Starting phenix.real_space_refine on Mon May 19 01:26:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bcp_15967/05_2025/8bcp_15967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bcp_15967/05_2025/8bcp_15967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bcp_15967/05_2025/8bcp_15967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bcp_15967/05_2025/8bcp_15967.map" model { file = "/net/cci-nas-00/data/ceres_data/8bcp_15967/05_2025/8bcp_15967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bcp_15967/05_2025/8bcp_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-5687/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: 10.17, per 1000 atoms: 0.56 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: 4.27 Conformation dependent library (CDL) restraints added in 2.4 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: 2.17 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: 6.70 Time building geometry restraints manager: 4.90 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: 0.04 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 40.720 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.170 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: 0.030 Load rotamer database and sin/cos tables:4.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18501 Z= 0.121 Angle : 0.528 7.063 25161 Z= 0.286 Chirality : 0.043 0.153 2919 Planarity : 0.004 0.057 3264 Dihedral : 17.057 89.469 6792 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.41 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 Details of bonding type rmsd hydrogen bonds : bond 0.19370 ( 386) hydrogen bonds : angle 7.48216 ( 1083) covalent geometry : bond 0.00266 (18501) covalent geometry : angle 0.52824 (25161) *********************** 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 : 1.806 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: 0.3096 time to fit residues: 265.4372 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 : 2.109 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121570 restraints weight = 27681.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121286 restraints weight = 21750.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121156 restraints weight = 19098.071| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 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= 0.242 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 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 386) hydrogen bonds : angle 5.28467 ( 1083) covalent geometry : bond 0.00524 (18501) covalent geometry : angle 0.69999 (25161) *********************** 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 : 1.934 Fit side-chains revert: symmetry clash REVERT: C 91 GLU cc_start: 0.6300 (tm-30) cc_final: 0.5723 (tm-30) REVERT: D 122 GLU cc_start: 0.6595 (pt0) cc_final: 0.6302 (pm20) REVERT: D 156 ARG cc_start: 0.4930 (pmt-80) cc_final: 0.3413 (tpm170) REVERT: H 197 MET cc_start: 0.7608 (mmm) cc_final: 0.7375 (ttm) REVERT: H 209 THR cc_start: 0.8255 (m) cc_final: 0.7984 (m) REVERT: H 239 TYR cc_start: 0.7078 (m-80) cc_final: 0.6441 (m-80) REVERT: H 347 ASP cc_start: 0.6399 (p0) cc_final: 0.5901 (t0) REVERT: A 29 ASN cc_start: 0.7728 (m110) cc_final: 0.7510 (m110) REVERT: A 67 GLN cc_start: 0.6575 (mt0) cc_final: 0.6251 (mt0) REVERT: B 1 MET cc_start: 0.3360 (pmm) cc_final: 0.1330 (mmm) REVERT: B 34 ASN cc_start: 0.5952 (t0) cc_final: 0.5640 (t0) REVERT: B 122 GLU cc_start: 0.6869 (pm20) cc_final: 0.6577 (mp0) REVERT: G 222 TYR cc_start: 0.8175 (m-10) cc_final: 0.7897 (m-10) REVERT: G 373 THR cc_start: 0.6621 (p) cc_final: 0.6262 (p) REVERT: E 2 ASP cc_start: 0.7379 (t0) cc_final: 0.7139 (t0) REVERT: E 26 GLU cc_start: 0.5795 (OUTLIER) cc_final: 0.5337 (mm-30) REVERT: E 37 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7244 (ttp80) REVERT: E 119 PHE cc_start: 0.6495 (m-10) cc_final: 0.6174 (m-10) REVERT: E 158 SER cc_start: 0.5939 (OUTLIER) cc_final: 0.5685 (p) REVERT: F 23 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.6085 (mp10) REVERT: F 58 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5465 (tm-30) REVERT: F 70 MET cc_start: 0.7265 (tpp) cc_final: 0.6928 (tpp) REVERT: I 120 MET cc_start: 0.4735 (ptm) cc_final: 0.4453 (ptt) REVERT: I 121 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.6975 (t) REVERT: I 180 ASP cc_start: 0.5507 (OUTLIER) cc_final: 0.5289 (t0) REVERT: I 357 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7518 (t80) outliers start: 125 outliers final: 58 residues processed: 515 average time/residue: 0.2628 time to fit residues: 208.2280 Evaluate side-chains 404 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 339 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 88 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 218 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 227 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.145348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123846 restraints weight = 27484.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123020 restraints weight = 26861.