p0) cc_final: 0.6369 (p0) REVERT: D 118 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8088 (t) REVERT: H 84 THR cc_start: 0.8164 (p) cc_final: 0.7853 (t) REVERT: H 120 MET cc_start: 0.8604 (pmm) cc_final: 0.8248 (ptp) REVERT: H 136 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8503 (mt) REVERT: H 142 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7464 (mttp) REVERT: H 306 GLU cc_start: 0.7629 (mp0) cc_final: 0.7202 (mm-30) REVERT: H 370 ASP cc_start: 0.7050 (t0) cc_final: 0.6732 (t70) REVERT: A 1 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7791 (mpp) REVERT: A 48 PHE cc_start: 0.8817 (m-80) cc_final: 0.8554 (m-80) REVERT: A 58 GLU cc_start: 0.7323 (tp30) cc_final: 0.7019 (tp30) REVERT: A 77 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7514 (pp) REVERT: A 86 ILE cc_start: 0.8055 (mm) cc_final: 0.7614 (mt) REVERT: A 91 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6456 (tm-30) REVERT: A 113 LYS cc_start: 0.7217 (tttt) cc_final: 0.6720 (mmtt) REVERT: B 69 TRP cc_start: 0.9076 (m100) cc_final: 0.8127 (m100) REVERT: B 70 MET cc_start: 0.7981 (tpp) cc_final: 0.7311 (mmt) REVERT: B 80 ASP cc_start: 0.7386 (t0) cc_final: 0.6846 (t0) REVERT: B 89 GLN cc_start: 0.7187 (mt0) cc_final: 0.6888 (mt0) REVERT: B 96 ASP cc_start: 0.7337 (t0) cc_final: 0.6691 (m-30) REVERT: B 113 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5840 (mmtt) REVERT: G 191 ILE cc_start: 0.7811 (pt) cc_final: 0.7488 (pt) REVERT: G 216 MET cc_start: 0.8064 (mpp) cc_final: 0.7580 (mpp) REVERT: G 247 ARG cc_start: 0.8084 (ttm110) cc_final: 0.7157 (mtm180) REVERT: G 255 PHE cc_start: 0.8202 (m-10) cc_final: 0.7941 (m-80) REVERT: G 306 GLU cc_start: 0.7289 (mp0) cc_final: 0.6671 (mm-30) REVERT: G 370 ASP cc_start: 0.7766 (t70) cc_final: 0.7354 (t70) REVERT: E 1 MET cc_start: 0.7859 (ptp) cc_final: 0.6533 (mmm) REVERT: E 11 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7141 (tpt) REVERT: E 16 SER cc_start: 0.8365 (m) cc_final: 0.7759 (t) REVERT: E 91 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6973 (tm-30) REVERT: F 17 LYS cc_start: 0.8191 (mttt) cc_final: 0.7762 (mttt) REVERT: F 44 GLU cc_start: 0.6228 (tp30) cc_final: 0.5158 (tt0) REVERT: F 70 MET cc_start: 0.7293 (tpp) cc_final: 0.7084 (mmt) REVERT: F 73 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7546 (tm-30) REVERT: F 91 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6969 (tm-30) REVERT: I 44 ASP cc_start: 0.7595 (m-30) cc_final: 0.7226 (t0) REVERT: I 49 GLU cc_start: 0.6750 (tp30) cc_final: 0.6417 (tt0) REVERT: I 148 ASP cc_start: 0.8021 (t70) cc_final: 0.7642 (t0) REVERT: I 200 GLN cc_start: 0.7862 (tp40) cc_final: 0.7202 (tt0) outliers start: 65 outliers final: 50 residues processed: 383 average time/residue: 0.2748 time to fit residues: 166.7993 Evaluate side-chains 355 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 299 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 164 ILE 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 295 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 51 VAL 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 B residue 78 VAL 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 71 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 51 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 E residue 158 SER 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 230 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 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 216 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 18 optimal weight: 0.0070 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 overall best weight: 3.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN H 115 ASN H 154 GLN ** H 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 GLN ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 1.0166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18501 Z= 0.299 Angle : 0.604 8.002 25161 Z= 0.315 Chirality : 0.046 0.197 2919 Planarity : 0.004 0.047 3264 Dihedral : 4.403 38.949 2513 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 3.21 % Allowed : 30.52 % Favored : 66.27 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.17), residues: 2319 helix: 1.54 (0.28), residues: 333 sheet: -0.73 (0.18), residues: 816 loop : -1.34 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 70 HIS 0.006 0.001 HIS I 318 PHE 0.022 0.002 PHE C 119 TYR 0.025 0.002 TYR H 303 ARG 0.007 0.001 ARG G 247 ********************** 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 368 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 303 time to evaluate : 1.989 Fit side-chains REVERT: C 58 GLU cc_start: 0.8145 (tt0) cc_final: 0.7939 (tt0) REVERT: C 91 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6987 (tm-30) REVERT: D 40 TYR cc_start: 0.5558 (m-80) cc_final: 0.5182 (m-80) REVERT: D 70 MET cc_start: 0.8140 (mpp) cc_final: 0.7743 (mmm) REVERT: D 115 ASN cc_start: 0.6484 (p0) cc_final: 0.6153 (p0) REVERT: D 118 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8097 (t) REVERT: H 120 MET cc_start: 0.8700 (pmm) cc_final: 0.8424 (ptp) REVERT: H 136 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8589 (mt) REVERT: H 142 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7462 (mttp) REVERT: H 306 GLU cc_start: 0.7804 (mp0) cc_final: 0.7328 (mm-30) REVERT: H 370 ASP cc_start: 0.7182 (t0) cc_final: 0.6940 (t70) REVERT: A 2 ASP cc_start: 0.7656 (t70) cc_final: 0.7255 (t0) REVERT: A 11 MET cc_start: 0.7968 (tpt) cc_final: 0.7639 (tpt) REVERT: A 48 PHE cc_start: 0.8854 (m-80) cc_final: 0.8578 (m-80) REVERT: A 58 GLU cc_start: 0.7514 (tp30) cc_final: 0.7193 (tp30) REVERT: A 77 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7591 (pp) REVERT: A 86 ILE cc_start: 0.8239 (mm) cc_final: 0.7783 (mt) REVERT: A 91 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6531 (tm-30) REVERT: A 113 LYS cc_start: 0.7212 (tttt) cc_final: 0.6743 (mmtt) REVERT: B 18 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: B 69 TRP cc_start: 0.9064 (m100) cc_final: 0.8070 (m100) REVERT: B 80 ASP cc_start: 0.7740 (t0) cc_final: 0.7058 (t0) REVERT: B 89 GLN cc_start: 0.7344 (mt0) cc_final: 0.7052 (mt0) REVERT: B 96 ASP cc_start: 0.7596 (t0) cc_final: 0.6981 (m-30) REVERT: B 113 LYS cc_start: 0.6215 (OUTLIER) cc_final: 0.5863 (mmtt) REVERT: G 191 ILE cc_start: 0.8067 (pt) cc_final: 0.7748 (pt) REVERT: G 216 MET cc_start: 0.8127 (mpp) cc_final: 0.7344 (mtt) REVERT: G 247 ARG cc_start: 0.8171 (ttm110) cc_final: 0.7220 (mtm180) REVERT: G 255 PHE cc_start: 0.8264 (m-10) cc_final: 0.7976 (m-80) REVERT: G 306 GLU cc_start: 0.7264 (mp0) cc_final: 0.6730 (mm-30) REVERT: G 348 GLU cc_start: 0.7331 (mp0) cc_final: 0.6977 (mp0) REVERT: G 370 ASP cc_start: 0.8008 (t70) cc_final: 0.7682 (t70) REVERT: E 1 MET cc_start: 0.8198 (ptp) cc_final: 0.6545 (mmm) REVERT: E 11 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7097 (tpt) REVERT: E 16 SER cc_start: 0.8775 (m) cc_final: 0.7988 (t) REVERT: E 91 GLU cc_start: 0.7458 (tm-30) cc_final: 0.6637 (tm-30) REVERT: F 17 LYS cc_start: 0.8235 (mttt) cc_final: 0.7805 (mttt) REVERT: F 73 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7493 (tm-30) REVERT: F 91 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6702 (tm-30) REVERT: I 44 ASP cc_start: 0.7707 (m-30) cc_final: 0.7292 (t0) REVERT: I 49 GLU cc_start: 0.6921 (tp30) cc_final: 0.6509 (tt0) REVERT: I 148 ASP cc_start: 0.8180 (t70) cc_final: 0.7875 (t0) REVERT: I 277 MET cc_start: 0.8776 (mmm) cc_final: 0.8399 (mmm) outliers start: 65 outliers final: 55 residues processed: 348 average time/residue: 0.2712 time to fit residues: 150.4038 Evaluate side-chains 359 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 298 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 118 THR 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 121 VAL Chi-restraints excluded: chain H residue 136 ILE 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 295 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 51 VAL 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 18 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 93 LEU 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 71 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 51 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 E residue 158 SER Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 230 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 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 192 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 26 optimal weight: 30.0000 chunk 50 optimal weight: 0.0570 chunk 181 optimal weight: 1.9990 chunk 75 optimal weight: 0.0170 chunk 186 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 ASN A 115 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 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 = 0.3530 r_free = 0.3530 target = 0.135887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113086 restraints weight = 27339.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112184 restraints weight = 27145.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113054 restraints weight = 25340.821| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 1.0214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 18501 Z= 0.160 Angle : 0.546 7.762 25161 Z= 0.282 Chirality : 0.044 0.176 2919 Planarity : 0.003 0.045 3264 Dihedral : 4.168 37.715 2513 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 3.21 % Allowed : 30.42 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2319 helix: 1.68 (0.28), residues: 333 sheet: -0.65 (0.19), residues: 807 loop : -1.32 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 69 HIS 0.005 0.001 HIS I 318 PHE 0.020 0.001 PHE C 119 TYR 0.024 0.001 TYR G 280 ARG 0.006 0.000 ARG G 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4003.24 seconds wall clock time: 74 minutes 14.55 seconds (4454.55 seconds total)