Starting phenix.real_space_refine on Sun Oct 25 02:07:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/38kz_78898/10_2026/38kz_78898.cif Found real_map, /net/cci-nas-00/data/ceres_data/38kz_78898/10_2026/38kz_78898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/38kz_78898/10_2026/38kz_78898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/38kz_78898/10_2026/38kz_78898.map" model { file = "/net/cci-nas-00/data/ceres_data/38kz_78898/10_2026/38kz_78898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/38kz_78898/10_2026/38kz_78898.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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: 6 Type Number sf(0) Gaussians Zn 10 6.06 5 P 30 5.49 5 S 80 5.16 5 C 9320 2.51 5 N 2710 2.21 5 O 2900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15050 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1471 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "B" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1471 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "C" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1471 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "D" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1471 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "E" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1471 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "F" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1471 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "G" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1471 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "H" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1471 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "I" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1471 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "J" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1471 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {' ZN': 1, '8GT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8GT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8GT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8GT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {' ZN': 1, '8GT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {' ZN': 1, '8GT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8GT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 624 SG CYS A 90 62.324 88.410 52.198 1.00145.33 S ATOM 1190 SG CYS A 163 63.943 86.322 49.600 1.00145.91 S ATOM 2095 SG CYS B 90 29.791 69.596 52.185 1.00155.14 S ATOM 2661 SG CYS B 163 32.057 70.433 49.482 1.00156.12 S ATOM 3566 SG CYS C 90 37.660 32.867 52.221 1.00155.96 S ATOM 4132 SG CYS C 163 37.559 35.423 49.592 1.00156.14 S ATOM 5037 SG CYS D 90 74.974 29.051 52.170 1.00158.42 S ATOM 5603 SG CYS D 163 72.572 29.511 49.471 1.00152.62 S ATOM 6508 SG CYS E 90 90.206 63.318 52.147 1.00155.47 S ATOM 7074 SG CYS E 163 88.861 61.299 49.431 1.00144.94 S ATOM 7979 SG CYS F 90 27.777 63.317 32.718 1.00160.29 S ATOM 8545 SG CYS F 163 29.219 61.346 35.431 1.00156.83 S ATOM 9450 SG CYS G 90 43.015 28.986 32.681 1.00166.32 S ATOM 10016 SG CYS G 163 45.276 29.772 35.477 1.00156.47 S ATOM 10921 SG CYS H 90 80.357 32.882 32.763 1.00155.09 S ATOM 11487 SG CYS H 163 80.499 35.291 35.524 1.00157.61 S ATOM 12392 SG CYS I 90 88.240 69.594 32.751 1.00159.15 S ATOM 12958 SG CYS I 163 85.890 70.329 35.453 1.00157.87 S ATOM 13863 SG CYS J 90 55.700 88.434 32.719 1.00155.57 S ATOM 14429 SG CYS J 163 54.205 86.529 35.422 1.00148.63 S Time building chain proxies: 3.35, per 1000 atoms: 0.22 Number of scatterers: 15050 At special positions: 0 Unit cell: (120.36, 116.82, 86.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 10 29.99 S 80 16.00 P 30 15.00 O 2900 8.00 N 2710 7.00 C 9320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 682.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 93 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 163 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 90 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 93 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 90 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 163 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 93 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" ND1 HIS D 93 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 163 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 90 " pdb=" ZN E 302 " pdb="ZN ZN E 302 " - pdb=" ND1 HIS E 93 " pdb="ZN ZN E 302 " - pdb=" SG CYS E 90 " pdb="ZN ZN E 302 " - pdb=" SG CYS E 163 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" ND1 HIS F 93 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 90 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 163 " pdb=" ZN G 302 " pdb="ZN ZN G 302 " - pdb=" ND1 HIS G 93 " pdb="ZN ZN G 302 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 302 " - pdb=" SG CYS G 163 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 93 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 163 " pdb=" ZN I 302 " pdb="ZN ZN I 302 " - pdb=" ND1 HIS I 93 " pdb="ZN ZN I 302 " - pdb=" SG CYS I 163 " pdb="ZN ZN I 302 " - pdb=" SG CYS I 90 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" ND1 HIS J 93 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 163 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 90 " 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3540 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 12 sheets defined 50.1% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 17 through 32 removed outlier: 3.729A pdb=" N ALA A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.788A pdb=" N SER A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.804A pdb=" N ILE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 149 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.503A pdb=" N MET A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 167 " --> pdb=" O CYS A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 167' Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.852A pdb=" N ARG A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.771A pdb=" N ALA B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.754A pdb=" N SER B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 128 removed outlier: 3.776A pdb=" N ILE B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 149 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 188 through 201 removed outlier: 4.070A pdb=" N ARG B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 32 removed outlier: 3.804A pdb=" N ALA C 21 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 56 Processing helix chain 'C' and resid 57 through 60 Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.750A pdb=" N SER C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.753A pdb=" N ILE C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 149 Processing helix chain 'C' and resid 162 through 166 removed outlier: 3.679A pdb=" N MET C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 162 through 166' Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'C' and resid 188 through 200 removed outlier: 3.646A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.734A pdb=" N ALA D 21 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 56 Processing helix chain 'D' and resid 57 through 60 Processing helix chain 'D' and resid 62 through 68 removed outlier: 3.594A pdb=" N SER D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 67 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 128 removed outlier: 3.769A pdb=" N ILE D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 149 Processing helix chain 'D' and resid 162 through 166 removed outlier: 3.504A pdb=" N MET D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 162 through 166' Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.958A pdb=" N ARG D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.854A pdb=" N ALA E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 