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123851 restraints weight = 24758.968| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18501 Z= 0.132 Angle : 0.562 8.236 25161 Z= 0.290 Chirality : 0.045 0.183 2919 Planarity : 0.004 0.050 3264 Dihedral : 4.156 30.948 2513 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 4.35 % Allowed : 26.32 % Favored : 69.33 % 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: -0.91 (0.17), residues: 2319 helix: 1.49 (0.27), residues: 330 sheet: -0.67 (0.19), residues: 828 loop : -1.13 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 69 HIS 0.006 0.001 HIS I 318 PHE 0.016 0.001 PHE H 119 TYR 0.037 0.002 TYR G 196 ARG 0.005 0.000 ARG E 4 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 386) hydrogen bonds : angle 4.94144 ( 1083) covalent geometry : bond 0.00297 (18501) covalent geometry : angle 0.56244 (25161) *********************** 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 449 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 361 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 69 TRP cc_start: 0.7443 (m100) cc_final: 0.7217 (m100) REVERT: C 91 GLU cc_start: 0.6398 (tm-30) cc_final: 0.5932 (tm-30) REVERT: C 158 SER cc_start: 0.7656 (t) cc_final: 0.7228 (t) REVERT: D 156 ARG cc_start: 0.5289 (pmt-80) cc_final: 0.3598 (tpm170) REVERT: H 23 THR cc_start: 0.8592 (p) cc_final: 0.8171 (t) REVERT: H 93 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.6031 (mtt) REVERT: H 197 MET cc_start: 0.7650 (mmm) cc_final: 0.7308 (ttm) REVERT: H 347 ASP cc_start: 0.6581 (p0) cc_final: 0.6175 (t0) REVERT: A 1 MET cc_start: 0.7179 (mpp) cc_final: 0.6821 (mpp) REVERT: A 113 LYS cc_start: 0.7736 (tttt) cc_final: 0.6980 (mmtt) REVERT: B 1 MET cc_start: 0.3366 (pmm) cc_final: 0.1587 (mmm) REVERT: B 34 ASN cc_start: 0.6223 (t0) cc_final: 0.5985 (t0) REVERT: B 91 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.4759 (tm-30) REVERT: B 126 MET cc_start: 0.7167 (mmm) cc_final: 0.6647 (mmt) REVERT: G 170 SER cc_start: 0.7304 (m) cc_final: 0.7054 (p) REVERT: G 373 THR cc_start: 0.6861 (p) cc_final: 0.6465 (p) REVERT: E 26 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.5540 (mm-30) REVERT: E 37 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7205 (ttp80) REVERT: E 119 PHE cc_start: 0.6737 (m-10) cc_final: 0.6371 (m-10) REVERT: E 158 SER cc_start: 0.5782 (OUTLIER) cc_final: 0.5520 (p) REVERT: F 23 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6434 (pm20) outliers start: 88 outliers final: 52 residues processed: 426 average time/residue: 0.2787 time to fit residues: 186.5127 Evaluate side-chains 384 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 327 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 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 93 MET Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 461 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 57 THR 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 91 GLU Chi-restraints excluded: chain B residue 150 VAL 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 252 ILE Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 26 GLU 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 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 46 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 327 ASP 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 124 optimal weight: 3.9990 chunk 57 optimal weight: 0.0370 chunk 150 optimal weight: 1.9990 chunk 198 optimal weight: 0.0770 chunk 191 optimal weight: 0.9980 chunk 72 optimal weight: 40.0000 chunk 161 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 133 optimal weight: 0.4980 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 68 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN B 89 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123780 restraints weight = 27284.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123171 restraints weight = 24774.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123785 restraints weight = 21718.762| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18501 Z= 0.105 Angle : 0.521 6.830 25161 Z= 0.270 Chirality : 0.044 0.251 2919 Planarity : 0.003 0.040 3264 Dihedral : 3.970 29.682 2513 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 4.20 % Allowed : 26.22 % Favored : 69.58 % 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: -0.80 (0.17), residues: 2319 helix: 1.52 (0.27), residues: 333 sheet: -0.53 (0.18), residues: 810 loop : -1.10 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 70 HIS 0.005 0.001 HIS I 318 PHE 0.016 0.001 PHE H 119 TYR 0.022 0.001 TYR G 196 ARG 0.006 0.000 ARG G 247 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 386) hydrogen bonds : angle 4.68818 ( 1083) covalent geometry : bond 0.00238 (18501) covalent geometry : angle 0.52110 (25161) *********************** 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 436 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 351 time to evaluate : 1.925 Fit side-chains revert: symmetry clash REVERT: C 69 TRP cc_start: 0.7858 (m100) cc_final: 0.7502 (m100) REVERT: C 91 GLU cc_start: 0.6366 (tm-30) cc_final: 0.5865 (tm-30) REVERT: C 158 SER cc_start: 0.7568 (t) cc_final: 0.7108 (t) REVERT: D 18 GLN cc_start: 0.7169 (mt0) cc_final: 0.6912 (mt0) REVERT: D 156 ARG cc_start: 0.5569 (pmt-80) cc_final: 0.3599 (tpm170) REVERT: H 23 THR cc_start: 0.8594 (p) cc_final: 0.8218 (t) REVERT: H 93 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.5943 (mtt) REVERT: H 113 HIS cc_start: 0.7151 (p-80) cc_final: 0.6719 (p90) REVERT: H 120 MET cc_start: 0.6708 (pmm) cc_final: 0.6324 (pmm) REVERT: H 142 LYS cc_start: 0.7332 (mmmt) cc_final: 0.6686 (mttp) REVERT: H 197 MET cc_start: 0.7587 (mmm) cc_final: 0.7219 (ttm) REVERT: H 239 TYR cc_start: 0.6896 (m-80) cc_final: 0.6220 (m-80) REVERT: H 347 ASP cc_start: 0.6605 (p0) cc_final: 0.6312 (t0) REVERT: A 113 LYS cc_start: 0.7693 (tttt) cc_final: 0.7018 (mmtt) REVERT: B 1 MET cc_start: 0.3456 (pmm) cc_final: 0.1695 (mmm) REVERT: B 18 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.5764 (mt0) REVERT: B 34 ASN cc_start: 0.6485 (t0) cc_final: 0.6196 (t0) REVERT: B 69 TRP cc_start: 0.7831 (m100) cc_final: 0.6895 (m100) REVERT: B 91 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.4702 (tm-30) REVERT: B 126 MET cc_start: 0.7617 (mmm) cc_final: 0.7111 (mmt) REVERT: B 132 SER cc_start: 0.7915 (t) cc_final: 0.7211 (m) REVERT: G 170 SER cc_start: 0.7633 (OUTLIER) cc_final: 0.7324 (p) REVERT: G 241 THR cc_start: 0.6215 (OUTLIER) cc_final: 0.5687 (p) REVERT: G 261 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8741 (tt) REVERT: G 373 THR cc_start: 0.7016 (p) cc_final: 0.6646 (p) REVERT: E 119 PHE cc_start: 0.6940 (m-80) cc_final: 0.6543 (m-10) REVERT: E 135 GLU cc_start: 0.6117 (pt0) cc_final: 0.5893 (pt0) REVERT: I 241 THR cc_start: 0.6663 (OUTLIER) cc_final: 0.6459 (p) outliers start: 85 outliers final: 47 residues processed: 410 average time/residue: 0.2557 time to fit residues: 165.8835 Evaluate side-chains 374 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 320 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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 146 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 93 MET Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU 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 295 ILE 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 57 THR Chi-restraints excluded: chain A residue 100 VAL 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 158 SER Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 78 VAL 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 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 140 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 380 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 136 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 overall best weight: 1.7982 ------------------------------------------------------------------------------- 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 A 115 ASN B 89 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN I 153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120354 restraints weight = 27651.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120056 restraints weight = 24468.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.120671 restraints weight = 22411.618| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.6623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18501 Z= 0.153 Angle : 0.573 10.750 25161 Z= 0.301 Chirality : 0.045 0.195 2919 Planarity : 0.004 0.047 3264 Dihedral : 4.059 18.758 2511 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 5.09 % Allowed : 25.68 % 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: -0.79 (0.17), residues: 2319 helix: 1.46 (0.27), residues: 336 sheet: -0.46 (0.18), residues: 807 loop : -1.13 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 70 HIS 0.008 0.001 HIS I 318 PHE 0.019 0.002 PHE A 71 TYR 0.017 0.002 TYR A 152 ARG 0.005 0.000 ARG I 60 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 386) hydrogen bonds : angle 4.64530 ( 1083) covalent geometry : bond 0.00352 (18501) covalent geometry : angle 0.57277 (25161) *********************** 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 452 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 349 time to evaluate : 1.962 Fit side-chains REVERT: C 11 MET cc_start: 0.7113 (ttm) cc_final: 0.6891 (mmm) REVERT: C 126 MET cc_start: 0.7568 (mmm) cc_final: 0.7275 (tpp) REVERT: D 69 TRP cc_start: 0.7950 (m100) cc_final: 0.7632 (m100) REVERT: D 91 GLU cc_start: 0.7231 (tp30) cc_final: 0.6698 (tp30) REVERT: D 151 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7658 (ttt180) REVERT: H 23 THR cc_start: 0.8784 (p) cc_final: 0.8455 (t) REVERT: H 142 LYS cc_start: 0.7701 (mmmt) cc_final: 0.7020 (mttp) REVERT: H 197 MET cc_start: 0.7570 (mmm) cc_final: 0.7218 (ttm) REVERT: A 77 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7578 (pp) REVERT: A 113 LYS cc_start: 0.7503 (tttt) cc_final: 0.7245 (mmtt) REVERT: B 18 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6405 (mp10) REVERT: B 69 TRP cc_start: 0.8447 (m100) cc_final: 0.7566 (m100) REVERT: B 70 MET cc_start: 0.7015 (tpp) cc_final: 0.6624 (mmt) REVERT: B 80 ASP cc_start: 0.6940 (t0) cc_final: 0.6398 (t0) REVERT: B 91 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5175 (tm-30) REVERT: G 63 ASP cc_start: 0.5108 (OUTLIER) cc_final: 0.4374 (m-30) REVERT: G 170 SER cc_start: 0.7807 (m) cc_final: 0.7552 (p) REVERT: G 241 THR cc_start: 0.7134 (OUTLIER) cc_final: 0.6535 (p) REVERT: G 261 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8840 (tt) REVERT: E 153 GLN cc_start: 0.8325 (tt0) cc_final: 0.8118 (tt0) REVERT: I 2 SER cc_start: 0.6782 (p) cc_final: 0.6378 (m) REVERT: I 34 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8314 (mt) REVERT: I 63 ASP cc_start: 0.5977 (p0) cc_final: 0.4713 (m-30) REVERT: I 238 THR cc_start: 0.7528 (m) cc_final: 0.6850 (p) outliers start: 103 outliers final: 65 residues processed: 422 average time/residue: 0.2596 time to fit residues: 172.3125 Evaluate side-chains 382 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 309 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 89 GLN Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 148 VAL 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 D residue 151 ARG Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 46 ARG 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 18 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 450 SER 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 81 LYS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 96 ASP 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 46 THR Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 25 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 72 optimal weight: 40.0000 chunk 177 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 184 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 101 optimal weight: 0.0020 chunk 122 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN A 61 GLN A 115 ASN B 89 GLN G 200 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.117600 restraints weight = 27667.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117182 restraints weight = 23478.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117689 restraints weight = 21186.743| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.8090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18501 Z= 0.166 Angle : 0.593 8.464 25161 Z= 0.312 Chirality : 0.046 0.210 2919 Planarity : 0.004 0.054 3264 Dihedral : 4.276 16.927 2511 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 5.19 % Allowed : 26.77 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.17), residues: 2319 helix: 1.39 (0.27), residues: 336 sheet: -0.58 (0.18), residues: 813 loop : -1.13 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 144 HIS 0.007 0.001 HIS I 318 PHE 0.019 0.002 PHE I 231 TYR 0.034 0.002 TYR H 303 ARG 0.007 0.001 ARG E 4 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 386) hydrogen bonds : angle 4.71703 ( 1083) covalent geometry : bond 0.00378 (18501) covalent geometry : angle 0.59322 (25161) *********************** 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 432 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 327 time to evaluate : 1.872 Fit side-chains REVERT: C 159 LEU cc_start: 0.6656 (mt) cc_final: 0.6325 (mt) REVERT: D 69 TRP cc_start: 0.8447 (m100) cc_final: 0.8201 (m100) REVERT: D 70 MET cc_start: 0.7824 (tpp) cc_final: 0.7622 (tpp) REVERT: D 126 MET cc_start: 0.7497 (tpp) cc_final: 0.7276 (tpp) REVERT: D 156 ARG cc_start: 0.6522 (pmt-80) cc_final: 0.3780 (tpm170) REVERT: H 2 SER cc_start: 0.6979 (p) cc_final: 0.6635 (m) REVERT: H 23 THR cc_start: 0.8936 (p) cc_final: 0.8547 (t) REVERT: H 142 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7328 (mttp) REVERT: H 197 MET cc_start: 0.7633 (mmm) cc_final: 0.7415 (ttm) REVERT: A 58 GLU cc_start: 0.8073 (mp0) cc_final: 0.7710 (mp0) REVERT: A 91 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6362 (tm-30) REVERT: A 113 LYS cc_start: 0.7415 (tttt) cc_final: 0.7094 (mmtt) REVERT: B 18 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6813 (mp10) REVERT: B 45 ILE cc_start: 0.6918 (mm) cc_final: 0.6448 (mm) REVERT: B 69 TRP cc_start: 0.8756 (m100) cc_final: 0.7942 (m100) REVERT: B 70 MET cc_start: 0.7434 (tpp) cc_final: 0.7066 (mmt) REVERT: B 80 ASP cc_start: 0.7257 (t0) cc_final: 0.6698 (t0) REVERT: B 91 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5291 (tm-30) REVERT: B 96 ASP cc_start: 0.7530 (t70) cc_final: 0.6679 (m-30) REVERT: B 113 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5325 (mptp) REVERT: B 122 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6913 (mt-10) REVERT: G 247 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7157 (mtm180) REVERT: G 261 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9006 (tt) REVERT: G 370 ASP cc_start: 0.7974 (t70) cc_final: 0.7509 (t70) REVERT: E 91 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6846 (tm-30) REVERT: E 135 GLU cc_start: 0.6099 (pt0) cc_final: 0.5840 (pt0) REVERT: I 63 ASP cc_start: 0.7031 (p0) cc_final: 0.5861 (m-30) REVERT: I 237 ILE cc_start: 0.8522 (mm) cc_final: 0.8238 (mm) REVERT: I 