56 Processing helix chain 'E' and resid 57 through 61 removed outlier: 3.906A pdb=" N THR E 61 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.553A pdb=" N SER E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.775A pdb=" N ILE E 119 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 149 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 188 through 200 removed outlier: 3.825A pdb=" N ARG E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 32 removed outlier: 3.559A pdb=" N ALA F 21 " --> pdb=" O ASP F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 56 Processing helix chain 'F' and resid 57 through 60 Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.664A pdb=" N SER F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 128 removed outlier: 3.718A pdb=" N ILE F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 149 Processing helix chain 'F' and resid 162 through 166 removed outlier: 3.590A pdb=" N MET F 166 " --> pdb=" O LEU F 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 162 through 166' Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'G' and resid 17 through 32 removed outlier: 3.532A pdb=" N ALA G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 56 Processing helix chain 'G' and resid 57 through 60 Processing helix chain 'G' and resid 62 through 68 removed outlier: 3.665A pdb=" N SER G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 128 removed outlier: 3.700A pdb=" N ILE G 119 " --> pdb=" O GLY G 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 149 Processing helix chain 'G' and resid 162 through 166 Processing helix chain 'G' and resid 184 through 188 Processing helix chain 'G' and resid 189 through 200 Processing helix chain 'H' and resid 17 through 32 Processing helix chain 'H' and resid 43 through 56 Processing helix chain 'H' and resid 57 through 60 Processing helix chain 'H' and resid 62 through 68 removed outlier: 3.582A pdb=" N SER H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 128 removed outlier: 3.741A pdb=" N ILE H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 149 Processing helix chain 'H' and resid 184 through 188 Processing helix chain 'H' and resid 188 through 200 removed outlier: 3.790A pdb=" N ARG H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 32 Processing helix chain 'I' and resid 43 through 56 Processing helix chain 'I' and resid 57 through 60 Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.766A pdb=" N SER I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 128 removed outlier: 3.742A pdb=" N ILE I 119 " --> pdb=" O GLY I 115 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 149 Processing helix chain 'I' and resid 184 through 188 Processing helix chain 'I' and resid 189 through 201 removed outlier: 3.699A pdb=" N ARG I 201 " --> pdb=" O ASP I 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 32 Processing helix chain 'J' and resid 43 through 56 Processing helix chain 'J' and resid 57 through 60 Processing helix chain 'J' and resid 62 through 68 removed outlier: 3.806A pdb=" N SER J 65 " --> pdb=" O ASP J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 128 removed outlier: 3.686A pdb=" N ILE J 119 " --> pdb=" O GLY J 115 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA J 120 " --> pdb=" O LEU J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 149 Processing helix chain 'J' and resid 162 through 166 removed outlier: 3.585A pdb=" N MET J 166 " --> pdb=" O LEU J 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 162 through 166' Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'J' and resid 189 through 200 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 90 removed outlier: 5.290A pdb=" N LEU A 80 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR A 105 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LYS A 82 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 103 " --> pdb=" O LYS A 82 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 96 through 106 current: chain 'A' and resid 175 through 183 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 175 through 183 current: chain 'B' and resid 96 through 106 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 96 through 106 current: chain 'B' and resid 175 through 183 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 175 through 183 current: chain 'C' and resid 96 through 106 removed outlier: 3.926A pdb=" N GLY C 152 " --> pdb=" O ILE C 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 175 through 183 current: chain 'D' and resid 96 through 106 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 96 through 106 current: chain 'D' and resid 175 through 183 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 175 through 183 current: chain 'E' and resid 96 through 106 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 96 through 106 current: chain 'E' and resid 175 through 183 Processing sheet with id=AA3, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 70 through 72 Processing sheet with id=AA6, first strand: chain 'E' and resid 70 through 72 Processing sheet with id=AA7, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'F' and resid 79 through 90 removed outlier: 5.286A pdb=" N LEU F 80 " --> pdb=" O TYR F 105 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR F 105 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LYS F 82 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL F 103 " --> pdb=" O LYS F 82 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 96 through 106 current: chain 'F' and resid 175 through 183 removed outlier: 5.295A pdb=" N LEU G 80 " --> pdb=" O TYR G 105 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N TYR G 105 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS G 82 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL G 103 " --> pdb=" O LYS G 82 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 96 through 106 current: chain 'G' and resid 175 through 183 removed outlier: 5.291A pdb=" N LEU H 80 " --> pdb=" O TYR H 105 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR H 105 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS H 82 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL H 103 " --> pdb=" O LYS H 82 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 96 through 106 current: chain 'H' and resid 175 through 183 removed outlier: 5.251A pdb=" N LEU I 80 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR I 105 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS I 82 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL I 103 " --> pdb=" O LYS I 82 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 96 through 106 current: chain 'I' and resid 175 through 183 removed outlier: 5.283A pdb=" N LEU J 80 " --> pdb=" O TYR J 105 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TYR J 105 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS J 82 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL J 103 " --> pdb=" O LYS J 82 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 96 through 106 current: chain 'J' and resid 175 through 183 Processing sheet with id=AA9, first strand: chain 'G' and resid 70 through 72 Processing sheet with id=AB1, first strand: chain 'H' and resid 70 through 72 Processing sheet with id=AB2, first strand: chain 'I' and resid 70 through 72 Processing sheet with id=AB3, first strand: chain 'J' and resid 70 through 72 652 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2524 1.31 - 1.43: 3676 1.43 - 1.56: 8900 1.56 - 1.68: 60 1.68 - 1.81: 140 Bond restraints: 15300 Sorted by residual: bond pdb=" C3' 8GT B 303 " pdb=" C4' 8GT B 303 " ideal model delta sigma weight residual 1.537 1.306 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3' 8GT E 301 " pdb=" C4' 8GT E 301 " ideal model delta sigma weight residual 1.537 1.307 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3' 8GT I 301 " pdb=" C4' 8GT I 301 " ideal model delta sigma weight