238 THR cc_start: 0.7988 (m) cc_final: 0.7254 (p) outliers start: 105 outliers final: 70 residues processed: 410 average time/residue: 0.2494 time to fit residues: 161.3278 Evaluate side-chains 367 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 293 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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 89 GLN Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 306 GLU Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 VAL 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 132 SER 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 91 GLU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 150 VAL 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 200 GLN Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 230 THR 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 250 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 46 THR 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 283 LEU Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 403 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 208 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 73 optimal weight: 50.0000 chunk 145 optimal weight: 30.0000 chunk 212 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN G 200 GLN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.122463 restraints weight = 27514.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121019 restraints weight = 43807.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.117978 restraints weight = 28136.225| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.8349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18501 Z= 0.123 Angle : 0.550 8.382 25161 Z= 0.287 Chirality : 0.044 0.242 2919 Planarity : 0.004 0.043 3264 Dihedral : 4.102 16.777 2511 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 4.10 % Allowed : 28.35 % Favored : 67.56 % 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: -0.88 (0.17), residues: 2319 helix: 1.53 (0.28), residues: 333 sheet: -0.68 (0.18), residues: 831 loop : -1.09 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 70 HIS 0.007 0.001 HIS I 318 PHE 0.015 0.001 PHE I 231 TYR 0.018 0.001 TYR G 196 ARG 0.005 0.000 ARG G 247 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 386) hydrogen bonds : angle 4.59984 ( 1083) covalent geometry : bond 0.00284 (18501) covalent geometry : angle 0.55041 (25161) *********************** 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 395 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 312 time to evaluate : 1.944 Fit side-chains REVERT: C 17 LYS cc_start: 0.6742 (mtpp) cc_final: 0.6373 (mmtm) REVERT: D 25 ASP cc_start: 0.8497 (m-30) cc_final: 0.8211 (m-30) REVERT: D 69 TRP cc_start: 0.8574 (m100) cc_final: 0.8254 (m100) REVERT: D 70 MET cc_start: 0.7775 (tpp) cc_final: 0.7569 (tpp) REVERT: H 2 SER cc_start: 0.7060 (p) cc_final: 0.6725 (m) REVERT: H 23 THR cc_start: 0.8866 (p) cc_final: 0.8488 (t) REVERT: H 142 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7377 (mttp) REVERT: H 327 ASP cc_start: 0.6554 (t0) cc_final: 0.4512 (p0) REVERT: A 91 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6565 (tm-30) REVERT: A 106 ASN cc_start: 0.7652 (m-40) cc_final: 0.7371 (m-40) REVERT: A 113 LYS cc_start: 0.7460 (tttt) cc_final: 0.7167 (mmtt) REVERT: B 18 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6768 (mp10) REVERT: B 45 ILE cc_start: 0.6905 (mm) cc_final: 0.6445 (mm) REVERT: B 69 TRP cc_start: 0.8745 (m100) cc_final: 0.7974 (m100) REVERT: B 70 MET cc_start: 0.7472 (tpp) cc_final: 0.7107 (mmt) REVERT: B 80 ASP cc_start: 0.7454 (t0) cc_final: 0.6900 (t0) REVERT: B 89 GLN cc_start: 0.7284 (pt0) cc_final: 0.6353 (pt0) REVERT: B 91 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5268 (tm-30) REVERT: B 96 ASP cc_start: 0.7648 (t70) cc_final: 0.6764 (m-30) REVERT: B 113 LYS cc_start: 0.6172 (OUTLIER) cc_final: 0.5394 (mptp) REVERT: G 241 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7030 (p) REVERT: G 247 ARG cc_start: 0.8003 (ttm110) cc_final: 0.7113 (mtm180) REVERT: G 261 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8961 (tt) REVERT: G 370 ASP cc_start: 0.7867 (t70) cc_final: 0.7452 (t70) REVERT: E 26 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6153 (tt0) REVERT: E 91 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6753 (tm-30) REVERT: F 47 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6992 (mm-30) REVERT: F 70 MET cc_start: 0.7243 (tpp) cc_final: 0.6914 (tpp) REVERT: I 29 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6997 (pp) REVERT: I 63 ASP cc_start: 0.6888 (p0) cc_final: 0.5909 (m-30) REVERT: I 211 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7896 (pp) REVERT: I 237 ILE cc_start: 0.8453 (mm) cc_final: 0.8221 (mm) REVERT: I 238 THR cc_start: 0.8029 (m) cc_final: 0.7392 (p) outliers start: 83 outliers final: 56 residues processed: 379 average time/residue: 0.2562 time to fit residues: 153.7232 Evaluate side-chains 360 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 296 time to evaluate : 1.950 ------------------------------------------------------------------------------- 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 89 GLN Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU 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 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL 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 100 VAL 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 16 SER Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 150 VAL 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 252 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 55 ILE 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 29 LEU Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 192 ASP 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 283 LEU Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 186 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 201 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 219 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN ** H 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 HIS ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114999 restraints weight = 27730.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.114196 restraints weight = 25651.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114910 restraints weight = 22402.407| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.8930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18501 Z= 0.159 Angle : 0.579 8.939 25161 Z= 0.301 Chirality : 0.045 0.217 2919 Planarity : 0.004 0.047 3264 Dihedral : 4.205 19.100 2511 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 4.35 % Allowed : 28.64 % Favored : 67.01 % 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: -0.92 (0.17), residues: 2319 helix: 1.51 (0.28), residues: 333 sheet: -0.66 (0.18), residues: 801 loop : -1.16 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 70 HIS 0.007 0.001 HIS I 318 PHE 0.014 0.001 PHE I 231 TYR 0.014 0.002 TYR G 196 ARG 0.005 0.000 ARG G 247 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 386) hydrogen bonds : angle 4.65238 ( 1083) covalent geometry : bond 0.00371 (18501) covalent geometry : angle 0.57886 (25161) *********************** 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 399 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 311 time to evaluate : 2.010 Fit side-chains REVERT: C 17 LYS cc_start: 0.7399 (mtpp) cc_final: 0.7125 (mmtm) REVERT: D 69 TRP cc_start: 0.8685 (m100) cc_final: 0.8400 (m100) REVERT: D 156 ARG cc_start: 0.6258 (pmt-80) cc_final: 0.3732 (tpm170) REVERT: H 23 THR cc_start: 0.8940 (p) cc_final: 0.8599 (t) REVERT: H 142 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7501 (mttp) REVERT: H 327 ASP cc_start: 0.6863 (t0) cc_final: 0.5098 (p0) REVERT: A 91 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6682 (tm-30) REVERT: A 113 LYS cc_start: 0.7395 (tttt) cc_final: 0.7065 (mmtt) REVERT: B 3 HIS cc_start: 0.5364 (OUTLIER) cc_final: 0.5060 (m90) REVERT: B 18 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: B 69 TRP cc_start: 0.8843 (m100) cc_final: 0.7967 (m100) REVERT: B 70 MET cc_start: 0.7722 (tpp) cc_final: 0.7394 (mmt) REVERT: B 78 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.9119 (m) REVERT: B 80 ASP cc_start: 0.7294 (t0) cc_final: 0.6599 (t0) REVERT: B 89 GLN cc_start: 0.7764 (pt0) cc_final: 0.6788 (pt0) REVERT: B 91 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5682 (tm-30) REVERT: B 96 ASP cc_start: 0.7647 (t70) cc_final: 0.6760 (m-30) REVERT: B 113 LYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5372 (mptp) REVERT: G 241 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7166 (p) REVERT: G 247 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7242 (mtm180) REVERT: G 277 MET cc_start: 0.7313 (mmm) cc_final: 0.7037 (mmm) REVERT: G 284 ILE cc_start: 0.8437 (pt) cc_final: 0.8013 (mt) REVERT: G 370 ASP cc_start: 0.7892 (t70) cc_final: 0.7508 (t70) REVERT: E 91 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6886 (tm-30) REVERT: F 17 LYS cc_start: 0.7876 (mttt) cc_final: 0.7534 (mttt) REVERT: I 29 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7183 (pp) REVERT: I 63 ASP cc_start: 0.6906 (p0) cc_final: 0.6187 (m-30) REVERT: I 200 GLN cc_start: 0.7772 (tp40) cc_final: 0.7337 (tt0) REVERT: I 238 THR cc_start: 0.8369 (m) cc_final: 0.7896 (p) outliers start: 88 outliers final: 62 residues processed: 378 average time/residue: 0.2560 time to fit residues: 153.6718 Evaluate side-chains 365 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 296 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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 89 GLN 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 68 GLN Chi-restraints excluded: chain D residue 99 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 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL 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 101 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 113 LYS 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 213 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 46 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 269 LEU Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 127 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116112 restraints weight = 27791.