residual 1.537 1.307 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3' 8GT G 303 " pdb=" C4' 8GT G 303 " ideal model delta sigma weight residual 1.537 1.307 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3' 8GT D 302 " pdb=" C4' 8GT D 302 " ideal model delta sigma weight residual 1.537 1.308 0.229 2.00e-02 2.50e+03 1.32e+02 ... (remaining 15295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 20359 2.57 - 5.15: 292 5.15 - 7.72: 67 7.72 - 10.29: 58 10.29 - 12.87: 14 Bond angle restraints: 20790 Sorted by residual: angle pdb=" O1A 8GT C 302 " pdb=" PA 8GT C 302 " pdb=" O2A 8GT C 302 " ideal model delta sigma weight residual 121.62 108.75 12.87 3.00e+00 1.11e-01 1.84e+01 angle pdb=" O1A 8GT D 302 " pdb=" PA 8GT D 302 " pdb=" O2A 8GT D 302 " ideal model delta sigma weight residual 121.62 108.94 12.68 3.00e+00 1.11e-01 1.79e+01 angle pdb=" O1A 8GT G 301 " pdb=" PA 8GT G 301 " pdb=" O2A 8GT G 301 " ideal model delta sigma weight residual 121.62 109.01 12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" O1A 8GT I 301 " pdb=" PA 8GT I 301 " pdb=" O2A 8GT I 301 " ideal model delta sigma weight residual 121.62 109.06 12.56 3.00e+00 1.11e-01 1.75e+01 angle pdb=" O1A 8GT G 303 " pdb=" PA 8GT G 303 " pdb=" O2A 8GT G 303 " ideal model delta sigma weight residual 121.62 109.14 12.48 3.00e+00 1.11e-01 1.73e+01 ... (remaining 20785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8095 17.98 - 35.95: 1082 35.95 - 53.93: 314 53.93 - 71.91: 45 71.91 - 89.89: 24 Dihedral angle restraints: 9560 sinusoidal: 4080 harmonic: 5480 Sorted by residual: dihedral pdb=" CA PRO D 130 " pdb=" C PRO D 130 " pdb=" N GLN D 131 " pdb=" CA GLN D 131 " ideal model delta harmonic sigma weight residual -180.00 -159.47 -20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PRO A 130 " pdb=" C PRO A 130 " pdb=" N GLN A 131 " pdb=" CA GLN A 131 " ideal model delta harmonic sigma weight residual -180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PRO H 130 " pdb=" C PRO H 130 " pdb=" N GLN H 131 " pdb=" CA GLN H 131 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 9557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1842 0.040 - 0.081: 334 0.081 - 0.121: 149 0.121 - 0.161: 45 0.161 - 0.202: 10 Chirality restraints: 2380 Sorted by residual: chirality pdb=" C3' 8GT D 302 " pdb=" C2' 8GT D 302 " pdb=" C4' 8GT D 302 " pdb=" O3' 8GT D 302 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C3' 8GT C 302 " pdb=" C2' 8GT C 302 " pdb=" C4' 8GT C 302 " pdb=" O3' 8GT C 302 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" C3' 8GT I 301 " pdb=" C2' 8GT I 301 " pdb=" C4' 8GT I 301 " pdb=" O3' 8GT I 301 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 2377 not shown) Planarity restraints: 2650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 44 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO J 45 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO J 45 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 45 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 44 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO G 45 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO G 45 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 45 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 44 " 0.020 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO H 45 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO H 45 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 45 " 0.018 5.00e-02 4.00e+02 ... (remaining 2647 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 15 2.45 - 3.06: 9866 3.06 - 3.67: 21724 3.67 - 4.29: 32221 4.29 - 4.90: 56405 Nonbonded interactions: 120231 Sorted by model distance: nonbonded pdb="ZN ZN J 301 " pdb=" O8 8GT J 302 " model vdw 1.833 2.230 nonbonded pdb="ZN ZN B 301 " pdb=" O8 8GT B 302 " model vdw 1.856 2.230 nonbonded pdb="ZN ZN H 301 " pdb=" O8 8GT I 301 " model vdw 1.857 2.230 nonbonded pdb=" O8 8GT C 302 " pdb="ZN ZN D 301 " model vdw 1.857 2.230 nonbonded pdb=" O8 8GT B 303 " pdb="ZN ZN C 301 " model vdw 1.858 2.230 ... (remaining 120226 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 13 through 201) selection = (chain 'B' and resid 13 through 201) selection = (chain 'C' and resid 13 through 201) selection = (chain 'D' and resid 13 through 201) selection = (chain 'E' and resid 13 through 201) selection = (chain 'F' and resid 13 through 201) selection = (chain 'G' and resid 13 through 201) selection = (chain 'H' and resid 13 through 201) selection = (chain 'I' and resid 13 through 201) selection = (chain 'J' and resid 13 through 201) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.790 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 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 : 0.015 0.272 15330 Z= 0.688 Angle : 0.919 12.865 20790 Z= 0.379 Chirality : 0.043 0.202 2380 Planarity : 0.003 0.033 2650 Dihedral : 17.785 89.885 6020 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.96 % Allowed : 19.17 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.20), residues: 1870 helix: 2.41 (0.20), residues: 780 sheet: 1.48 (0.23), residues: 470 loop : -1.18 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 167 TYR 0.004 0.001 TYR I 126 PHE 0.008 0.001 PHE I 97 HIS 0.008 0.001 HIS I 93 Details of bonding type rmsd/Z covalent geometry : bond 0.01296 / 0.65 (15300) covalent geometry : angle 0.91947 / 0.38 (20790) hydrogen bonds : bond 0.14045 / 8.54 ( 652) hydrogen bonds : angle 6.04386 / 4.13 ( 1821) metal coordination : bond 0.15845 / 10.70 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 505 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8887 (mm-30) REVERT: A 77 GLU cc_start: 0.9098 (mp0) cc_final: 0.8734 (mp0) REVERT: A 83 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9267 (mm-30) REVERT: A 87 TYR cc_start: 0.9512 (m-80) cc_final: 0.9296 (m-80) REVERT: A 171 LYS cc_start: 0.9671 (mmtt) cc_final: 0.9386 (mmmt) REVERT: A 176 THR cc_start: 0.9598 (m) cc_final: 0.9055 (t) REVERT: A 197 ASP cc_start: 0.9441 (t0) cc_final: 0.9185 (m-30) REVERT: B 22 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8689 (mm-30) REVERT: B 70 MET cc_start: 0.9012 (mmm) cc_final: 0.8658 (mmm) REVERT: B 83 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9254 (mm-30) REVERT: B 131 GLN cc_start: 0.8576 (tt0) cc_final: 0.8371 (tt0) REVERT: B 171 LYS cc_start: 0.9675 (mmtt) cc_final: 0.9226 (mmmt) REVERT: B 174 SER cc_start: 0.9709 (m) cc_final: 0.9349 (p) REVERT: B 176 THR cc_start: 0.9617 (m) cc_final: 0.9098 (t) REVERT: C 22 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8969 (mm-30) REVERT: C 77 GLU cc_start: 0.9082 (mp0) cc_final: 0.8674 (mp0) REVERT: C 147 LYS cc_start: 0.9488 (tptt) cc_final: 0.9125 (tptm) REVERT: C 171 LYS cc_start: 0.9706 (mmtt) cc_final: 0.9142 (mmmt) REVERT: C 176 THR cc_start: 0.9595 (m) cc_final: 0.9095 (t) REVERT: C 188 ASN cc_start: 0.9388 (t0) cc_final: 0.9075 (t0) REVERT: D 22 GLU cc_start: 0.9387 (mt-10) cc_final: 0.8862 (mm-30) REVERT: D 77 GLU cc_start: 0.8795 (mp0) cc_final: 0.8352 (mp0) REVERT: D 174 SER cc_start: 0.9698 (m) cc_final: 0.9411 (p) REVERT: D 176 THR cc_start: 0.9566 (m) cc_final: 0.8955 (t) REVERT: D 197 ASP cc_start: 0.9426 (t0) cc_final: 0.9225 (m-30) REVERT: E 22 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8987 (mm-30) REVERT: E 77 GLU cc_start: 0.8776 (mp0) cc_final: 0.8219 (mp0) REVERT: E 83 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9210 (mm-30) REVERT: E 86 MET cc_start: 0.9325 (tmm) cc_final: 0.9125 (tmm) REVERT: E 128 LYS cc_start: 0.9472 (mmtt) cc_final: 0.9201 (mmtp) REVERT: E 160 GLU cc_start: 0.9054 (tt0) cc_final: 0.8841 (tt0) REVERT: E 171 LYS cc_start: 0.9745 (mmtt) cc_final: 0.9282 (mmmt) REVERT: E 174 SER cc_start: 0.9659 (m) cc_final: 0.9269 (p) REVERT: E 176 THR cc_start: 0.9620 (m) cc_final: 0.9230 (t) REVERT: F 54 GLU cc_start: 0.9420 (tp30) cc_final: 0.9144 (tt0) REVERT: F 77 GLU cc_start: 0.8221 (mp0) cc_final: 0.7887 (mp0) REVERT: F 160 GLU cc_start: 0.9111 (tt0) cc_final: 0.8907 (tt0) REVERT: F 171 LYS cc_start: 0.9730 (mmtt) cc_final: 0.9100 (mmmt) REVERT: F 176 THR cc_start: 0.9585 (m) cc_final: 0.9186 (t) REVERT: F 194 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9135 (mt-10) REVERT: F 197 ASP cc_start: 0.9332 (m-30) cc_final: 0.8971 (m-30) REVERT: G 22 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8860 (mm-30) REVERT: G 83 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9056 (mm-30) REVERT: G 171 LYS cc_start: 0.9786 (mmtt) cc_final: 0.9061 (mmmt) REVERT: G 176 THR cc_start: 0.9569 (m) cc_final: 0.9077 (t) REVERT: G 188 ASN cc_start: 0.9232 (t0) cc_final: 0.8864 (t0) REVERT: G 194 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9126 (mt-10) REVERT: H 51 SER cc_start: 0.9638 (t) cc_final: 0.9430 (p) REVERT: H 83 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9227 (mm-30) REVERT: H 86 MET cc_start: 0.9301 (ttp) cc_final: 0.9082 (tmm) REVERT: H 132 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9018 (p) REVERT: H 171 LYS cc_start: 0.9787 (mmtt) cc_final: 0.9268 (mmmt) REVERT: H 176 THR cc_start: 0.9583 (m) cc_final: 0.9260 (t) REVERT: I 30 TYR cc_start: 0.9424 (m-80) cc_final: 0.9209 (m-80) REVERT: I 70 MET cc_start: 0.9056 (mmm) cc_final: 0.8797 (mmm) REVERT: I 77 GLU cc_start: 0.8897 (mp0) cc_final: 0.8343 (mt-10) REVERT: I 83 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9202 (mm-30) REVERT: I 131 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8420 (tt0) REVERT: I 158 GLU cc_start: 0.8725 (pp20) cc_final: 0.8410 (pp20) REVERT: I 171 LYS cc_start: 0.9736 (mmtt) cc_final: 0.9246 (mmmt) REVERT: I 174 SER cc_start: 0.9671 (m) cc_final: 0.9275 (p) REVERT: I 176 THR cc_start: 0.9607 (m) cc_final: 0.9147 (t) REVERT: I 197 ASP cc_start: 0.9281 (m-30) cc_final: 0.8919 (m-30) REVERT: J 22 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9036 (mm-30) REVERT: J 77 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8324 (mt-10) REVERT: J 83 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9209 (mm-30) REVERT: J 87 TYR cc_start: 0.9448 (m-80) cc_final: 0.9212 (m-80) REVERT: J 145 MET cc_start: 0.9418 (mmm) cc_final: 0.9197 (tpp) REVERT: J 158 GLU cc_start: 0.8829 (pt0) cc_final: 0.8369 (pp20) REVERT: J 171 LYS cc_start: 0.9724 (mmtt) cc_final: 0.9146 (mmmt) REVERT: J 176 THR cc_start: 0.9636 (m) cc_final: 0.9282 (t) REVERT: J 188 ASN cc_start: 0.9151 (t0) cc_final: 0.8894 (t0) REVERT: J 194 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9295 (mt-10) REVERT: J 197 ASP cc_start: 0.9478 (m-30) cc_final: 0.9109 (m-30) outliers start: 15 outliers final: 7 residues processed: 520 average time/residue: 0.1264 time to fit residues: 94.4128 Evaluate side-chains 359 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 351 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 132 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS G 18 GLN I 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.050788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.038827 restraints weight = 49712.859| |-----------------------------------------------------------------------------| r_work (start): 0.2452 rms_B_bonded: 4.38 r_work: 0.2273 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15330 Z= 0.188 Angle : 0.576 7.048 20790 Z= 0.298 Chirality : 0.044 0.161 2380 Planarity : 0.004 0.034 2650 Dihedral : 9.897 59.781 2502 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.93 % Allowed : 21.53 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.20), residues: 1870 helix: 2.51 (0.19), residues: 780 sheet: 1.98 (0.23), residues: 460 loop : -1.02 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 201 TYR 0.007 0.001 TYR H 87 PHE 0.013 0.001 PHE G 97 HIS 0.002 0.000 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (15300) covalent geometry : angle 0.57633 / 0.30 (20790) hydrogen bonds : bond 0.03910 / 2.54 ( 652) hydrogen bonds : angle 4.80674 / 3.33 ( 1821) metal coordination : bond 0.01565 / 1.06 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 341 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9448 (mt-10) cc_final: 0.8935 (mm-30) REVERT: A 77 GLU cc_start: 0.9083 (mp0) cc_final: 0.8668 (mp0) REVERT: A 83 GLU cc_start: 0.9644 (mm-30) cc_final: 0.9390 (mm-30) REVERT: A 86 MET cc_start: 0.9247 (tmm) cc_final: 0.9013 (tmm) REVERT: A 131 GLN cc_start: 0.8947 (tp40) cc_final: 0.8442 (tp40) REVERT: A 145 MET cc_start: 0.9399 (tpp) cc_final: 0.9173 (tpp) REVERT: A 176 THR cc_start: 0.9640 (m) cc_final: 0.9079 (t) REVERT: A 197 ASP cc_start: 0.9617 (t0) cc_final: 0.9278 (m-30) REVERT: B 69 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9029 (p) REVERT: B 70 MET cc_start: 0.8966 (mmm) cc_final: 0.8602 (mmm) REVERT: B 86 MET cc_start: 0.9313 (tmm) cc_final: 0.9062 (tmm) REVERT: B 131 GLN cc_start: 0.8781 (tt0) cc_final: 0.8514 (tt0) REVERT: B 171 LYS cc_start: 0.9705 (mmtt) cc_final: 0.9157 (mmmt) REVERT: B 176 THR cc_start: 0.9587 (m) cc_final: 0.9056 (t) REVERT: C 70 MET cc_start: 0.9229 (mmm) cc_final: 0.8956 (mmm) REVERT: C 86 MET cc_start: 0.9187 (tmm) cc_final: 0.8839 (tmm) REVERT: C 171 LYS cc_start: 0.9756 (mmtt) cc_final: 0.9079 (mmmt) REVERT: C 176 THR cc_start: 0.9656 (m) cc_final: 0.9162 (t) REVERT: C 188 ASN cc_start: 0.9239 (t0) cc_final: 0.8827 (t0) REVERT: D 69 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9159 (p) REVERT: D 171 LYS cc_start: 0.9748 (mmtt) cc_final: 0.9095 (mmmt) REVERT: D 176 THR cc_start: 0.9692 (m) cc_final: 0.9064 (t) REVERT: D 188 ASN cc_start: 0.8902 (t0) cc_final: 0.8664 (t0) REVERT: D 197 ASP cc_start: 0.9609 (t0) cc_final: 0.9334 (m-30) REVERT: E 22 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9111 (mm-30) REVERT: E 54 GLU cc_start: 0.9240 (tt0) cc_final: 0.8905 (tm-30) REVERT: E 70 MET cc_start: 0.9283 (mmm) cc_final: 0.8965 (mmm) REVERT: E 83 GLU cc_start: 0.9555 (mm-30) cc_final: 0.9304 (mm-30) REVERT: E 86 MET cc_start: 0.9509 (tmm) cc_final: 0.9205 (tmm) REVERT: E 131 GLN cc_start: 0.8850 (tt0) cc_final: 0.8480 (mt0) REVERT: E 160 GLU cc_start: 0.9409 (tt0) cc_final: 0.9132 (tt0) REVERT: E 171 LYS cc_start: 0.9748 (mmtt) cc_final: 0.9225 (mmmt) REVERT: E 174 SER cc_start: 0.9738 (m) cc_final: 0.9344 (p) REVERT: E 176 THR cc_start: 0.9670 (m) cc_final: 0.9233 (t) REVERT: F 160 GLU cc_start: 0.9382 (tt0) cc_final: 0.9135 (tt0) REVERT: F 171 LYS cc_start: 0.9735 (mmtt) cc_final: 0.9161 (mmmt) REVERT: F 176 THR cc_start: 0.9732 (m) cc_final: 0.9321 (t) REVERT: F 197 ASP cc_start: 0.9464 (m-30) cc_final: 0.9078 (m-30) REVERT: G 54 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.9027 (tm-30) REVERT: G 86 MET cc_start: 0.9252 (tmm) cc_final: 0.9014 (tmm) REVERT: G 158 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8833 (pp20) REVERT: G 171 LYS cc_start: 0.9782 (mmtt) cc_final: 0.8910 (mmmt) REVERT: G 176 THR cc_start: 0.9697 (m) cc_final: 0.9163 (t) REVERT: G 188 ASN cc_start: 0.9063 (t0) cc_final: 0.8726 (t0) REVERT: G 197 ASP cc_start: 0.9542 (m-30) cc_final: 0.9179 (m-30) REVERT: H 22 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8919 (tp30) REVERT: H 27 GLU cc_start: 0.9579 (tp30) cc_final: 0.9373 (tp30) REVERT: H 70 MET cc_start: 0.9271 (mmm) cc_final: 0.8985 (mmm) REVERT: H 77 GLU cc_start: 0.8294 (mp0) cc_final: 0.7798 (mp0) REVERT: H 83 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9265 (mm-30) REVERT: H 86 MET cc_start: 0.9588 (ttp) cc_final: 0.9163 (tmm) REVERT: H 131 GLN cc_start: 0.8956 (mt0) cc_final: 0.8577 (tt0) REVERT: H 145 MET cc_start: 0.9382 (tpp) cc_final: 0.8731 (tpp) REVERT: H 164 MET cc_start: 0.9692 (mtp) cc_final: 0.9487 (mtp) REVERT: H 171 LYS cc_start: 0.9756 (mmtt) cc_final: 0.9215 (mmmt) REVERT: H 176 THR cc_start: 0.9745 (m) cc_final: 0.9348 (t) REVERT: H 188 ASN cc_start: 0.8664 (t0) cc_final: 0.8354 (t0) REVERT: H 197 ASP cc_start: 0.9438 (m-30) cc_final: 0.8950 (m-30) REVERT: I 22 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8650 (mm-30) REVERT: I 30 