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115190 restraints weight = 31113.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116639 restraints weight = 29726.142| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.9229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18501 Z= 0.135 Angle : 0.563 7.285 25161 Z= 0.294 Chirality : 0.045 0.212 2919 Planarity : 0.004 0.043 3264 Dihedral : 4.149 17.218 2511 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.32 % Favored : 96.55 % Rotamer: Outliers : 3.85 % Allowed : 29.38 % Favored : 66.77 % 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: 1.57 (0.28), residues: 333 sheet: -0.59 (0.18), residues: 807 loop : -1.15 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 70 HIS 0.006 0.001 HIS I 318 PHE 0.017 0.001 PHE I 231 TYR 0.024 0.001 TYR E 141 ARG 0.004 0.000 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 386) hydrogen bonds : angle 4.58506 ( 1083) covalent geometry : bond 0.00314 (18501) covalent geometry : angle 0.56343 (25161) *********************** 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 398 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 320 time to evaluate : 2.072 Fit side-chains revert: symmetry clash REVERT: C 17 LYS cc_start: 0.7418 (mtpp) cc_final: 0.7063 (mmtm) REVERT: C 62 TYR cc_start: 0.8564 (m-80) cc_final: 0.8242 (m-10) REVERT: D 11 MET cc_start: 0.7966 (tpp) cc_final: 0.7763 (tpp) REVERT: D 69 TRP cc_start: 0.8679 (m100) cc_final: 0.8360 (m100) REVERT: H 23 THR cc_start: 0.8988 (p) cc_final: 0.8667 (t) REVERT: H 142 LYS cc_start: 0.7897 (mmmt) cc_final: 0.7483 (mttp) REVERT: H 327 ASP cc_start: 0.6955 (t0) cc_final: 0.5176 (p0) REVERT: H 370 ASP cc_start: 0.6780 (t70) cc_final: 0.6007 (p0) REVERT: H 455 THR cc_start: -0.1446 (OUTLIER) cc_final: -0.1710 (t) REVERT: A 113 LYS cc_start: 0.7303 (tttt) cc_final: 0.7047 (mmtt) REVERT: B 18 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: B 69 TRP cc_start: 0.8833 (m100) cc_final: 0.7954 (m100) REVERT: B 70 MET cc_start: 0.7806 (tpp) cc_final: 0.7529 (mmm) REVERT: B 80 ASP cc_start: 0.7380 (t0) cc_final: 0.6702 (t0) REVERT: B 89 GLN cc_start: 0.7666 (pt0) cc_final: 0.6572 (pt0) REVERT: B 91 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5671 (tm-30) REVERT: B 96 ASP cc_start: 0.7297 (t70) cc_final: 0.6840 (m-30) REVERT: B 113 LYS cc_start: 0.6361 (OUTLIER) cc_final: 0.5585 (mptp) REVERT: G 216 MET cc_start: 0.8070 (mpp) cc_final: 0.6959 (mtt) REVERT: G 247 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7272 (mtm180) REVERT: G 277 MET cc_start: 0.7321 (mmm) cc_final: 0.6971 (mmm) REVERT: G 284 ILE cc_start: 0.8470 (pt) cc_final: 0.8063 (mt) REVERT: G 306 GLU cc_start: 0.7080 (mp0) cc_final: 0.6509 (mm-30) REVERT: G 370 ASP cc_start: 0.7803 (t70) cc_final: 0.7519 (t70) REVERT: E 91 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6852 (tm-30) REVERT: F 17 LYS cc_start: 0.8002 (mttt) cc_final: 0.7672 (mttt) REVERT: F 47 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7055 (mm-30) REVERT: I 29 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7284 (pp) REVERT: I 38 GLN cc_start: 0.8458 (tt0) cc_final: 0.8210 (tt0) REVERT: I 44 ASP cc_start: 0.7700 (m-30) cc_final: 0.7247 (t0) REVERT: I 63 ASP cc_start: 0.6980 (p0) cc_final: 0.6181 (m-30) REVERT: I 200 GLN cc_start: 0.7708 (tp40) cc_final: 0.7241 (tt0) outliers start: 78 outliers final: 62 residues processed: 381 average time/residue: 0.2531 time to fit residues: 152.3700 Evaluate side-chains 364 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 297 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 89 GLN Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU 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 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 455 THR 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 101 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 113 LYS 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 213 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 133 THR 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 150 VAL 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 211 LEU Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 93 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 29 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 198 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 8 optimal weight: 0.0470 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 GLN ** H 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116058 restraints weight = 27584.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115735 restraints weight = 28212.