TYR cc_start: 0.9534 (m-80) cc_final: 0.9301 (m-80) REVERT: I 70 MET cc_start: 0.9110 (mmm) cc_final: 0.8696 (mmm) REVERT: I 83 GLU cc_start: 0.9435 (mm-30) cc_final: 0.9210 (mm-30) REVERT: I 86 MET cc_start: 0.9152 (tmm) cc_final: 0.8868 (tmm) REVERT: I 131 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8855 (mt0) REVERT: I 158 GLU cc_start: 0.9093 (pp20) cc_final: 0.8674 (pp20) REVERT: I 171 LYS cc_start: 0.9733 (mmtt) cc_final: 0.9141 (mmmt) REVERT: I 176 THR cc_start: 0.9708 (m) cc_final: 0.9220 (t) REVERT: I 197 ASP cc_start: 0.9489 (m-30) cc_final: 0.9092 (m-30) REVERT: J 70 MET cc_start: 0.9280 (mmm) cc_final: 0.9042 (mmm) REVERT: J 86 MET cc_start: 0.9201 (tmm) cc_final: 0.8971 (tmm) REVERT: J 100 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8600 (p) REVERT: J 128 LYS cc_start: 0.9436 (mmtp) cc_final: 0.9211 (mmmm) REVERT: J 131 GLN cc_start: 0.8972 (mt0) cc_final: 0.8748 (tt0) REVERT: J 132 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8570 (p) REVERT: J 176 THR cc_start: 0.9673 (m) cc_final: 0.9284 (t) REVERT: J 188 ASN cc_start: 0.9023 (t0) cc_final: 0.8689 (t0) REVERT: J 197 ASP cc_start: 0.9706 (m-30) cc_final: 0.9292 (m-30) outliers start: 46 outliers final: 13 residues processed: 373 average time/residue: 0.1160 time to fit residues: 63.9492 Evaluate side-chains 336 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 317 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 177 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [173, 20, 5, 96, 127, 106, 141, 81, 149, 38, 51] chunk 173 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 141 optimal weight: 0.4980 chunk 81 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS ** E 75 HIS ** 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 = 0.2820 r_free = 0.2820 target = 0.051329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.039696 restraints weight = 49361.197| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 4.28 r_work: 0.2319 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15330 Z= 0.107 Angle : 0.497 5.614 20790 Z= 0.262 Chirality : 0.042 0.153 2380 Planarity : 0.003 0.033 2650 Dihedral : 9.142 57.046 2499 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.10 % Allowed : 21.53 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.20), residues: 1870 helix: 2.56 (0.19), residues: 780 sheet: 1.95 (0.24), residues: 460 loop : -0.73 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 151 TYR 0.012 0.001 TYR J 87 PHE 0.010 0.001 PHE G 97 HIS 0.004 0.000 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15300) covalent geometry : angle 0.49657 / 0.26 (20790) hydrogen bonds : bond 0.03238 / 2.13 ( 652) hydrogen bonds : angle 4.51133 / 3.13 ( 1821) metal coordination : bond 0.00399 / 0.27 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 350 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9447 (mt-10) cc_final: 0.9145 (mm-30) REVERT: A 54 GLU cc_start: 0.9243 (tt0) cc_final: 0.9025 (tt0) REVERT: A 70 MET cc_start: 0.9071 (mmm) cc_final: 0.8753 (mmm) REVERT: A 77 GLU cc_start: 0.8999 (mp0) cc_final: 0.8621 (mp0) REVERT: A 83 GLU cc_start: 0.9633 (mm-30) cc_final: 0.9023 (mp0) REVERT: A 86 MET cc_start: 0.9232 (tmm) cc_final: 0.8895 (tmm) REVERT: A 131 GLN cc_start: 0.8947 (tp40) cc_final: 0.8365 (tp40) REVERT: A 145 MET cc_start: 0.9412 (tpp) cc_final: 0.9074 (tpp) REVERT: A 147 LYS cc_start: 0.9565 (mmmm) cc_final: 0.9354 (tppp) REVERT: A 171 LYS cc_start: 0.9661 (mmtt) cc_final: 0.9372 (mmmt) REVERT: A 176 THR cc_start: 0.9667 (m) cc_final: 0.9161 (t) REVERT: A 197 ASP cc_start: 0.9625 (t0) cc_final: 0.9269 (m-30) REVERT: B 70 MET cc_start: 0.8874 (mmm) cc_final: 0.8529 (mmm) REVERT: B 86 MET cc_start: 0.9363 (tmm) cc_final: 0.9061 (tmm) REVERT: B 131 GLN cc_start: 0.8639 (tt0) cc_final: 0.8076 (tt0) REVERT: B 171 LYS cc_start: 0.9769 (mmtt) cc_final: 0.9147 (mmmt) REVERT: B 176 THR cc_start: 0.9612 (m) cc_final: 0.9108 (t) REVERT: B 197 ASP cc_start: 0.9386 (m-30) cc_final: 0.9073 (m-30) REVERT: C 70 MET cc_start: 0.9231 (mmm) cc_final: 0.8973 (mmm) REVERT: C 76 ASP cc_start: 0.9417 (OUTLIER) cc_final: 0.9110 (t0) REVERT: C 86 MET cc_start: 0.9272 (tmm) cc_final: 0.8829 (tmm) REVERT: C 145 MET cc_start: 0.9277 (tpp) cc_final: 0.8585 (tpp) REVERT: C 171 LYS cc_start: 0.9755 (mmtt) cc_final: 0.9058 (mmmt) REVERT: C 176 THR cc_start: 0.9666 (m) cc_final: 0.9154 (t) REVERT: C 188 ASN cc_start: 0.9291 (t0) cc_final: 0.8838 (t0) REVERT: D 131 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8654 (pp30) REVERT: D 136 LEU cc_start: 0.9780 (tt) cc_final: 0.9550 (tp) REVERT: D 171 LYS cc_start: 0.9786 (mmtt) cc_final: 0.8954 (mmmt) REVERT: D 176 THR cc_start: 0.9756 (m) cc_final: 0.9195 (t) REVERT: D 188 ASN cc_start: 0.9039 (t0) cc_final: 0.8679 (t0) REVERT: E 22 GLU cc_start: 0.9432 (mt-10) cc_final: 0.9084 (mm-30) REVERT: E 54 GLU cc_start: 0.9281 (tt0) cc_final: 0.8965 (tm-30) REVERT: E 68 ASN cc_start: 0.8627 (m110) cc_final: 0.8283 (m110) REVERT: E 70 MET cc_start: 0.9228 (mmm) cc_final: 0.8924 (mmm) REVERT: E 77 GLU cc_start: 0.9082 (mm-30) cc_final: 0.7965 (mt-10) REVERT: E 83 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9276 (mm-30) REVERT: E 86 MET cc_start: 0.9468 (tmm) cc_final: 0.9161 (tmm) REVERT: E 160 GLU cc_start: 0.9415 (tt0) cc_final: 0.9067 (tt0) REVERT: E 171 LYS cc_start: 0.9734 (mmtt) cc_final: 0.9104 (mmmt) REVERT: E 176 THR cc_start: 0.9665 (m) cc_final: 0.9212 (t) REVERT: E 188 ASN cc_start: 0.8928 (t0) cc_final: 0.8419 (t0) REVERT: F 147 LYS cc_start: 0.9232 (tppp) cc_final: 0.9013 (tppp) REVERT: F 160 GLU cc_start: 0.9376 (tt0) cc_final: 0.9120 (tt0) REVERT: F 171 LYS cc_start: 0.9775 (mmtt) cc_final: 0.9104 (mmmt) REVERT: F 176 THR cc_start: 0.9738 (m) cc_final: 0.9295 (t) REVERT: F 197 ASP cc_start: 0.9481 (m-30) cc_final: 0.9101 (m-30) REVERT: G 86 MET cc_start: 0.9341 (tmm) cc_final: 0.9039 (tmm) REVERT: G 124 ASP cc_start: 0.9453 (t0) cc_final: 0.9168 (t0) REVERT: G 131 GLN cc_start: 0.8870 (mt0) cc_final: 0.8517 (tt0) REVERT: G 145 MET cc_start: 0.9199 (tpp) cc_final: 0.8887 (tpp) REVERT: G 171 LYS cc_start: 0.9747 (mmtt) cc_final: 0.8854 (mmmt) REVERT: G 188 ASN cc_start: 0.9043 (t0) cc_final: 0.8741 (t0) REVERT: G 197 ASP cc_start: 0.9506 (m-30) cc_final: 0.9219 (m-30) REVERT: H 22 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8803 (mm-30) REVERT: H 27 GLU cc_start: 0.9562 (tp30) cc_final: 0.9329 (tp30) REVERT: H 70 MET cc_start: 0.9271 (mmm) cc_final: 0.8971 (mmm) REVERT: H 73 GLU cc_start: 0.8957 (mp0) cc_final: 0.8431 (mp0) REVERT: H 77 GLU cc_start: 0.8278 (mp0) cc_final: 0.7844 (mp0) REVERT: H 83 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9156 (mm-30) REVERT: H 86 MET cc_start: 0.9590 (ttp) cc_final: 0.8928 (tmm) REVERT: H 131 GLN cc_start: 0.8877 (mt0) cc_final: 0.8591 (tt0) REVERT: H 145 MET cc_start: 0.9387 (tpp) cc_final: 0.8664 (tpp) REVERT: H 171 LYS cc_start: 0.9742 (mmtt) cc_final: 0.9194 (mmmt) REVERT: H 176 THR cc_start: 0.9743 (m) cc_final: 0.9332 (t) REVERT: H 188 ASN cc_start: 0.8805 (t0) cc_final: 0.8407 (t0) REVERT: H 197 ASP cc_start: 0.9439 (m-30) cc_final: 0.8936 (m-30) REVERT: I 22 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8612 (mm-30) REVERT: I 30 TYR cc_start: 0.9503 (m-80) cc_final: 0.9248 (m-80) REVERT: I 54 GLU cc_start: 0.9347 (tt0) cc_final: 0.9016 (tm-30) REVERT: I 70 MET cc_start: 0.9058 (mmm) cc_final: 0.8653 (mmm) REVERT: I 77 GLU cc_start: 0.8972 (mp0) cc_final: 0.8416 (mt-10) REVERT: I 83 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9210 (mm-30) REVERT: I 86 MET cc_start: 0.9209 (tmm) cc_final: 0.8859 (tmm) REVERT: I 158 GLU cc_start: 0.9066 (pp20) cc_final: 0.8590 (pp20) REVERT: I 171 LYS cc_start: 0.9799 (mmtt) cc_final: 0.9126 (mmmt) REVERT: I 176 THR cc_start: 0.9691 (m) cc_final: 0.9143 (t) REVERT: I 197 ASP cc_start: 0.9478 (m-30) cc_final: 0.9194 (m-30) REVERT: J 70 MET cc_start: 0.9276 (mmm) cc_final: 0.9035 (mmm) REVERT: J 86 MET cc_start: 0.9211 (tmm) cc_final: 0.8871 (tmm) REVERT: J 100 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8618 (p) REVERT: J 128 LYS cc_start: 0.9448 (mmtp) cc_final: 0.9179 (mmmm) REVERT: J 131 GLN cc_start: 0.8802 (mt0) cc_final: 0.8560 (tt0) REVERT: J 132 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8570 (p) REVERT: J 176 THR cc_start: 0.9668 (m) cc_final: 0.9334 (t) REVERT: J 188 ASN cc_start: 0.8960 (t0) cc_final: 0.8625 (t0) REVERT: J 197 ASP cc_start: 0.9706 (m-30) cc_final: 0.9280 (m-30) outliers start: 33 outliers final: 15 residues processed: 370 average time/residue: 0.1257 time to fit residues: 68.5703 Evaluate side-chains 348 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 329 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 177 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [7, 74, 103, 104, 84, 25, 134, 97, 139, 82, 135] chunk 7 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 139 optimal weight: 0.0010 chunk 82 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 HIS ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 HIS I 68 ASN I 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.051091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.039475 restraints weight = 50030.099| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 4.32 r_work: 0.2322 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15330 Z= 0.115 Angle : 0.482 5.699 20790 Z= 0.254 Chirality : 0.042 0.149 2380 Planarity : 0.003 0.031 2650 Dihedral : 8.751 57.457 2499 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.29 % Allowed : 21.46 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.20), residues: 1870 helix: 2.58 (0.19), residues: 780 sheet: 2.06 (0.24), residues: 460 loop : -0.63 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 151 TYR 0.016 0.001 TYR J 87 PHE 0.011 0.001 PHE J 97 HIS 0.002 0.000 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15300) covalent geometry : angle 0.48178 / 0.25 (20790) hydrogen bonds : bond 0.03120 / 2.05 ( 652) hydrogen bonds : angle 4.39493 / 3.06 ( 1821) metal coordination : bond 0.00390 / 0.27 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 334 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9140 (mm-30) REVERT: A 54 GLU cc_start: 0.9239 (tt0) cc_final: 0.8968 (tm-30) REVERT: A 70 MET cc_start: 0.8983 (mmm) cc_final: 0.8598 (mmm) REVERT: A 77 GLU cc_start: 0.8998 (mp0) cc_final: 0.8590 (mp0) REVERT: A 83 GLU cc_start: 0.9627 (mm-30) cc_final: 0.9015 (mp0) REVERT: A 86 MET cc_start: 0.9200 (tmm) cc_final: 0.8823 (tmm) REVERT: A 131 GLN cc_start: 0.8968 (tp40) cc_final: 0.8383 (tp40) REVERT: A 145 MET cc_start: 0.9438 (tpp) cc_final: 0.9089 (tpp) REVERT: A 176 THR cc_start: 0.9683 (m) cc_final: 0.9233 (t) REVERT: A 197 ASP cc_start: 0.9607 (t0) cc_final: 0.9272 (m-30) REVERT: B 69 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9009 (p) REVERT: B 70 MET cc_start: 0.8866 (mmm) cc_final: 0.8452 (mmm) REVERT: B 86 MET cc_start: 0.9388 (tmm) cc_final: 0.9047 (tmm) REVERT: B 131 GLN cc_start: 0.8615 (tt0) cc_final: 0.8317 (tt0) REVERT: B 176 THR cc_start: 0.9601 (m) cc_final: 0.9117 (t) REVERT: B 197 ASP cc_start: 0.9387 (m-30) cc_final: 0.9120 (m-30) REVERT: C 70 MET cc_start: 0.9201 (mmm) cc_final: 0.8942 (mmm) REVERT: C 76 ASP cc_start: 0.9409 (OUTLIER) cc_final: 0.9112 (t0) REVERT: C 86 MET cc_start: 0.9335 (tmm) cc_final: 0.8967 (tmm) REVERT: C 171 LYS cc_start: 0.9721 (mmtt) cc_final: 0.9033 (mmmt) REVERT: C 176 THR cc_start: 0.9686 (m) cc_final: 0.9179 (t) REVERT: C 188 ASN cc_start: 0.9282 (t0) cc_final: 0.8823 (t0) REVERT: D 69 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9151 (p) REVERT: D 131 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8461 (pp30) REVERT: D 136 LEU cc_start: 0.9769 (tt) cc_final: 0.9535 (tp) REVERT: D 171 LYS cc_start: 0.9790 (mmtt) cc_final: 0.9054 (mmmt) REVERT: D 176 THR cc_start: 0.9760 (m) cc_final: 0.9188 (t) REVERT: D 188 ASN cc_start: 0.8983 (t0) cc_final: 0.8629 (t0) REVERT: D 197 ASP cc_start: 0.9581 (t0) cc_final: 0.9351 (m-30) REVERT: E 22 GLU cc_start: 0.9456 (mt-10) cc_final: 0.9111 (mm-30) REVERT: E 27 GLU cc_start: 0.9534 (mm-30) cc_final: 0.9180 (tp30) REVERT: E 54 GLU cc_start: 0.9299 (tt0) cc_final: 0.8934 (tm-30) REVERT: E 70 MET cc_start: 0.9194 (mmm) cc_final: 0.8903 (mmm) REVERT: E 86 MET cc_start: 0.9472 (tmm) cc_final: 0.9076 (tmm) REVERT: E 131 GLN cc_start: 0.8517 (tt0) cc_final: 0.8221 (tt0) REVERT: E 145 MET cc_start: 0.9211 (tpp) cc_final: 0.8823 (tpp) REVERT: E 171 LYS cc_start: 0.9727 (mmtt) cc_final: 0.9092 (mmmt) REVERT: E 176 THR cc_start: 0.9700 (m) cc_final: 0.9241 (t) REVERT: E 188 ASN cc_start: 0.8924 (t0) cc_final: 0.8401 (t0) REVERT: F 147 LYS cc_start: 0.9299 (tppp) cc_final: 0.9071 (tppp) REVERT: F 160 GLU cc_start: 0.9362 (tt0) cc_final: 0.9100 (tt0) REVERT: F 171 LYS cc_start: 0.9763 (mmtt) cc_final: 0.9084 (mmmt) REVERT: F 176 THR cc_start: 0.9705 (m) cc_final: 0.9138 (t) REVERT: F 197 ASP cc_start: 0.9502 (m-30) cc_final: 0.9125 (m-30) REVERT: G 86 MET cc_start: 0.9323 (tmm) cc_final: 0.8984 (tmm) REVERT: G 124 ASP cc_start: 0.9452 (t0) cc_final: 0.9243 (t0) REVERT: G 131 GLN cc_start: 0.8817 (mt0) cc_final: 0.8533 (tt0) REVERT: G 171 LYS cc_start: 0.9730 (mmtt) cc_final: 0.8834 (mmmt) REVERT: G 188 ASN cc_start: 0.9028 (t0) cc_final: 0.8721 (t0) REVERT: G 197 ASP cc_start: 0.9534 (m-30) cc_final: 0.9232 (m-30) REVERT: H 70 MET cc_start: 0.9236 (mmm) cc_final: 0.8997 (mmm) REVERT: H 86 MET cc_start: 0.9565 (ttp) cc_final: 0.9015 (tmm) REVERT: H 131 GLN cc_start: 0.8848 (mt0) cc_final: 0.8595 (tt0) REVERT: H 145 MET cc_start: 0.9437 (tpp) cc_final: 0.8832 (tpp) REVERT: H 167 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8258 (ttp80) REVERT: H 171 LYS cc_start: 0.9725 (mmtt) cc_final: 0.9170 (mmmt) REVERT: H 176 THR cc_start: 0.9764 (m) cc_final: 0.9351 (t) REVERT: H 188 ASN cc_start: 0.8814 (t0) cc_final: 0.8393 (t0) REVERT: H 197 ASP cc_start: 0.9432 (m-30) cc_final: 0.8918 (m-30) REVERT: I 30 TYR cc_start: 0.9503 (m-80) cc_final: 0.9259 (m-80) REVERT: I 70 MET cc_start: 0.9062 (mmm) cc_final: 0.8659 (mmm) REVERT: I 86 MET cc_start: 0.9237 (tmm) cc_final: 0.8851 (tmm) REVERT: I 131 GLN cc_start: 0.8802 (mt0) cc_final: 0.8338 (tt0) REVERT: I 171 LYS cc_start: 0.9797 (mmtt) cc_final: 0.9126 (mmmt) REVERT: I 176 THR cc_start: 0.9685 (m) cc_final: 0.9164 (t) REVERT: I 197 ASP cc_start: 0.9486 (m-30) cc_final: 0.9193 (m-30) REVERT: J 70 MET cc_start: 0.9248 (mmm) cc_final: 0.8945 (mmm) REVERT: J 86 MET cc_start: 0.9175 (tmm) cc_final: 0.8826 (tmm) REVERT: J 100 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8578 (p) REVERT: J 128 LYS cc_start: 0.9449 (mmtp) cc_final: 0.9186 (mmmm) REVERT: J 131 GLN cc_start: 0.8766 (mt0) cc_final: 0.8418 (tt0) REVERT: J 132 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8401 (p) REVERT: J 176 THR cc_start: 0.9657 (m) cc_final: 0.9341 (t) REVERT: J 188 ASN cc_start: 0.8967 (t0) cc_final: 0.8630 (t0) REVERT: J 197 ASP cc_start: 0.9713 (m-30) cc_final: 0.9281 (m-30) outliers start: 36 outliers final: 17 residues processed: 355 average time/residue: 0.1259 time to fit residues: 65.8416 Evaluate side-chains 339 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 315 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 177 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [175, 45, 151, 98, 75, 85, 139, 10, 34, 79, 154] chunk 175 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.048395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.037142 restraints weight = 49004.031| |-----------------------------------------------------------------------------| r_work (start): 0.2432 rms_B_bonded: 4.10 r_work: 0.2259 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 15330 Z= 0.314 Angle : 0.625 7.488 20790 Z= 0.316 Chirality : 0.045 0.146 2380 Planarity : 0.003 0.032 2650 Dihedral : 8.631 59.752 2495 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.55 % Allowed : 21.27 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.19), residues: 1870 helix: 2.27 (0.19), residues: 790 sheet: 2.53 (0.23), residues: 430 loop : -0.90 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.025 0.001 TYR A 87 PHE 0.013 0.001 PHE I 97 HIS 0.005 0.001 HIS J 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.31 (15300) covalent geometry : angle 0.62513 / 0.32 (20790) hydrogen bonds : bond 0.03766 / 2.50 ( 652) hydrogen bonds : angle 4.57287 / 3.21 ( 1821) metal coordination : bond 0.01058 / 0.73 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9071 (p) REVERT: A 70 MET cc_start: 0.8955 (mmm) cc_final: 0.8521 (mmm) REVERT: A 86 MET cc_start: 0.9293 (tmm) cc_final: 0.8964 (tmm) REVERT: A 131 GLN cc_start: 0.9098 (tp40) cc_final: 0.8377 (tp40) REVERT: A 145 MET cc_start: 0.9467 (tpp) cc_final: 0.9070 (tpp) REVERT: A 176 THR cc_start: 0.9718 (m) cc_final: 0.9274 (t) REVERT: A 197 ASP cc_start: 0.9622 (t0) cc_final: 0.9283 (m-30) REVERT: B 70 MET cc_start: 0.8844 (mmm) cc_final: 0.8502 (mmm) REVERT: B 86 MET cc_start: 0.9426 (tmm) cc_final: 0.9073 (tmm) REVERT: B 131 GLN cc_start: 0.8677 (tt0) cc_final: 0.8267 (tt0) REVERT: B 176 THR cc_start: 0.9647 (m) cc_final: 0.9185 (t) REVERT: B 197 ASP cc_start: 0.9414 (m-30) cc_final: 0.9136 (m-30) REVERT: C 30 TYR cc_start: 0.9594 (m-80) cc_final: 0.9269 (m-10) REVERT: C 69 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.9059 (p) REVERT: C 70 MET cc_start: 0.9159 (mmm) cc_final: 0.8818 (mmm) REVERT: C 76 ASP cc_start: 0.9428 (OUTLIER) cc_final: 0.9136 (t0) REVERT: C 86 MET cc_start: 0.9484 (tmm) cc_final: 0.9134 (tmm) REVERT: C 171 LYS cc_start: 0.9711 (mmtt) cc_final: 0.9013 (mmmt) REVERT: C 176 THR cc_start: 0.9698 (m) cc_final: 0.9191 (t) REVERT: C 188 ASN cc_start: 0.9219 (t0) cc_final: 0.8829 (t0) REVERT: D 30 TYR cc_start: 0.9427 (m-80) cc_final: 0.9125 (m-80) REVERT: D 69 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9104 (p) REVERT: D 171 LYS cc_start: 0.9808 (mmtt) cc_final: 0.9131 (mmmt) REVERT: D 176 THR cc_start: 0.9762 (m) cc_final: 0.9167 (t) REVERT: D 188 ASN cc_start: 0.9034 (t0) cc_final: 0.8692 (t0) REVERT: E 68 ASN cc_start: 0.8830 (m110) cc_final: 0.8438 (m110) REVERT: E 70 MET cc_start: 0.9108 (mmm) cc_final: 0.8782 (mmm) REVERT: E 86 MET cc_start: 0.9501 (tmm) cc_final: 0.9095 (tmm) REVERT: E 131 GLN cc_start: 0.8655 (tt0) cc_final: 0.8258 (tt0) REVERT: E 171 LYS cc_start: 0.9720 (mmtt) cc_final: 0.9080 (mmmt) REVERT: E 176 THR cc_start: 0.9698 (m) cc_final: 0.9194 (t) REVERT: F 145 MET cc_start: 0.9261 (tpp) cc_final: 0.8861 (tpp) REVERT: F 147 LYS cc_start: 0.9383 (tppp) cc_final: 0.9144 (tppp) REVERT: F 160 GLU cc_start: 0.9370 (tt0) cc_final: 0.9118 (tt0) REVERT: F 171 LYS cc_start: 0.9792 (mmtt) cc_final: 0.9136 (mmmt) REVERT: F 176 THR cc_start: 0.9720 (m) cc_final: 0.9190 (t) REVERT: F 197 ASP cc_start: 0.9519 (m-30) cc_final: 0.9162 (m-30) REVERT: G 86 MET cc_start: 0.9376 (tmm) cc_final: 0.9105 (tmm) REVERT: G 100 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8772 (p) REVERT: G 131 GLN cc_start: 0.8957 (mt0) cc_final: 0.8398 (tt0) REVERT: G 145 MET cc_start: 0.9236 (tpp) cc_final: 0.8944 (tpp) REVERT: G 171 LYS cc_start: 0.9734 (mmtt) cc_final: 0.8979 (mmmt) REVERT: G 176 THR cc_start: 0.9657 (m) cc_final: 0.9096 (t) REVERT: G 188 ASN cc_start: 0.9005 (t0) cc_final: 0.8626 (t0) REVERT: G 197 ASP cc_start: 0.9551 (m-30) cc_final: 0.9270 (m-30) REVERT: H 70 MET cc_start: 0.9214 (mmm) cc_final: 0.8915 (mmm) REVERT: H 86 MET cc_start: 0.9596 (ttp) cc_final: 0.8967 (tmm) REVERT: H 145 MET cc_start: 0.9454 (tpp) cc_final: 0.8861 (tpp) REVERT: H 167 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.8348 (ttp80) REVERT: H 171 LYS cc_start: 0.9745 (mmtt) cc_final: 0.9058 (mmmt) REVERT: H 176 THR cc_start: 0.9753 (m) cc_final: 0.9310 (t) REVERT: H 197 ASP cc_start: 0.9458 (m-30) cc_final: 0.8972 (m-30) REVERT: I 30 TYR cc_start: 0.9536 (m-80) cc_final: 0.9319 (m-80) REVERT: I 70 MET cc_start: 0.9078 (mmm) cc_final: 0.8607 (mmm) REVERT: I 171 LYS cc_start: 0.9799 (mmtt) cc_final: 0.9118 (mmmt) REVERT: I 176 THR cc_start: 0.9709 (m) cc_final: 0.9168 (t) REVERT: I 197 ASP cc_start: 0.9521 (m-30) cc_final: 0.9247 (m-30) REVERT: J 86 MET cc_start: 0.9274 (tmm) cc_final: 0.8886 (tmm) REVERT: J 100 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8745 (p) REVERT: J 128 LYS cc_start: 0.9478 (mmtp) cc_final: 0.9273 (mmmm) REVERT: J 131 GLN cc_start: 0.8872 (mt0) cc_final: 0.8592 (tt0) REVERT: J 132 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8760 (p) REVERT: J 176 THR cc_start: 0.9661 (m) cc_final: 0.9331 (t) REVERT: J 188 ASN cc_start: 0.9002 (t0) cc_final: 0.8642 (t0) REVERT: J 197 ASP cc_start: 0.9715 (m-30) cc_final: 0.9301 (m-30) outliers start: 40 outliers final: 23 residues processed: 321 average time/residue: 0.1254 time to fit residues: 59.1728 Evaluate side-chains 320 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 177 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [88, 178, 22, 111, 83, 145, 105, 39, 156, 35, 109] chunk 88 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 chunk 145 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS D 75 HIS D 131 GLN E 75 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.050661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.039223 restraints weight = 49555.161| |-----------------------------------------------------------------------------| r_work (start): 0.2510 rms_B_bonded: 4.29 r_work: 0.2342 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15330 Z= 0.099 Angle : 0.491 6.693 20790 Z= 0.260 Chirality : 0.042 0.145 2380 Planarity : 0.003 0.030 2650 Dihedral : 8.243 59.927 2494 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.91 % Allowed : 22.74 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.19), residues: 1870 helix: 2.40 (0.19), residues: 790 sheet: 2.00 (0.23), residues: 460 loop : -0.66 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 151 TYR 0.010 0.001 TYR A 87 PHE 0.010 0.001 PHE J 97 HIS 0.002 0.000 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (15300) covalent geometry : angle 0.49147 / 0.26 (20790) hydrogen bonds : bond 0.03035 / 2.01 ( 652) hydrogen bonds : angle 4.31729 / 3.02 ( 1821) metal coordination : bond 0.00209 / 0.14 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 324 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9067 (p) REVERT: A 70 MET cc_start: 0.9012 (mmm) cc_final: 0.8660 (mmm) REVERT: A 86 MET cc_start: 0.9296 (tmm) cc_final: 0.8912 (tmm) REVERT: A 131 GLN cc_start: 0.9014 (tp40) cc_final: 0.8315 (tp40) REVERT: A 176 THR cc_start: 0.9711 (m) cc_final: 0.9364 (t) REVERT: A 197 ASP cc_start: 0.9615 (t0) cc_final: 0.9279 (m-30) REVERT: B 69 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.9056 (p) REVERT: B 70 MET cc_start: 0.8891 (mmm) cc_final: 0.8483 (mmm) REVERT: B 86 MET cc_start: 0.9443 (tmm) cc_final: 0.9101 (tmm) REVERT: B 131 GLN cc_start: 0.8531 (tt0) cc_final: 0.8210 (tt0) REVERT: B 176 THR cc_start: 0.9641 (m) cc_final: 0.9198 (t) REVERT: B 197 ASP cc_start: 0.9395 (m-30) cc_final: 0.9113 (m-30) REVERT: C 76 ASP cc_start: 0.9395 (OUTLIER) cc_final: 0.9107 (t0) REVERT: C 86 MET cc_start: 0.9499 (tmm) cc_final: 0.9149 (tmm) REVERT: C 145 MET cc_start: 0.9387 (tpp) cc_final: 0.8858 (tpp) REVERT: C 171 LYS cc_start: 0.9712 (mmtt) cc_final: 0.9007 (mmmt) REVERT: C 176 THR cc_start: 0.9705 (m) cc_final: 0.9172 (t) REVERT: C 188 ASN cc_start: 0.9191 (t0) cc_final: 0.8877 (t0) REVERT: D 18 GLN cc_start: 0.8705 (tt0) cc_final: 0.8320 (tp40) REVERT: D 69 THR cc_start: 0.9478 (OUTLIER) cc_final: 0.9165 (p) REVERT: D 131 GLN cc_start: 0.9122 (pt0) cc_final: 0.8583 (pp30) REVERT: D 171 LYS cc_start: 0.9796 (mmtt) cc_final: 0.9121 (mmmt) REVERT: D 176 THR cc_start: 0.9779 (m) cc_final: 0.9220 (t) REVERT: D 188 ASN cc_start: 0.9023 (t0) cc_final: 0.8650 (t0) REVERT: E 68 ASN cc_start: 0.8707 (m110) cc_final: 0.8357 (m110) REVERT: E 69 THR cc_start: 0.9527 (OUTLIER) cc_final: 