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116267 restraints weight = 25614.345| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.9306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18501 Z= 0.100 Angle : 0.542 8.127 25161 Z= 0.280 Chirality : 0.044 0.192 2919 Planarity : 0.003 0.042 3264 Dihedral : 3.962 16.733 2511 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.85 % Favored : 97.02 % Rotamer: Outliers : 3.21 % Allowed : 29.98 % 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: -0.78 (0.17), residues: 2319 helix: 1.66 (0.28), residues: 333 sheet: -0.53 (0.18), residues: 807 loop : -1.11 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 70 HIS 0.006 0.001 HIS I 318 PHE 0.018 0.001 PHE I 231 TYR 0.017 0.001 TYR G 303 ARG 0.004 0.000 ARG G 247 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 386) hydrogen bonds : angle 4.50538 ( 1083) covalent geometry : bond 0.00222 (18501) covalent geometry : angle 0.54222 (25161) ********************** 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 383 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 318 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: C 17 LYS cc_start: 0.7242 (mtpp) cc_final: 0.7006 (mmtm) REVERT: C 62 TYR cc_start: 0.8516 (m-80) cc_final: 0.8201 (m-10) REVERT: D 69 TRP cc_start: 0.8620 (m100) cc_final: 0.8246 (m100) REVERT: D 91 GLU cc_start: 0.7869 (tp30) cc_final: 0.7397 (tm-30) REVERT: D 126 MET cc_start: 0.7734 (tpp) cc_final: 0.7343 (tpp) REVERT: H 23 THR cc_start: 0.8930 (p) cc_final: 0.8628 (t) REVERT: H 142 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7553 (mttt) REVERT: H 327 ASP cc_start: 0.6927 (t0) cc_final: 0.5297 (p0) REVERT: H 455 THR cc_start: -0.1602 (OUTLIER) cc_final: -0.1877 (t) REVERT: A 1 MET cc_start: 0.7910 (mpp) cc_final: 0.7583 (pmm) REVERT: A 48 PHE cc_start: 0.8736 (m-80) cc_final: 0.8479 (m-80) REVERT: B 69 TRP cc_start: 0.8836 (m100) cc_final: 0.7987 (m100) REVERT: B 70 MET cc_start: 0.7746 (tpp) cc_final: 0.7338 (mmm) REVERT: B 80 ASP cc_start: 0.7457 (t0) cc_final: 0.6872 (t0) REVERT: B 89 GLN cc_start: 0.7693 (pt0) cc_final: 0.6700 (pt0) REVERT: B 91 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.5610 (tm-30) REVERT: B 96 ASP cc_start: 0.7259 (t70) cc_final: 0.6582 (m-30) REVERT: B 113 LYS cc_start: 0.6341 (OUTLIER) cc_final: 0.5552 (mptp) REVERT: G 63 ASP cc_start: 0.6045 (p0) cc_final: 0.5797 (m-30) REVERT: G 247 ARG cc_start: 0.8044 (ttm110) cc_final: 0.7215 (mtm180) REVERT: G 277 MET cc_start: 0.7227 (mmm) cc_final: 0.6969 (mmm) REVERT: G 284 ILE cc_start: 0.8419 (pt) cc_final: 0.8060 (mt) REVERT: G 306 GLU cc_start: 0.7077 (mp0) cc_final: 0.6467 (mm-30) REVERT: F 17 LYS cc_start: 0.8059 (mttt) cc_final: 0.7709 (mttt) REVERT: F 47 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6999 (mm-30) REVERT: I 29 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7168 (pp) REVERT: I 44 ASP cc_start: 0.7582 (m-30) cc_final: 0.7172 (t0) REVERT: I 63 ASP cc_start: 0.6831 (p0) cc_final: 0.6107 (m-30) REVERT: I 200 GLN cc_start: 0.7580 (tp40) cc_final: 0.7193 (tt0) REVERT: I 211 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7853 (pp) outliers start: 65 outliers final: 47 residues processed: 370 average time/residue: 0.2537 time to fit residues: 149.1011 Evaluate side-chains 350 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 89 GLN Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU 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 455 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 266 THR 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 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 18 THR Chi-restraints excluded: chain I residue 29 LEU 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 269 LEU Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 174 optimal weight: 2.9990 chunk 64 optimal weight: 0.0470 chunk 137 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 225 optimal weight: 20.0000 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN C 61 GLN ** H 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 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** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110545 restraints weight = 27849.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109433 restraints weight = 34327.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110726 restraints weight = 29447.747| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.9853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18501 Z= 0.203 Angle : 0.634 8.114 25161 Z= 0.331 Chirality : 0.047 0.212 2919 Planarity : 0.004 0.044 3264 Dihedral : 4.433 17.675 2511 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.10 % Favored : 95.77 % Rotamer: Outliers : 3.41 % Allowed : 29.63 % Favored : 66.96 % 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: 1.37 (0.28), residues: 333 sheet: -0.72 (0.18), residues: 822 loop : -1.16 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 70 HIS 0.007 0.001 HIS I 318 PHE 0.017 0.002 PHE I 231 TYR 0.026 0.002 TYR H 303 ARG 0.008 0.001 ARG H 56 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 386) hydrogen bonds : angle 4.72585 ( 1083) covalent geometry : bond 0.00478 (18501) covalent geometry : angle 0.63378 (25161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5345.41 seconds wall clock time: 95 minutes 3.09 seconds (5703.09 seconds total)