0.9182 (p) REVERT: E 70 MET cc_start: 0.9192 (mmm) cc_final: 0.8824 (mmm) REVERT: E 86 MET cc_start: 0.9457 (tmm) cc_final: 0.9118 (tmm) REVERT: E 131 GLN cc_start: 0.8503 (tt0) cc_final: 0.8195 (tt0) REVERT: E 147 LYS cc_start: 0.9538 (tppp) cc_final: 0.9233 (tppp) REVERT: E 171 LYS cc_start: 0.9725 (mmtt) cc_final: 0.9085 (mmmt) REVERT: E 176 THR cc_start: 0.9705 (m) cc_final: 0.9218 (t) REVERT: E 188 ASN cc_start: 0.8911 (t0) cc_final: 0.8566 (t0) REVERT: F 160 GLU cc_start: 0.9350 (tt0) cc_final: 0.9119 (tt0) REVERT: F 171 LYS cc_start: 0.9776 (mmtt) cc_final: 0.9094 (mmmt) REVERT: F 176 THR cc_start: 0.9728 (m) cc_final: 0.9224 (t) REVERT: F 197 ASP cc_start: 0.9503 (m-30) cc_final: 0.9121 (m-30) REVERT: G 86 MET cc_start: 0.9419 (tmm) cc_final: 0.9033 (tmm) REVERT: G 100 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8732 (p) REVERT: G 124 ASP cc_start: 0.9457 (t0) cc_final: 0.9160 (t0) REVERT: G 131 GLN cc_start: 0.8784 (mt0) cc_final: 0.8474 (tt0) REVERT: G 171 LYS cc_start: 0.9720 (mmtt) cc_final: 0.8908 (mmmt) REVERT: G 176 THR cc_start: 0.9657 (m) cc_final: 0.9209 (t) REVERT: G 188 ASN cc_start: 0.8962 (t0) cc_final: 0.8615 (t0) REVERT: G 197 ASP cc_start: 0.9517 (m-30) cc_final: 0.9227 (m-30) REVERT: H 70 MET cc_start: 0.9165 (mmm) cc_final: 0.8964 (mmm) REVERT: H 86 MET cc_start: 0.9575 (ttp) cc_final: 0.9048 (tmm) REVERT: H 131 GLN cc_start: 0.8975 (mt0) cc_final: 0.8660 (tt0) REVERT: H 145 MET cc_start: 0.9433 (tpp) cc_final: 0.8852 (tpp) REVERT: H 167 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8250 (ttp80) REVERT: H 171 LYS cc_start: 0.9731 (mmtt) cc_final: 0.9160 (mmmt) REVERT: H 176 THR cc_start: 0.9758 (m) cc_final: 0.9339 (t) REVERT: H 197 ASP cc_start: 0.9406 (m-30) cc_final: 0.8888 (m-30) REVERT: I 30 TYR cc_start: 0.9479 (m-80) cc_final: 0.9212 (m-80) REVERT: I 70 MET cc_start: 0.9098 (mmm) cc_final: 0.8681 (mmm) REVERT: I 131 GLN cc_start: 0.8816 (mt0) cc_final: 0.8490 (tt0) REVERT: I 171 LYS cc_start: 0.9774 (mmtt) cc_final: 0.9093 (mmmt) REVERT: I 176 THR cc_start: 0.9747 (m) cc_final: 0.9240 (t) REVERT: I 197 ASP cc_start: 0.9489 (m-30) cc_final: 0.9199 (m-30) REVERT: J 86 MET cc_start: 0.9280 (tmm) cc_final: 0.8880 (tmm) REVERT: J 100 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8734 (p) REVERT: J 131 GLN cc_start: 0.8696 (mt0) cc_final: 0.8387 (tt0) REVERT: J 176 THR cc_start: 0.9663 (m) cc_final: 0.9394 (t) REVERT: J 188 ASN cc_start: 0.8924 (t0) cc_final: 0.8555 (t0) REVERT: J 197 ASP cc_start: 0.9703 (m-30) cc_final: 0.9255 (m-30) outliers start: 30 outliers final: 12 residues processed: 343 average time/residue: 0.1190 time to fit residues: 60.0327 Evaluate side-chains 327 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 307 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 177 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [145, 82, 173, 48, 169, 23, 13, 97, 41, 31, 93] chunk 145 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.049446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.038209 restraints weight = 48754.046| |-----------------------------------------------------------------------------| r_work (start): 0.2453 rms_B_bonded: 4.30 r_work: 0.2269 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15330 Z= 0.167 Angle : 0.515 6.852 20790 Z= 0.270 Chirality : 0.043 0.165 2380 Planarity : 0.003 0.028 2650 Dihedral : 7.980 56.895 2493 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.78 % Allowed : 23.44 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 1870 helix: 2.39 (0.19), residues: 790 sheet: 2.00 (0.23), residues: 460 loop : -0.61 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.019 0.001 TYR A 87 PHE 0.010 0.001 PHE A 97 HIS 0.003 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (15300) covalent geometry : angle 0.51476 / 0.27 (20790) hydrogen bonds : bond 0.03243 / 2.16 ( 652) hydrogen bonds : angle 4.34946 / 3.05 ( 1821) metal coordination : bond 0.00528 / 0.36 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8888 (p) REVERT: A 70 MET cc_start: 0.8918 (mmm) cc_final: 0.8540 (mmm) REVERT: A 86 MET cc_start: 0.9190 (tmm) cc_final: 0.8700 (tmm) REVERT: A 131 GLN cc_start: 0.9094 (tp40) cc_final: 0.8209 (tp40) REVERT: A 145 MET cc_start: 0.9314 (tpp) cc_final: 0.8803 (tpp) REVERT: A 176 THR cc_start: 0.9616 (m) cc_final: 0.9244 (t) REVERT: A 197 ASP cc_start: 0.9660 (t0) cc_final: 0.9300 (m-30) REVERT: B 69 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8871 (p) REVERT: B 70 MET cc_start: 0.8761 (mmm) cc_final: 0.8320 (mmm) REVERT: B 86 MET cc_start: 0.9397 (tmm) cc_final: 0.9054 (tmm) REVERT: B 131 GLN cc_start: 0.8625 (tt0) cc_final: 0.7959 (tt0) REVERT: B 176 THR cc_start: 0.9576 (m) cc_final: 0.9118 (t) REVERT: B 197 ASP cc_start: 0.9430 (m-30) cc_final: 0.9152 (m-30) REVERT: C 76 ASP cc_start: 0.9432 (OUTLIER) cc_final: 0.9160 (t0) REVERT: C 86 MET cc_start: 0.9429 (tmm) cc_final: 0.8995 (tmm) REVERT: C 171 LYS cc_start: 0.9619 (mmtt) cc_final: 0.8881 (mmmt) REVERT: C 176 THR cc_start: 0.9581 (m) cc_final: 0.8955 (p) REVERT: C 188 ASN cc_start: 0.8990 (t0) cc_final: 0.8579 (t0) REVERT: D 18 GLN cc_start: 0.8644 (tt0) cc_final: 0.8251 (tp40) REVERT: D 69 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.8982 (p) REVERT: D 171 LYS cc_start: 0.9737 (mmtt) cc_final: 0.9062 (mmmt) REVERT: D 176 THR cc_start: 0.9690 (m) cc_final: 0.9127 (t) REVERT: E 68 ASN cc_start: 0.8788 (m110) cc_final: 0.8433 (m110) REVERT: E 69 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.8953 (p) REVERT: E 70 MET cc_start: 0.9068 (mmm) cc_final: 0.8665 (mmm) REVERT: E 86 MET cc_start: 0.9422 (tmm) cc_final: 0.9186 (tmm) REVERT: E 131 GLN cc_start: 0.8619 (tt0) cc_final: 0.8115 (tt0) REVERT: E 147 LYS cc_start: 0.9416 (tppp) cc_final: 0.9103 (tppp) REVERT: E 171 LYS cc_start: 0.9669 (mmtt) cc_final: 0.9009 (mmmt) REVERT: E 176 THR cc_start: 0.9563 (m) cc_final: 0.9064 (t) REVERT: F 145 MET cc_start: 0.9115 (tpp) cc_final: 0.8746 (tpp) REVERT: F 160 GLU cc_start: 0.9309 (tt0) cc_final: 0.9072 (tt0) REVERT: F 171 LYS cc_start: 0.9703 (mmtt) cc_final: 0.9042 (mmmt) REVERT: F 176 THR cc_start: 0.9632 (m) cc_final: 0.9099 (t) REVERT: F 197 ASP cc_start: 0.9544 (m-30) cc_final: 0.9172 (m-30) REVERT: G 86 MET cc_start: 0.9224 (tmm) cc_final: 0.8834 (tmm) REVERT: G 100 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8368 (p) REVERT: G 131 GLN cc_start: 0.8890 (mt0) cc_final: 0.8333 (tt0) REVERT: G 145 MET cc_start: 0.9076 (tpp) cc_final: 0.8823 (tpp) REVERT: G 171 LYS cc_start: 0.9615 (mmtt) cc_final: 0.8869 (mmmt) REVERT: G 176 THR cc_start: 0.9533 (m) cc_final: 0.9020 (t) REVERT: G 188 ASN cc_start: 0.8619 (t0) cc_final: 0.8229 (t0) REVERT: G 197 ASP cc_start: 0.9546 (m-30) cc_final: 0.9251 (m-30) REVERT: H 70 MET cc_start: 0.9107 (mmm) cc_final: 0.8762 (mmm) REVERT: H 86 MET cc_start: 0.9617 (ttp) cc_final: 0.8899 (tmm) REVERT: H 131 GLN cc_start: 0.9118 (mt0) cc_final: 0.8560 (tt0) REVERT: H 145 MET cc_start: 0.9365 (tpp) cc_final: 0.8720 (tpp) REVERT: H 167 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8130 (ttp80) REVERT: H 171 LYS cc_start: 0.9631 (mmtt) cc_final: 0.8938 (mmmt) REVERT: H 176 THR cc_start: 0.9642 (m) cc_final: 0.9161 (t) REVERT: H 197 ASP cc_start: 0.9461 (m-30) cc_final: 0.8978 (m-30) REVERT: I 30 TYR cc_start: 0.9402 (m-80) cc_final: 0.9165 (m-80) REVERT: I 70 MET cc_start: 0.9015 (mmm) cc_final: 0.8564 (mmm) REVERT: I 131 GLN cc_start: 0.8906 (mt0) cc_final: 0.8364 (tt0) REVERT: I 171 LYS cc_start: 0.9699 (mmtt) cc_final: 0.9056 (mmmt) REVERT: I 176 THR cc_start: 0.9638 (m) cc_final: 0.9050 (t) REVERT: I 197 ASP cc_start: 0.9519 (m-30) cc_final: 0.9240 (m-30) REVERT: J 86 MET cc_start: 0.9200 (tmm) cc_final: 0.8743 (tmm) REVERT: J 100 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8393 (p) REVERT: J 131 GLN cc_start: 0.8799 (mt0) cc_final: 0.8340 (tt0) REVERT: J 176 THR cc_start: 0.9557 (m) cc_final: 0.9264 (t) REVERT: J 188 ASN cc_start: 0.8691 (t0) cc_final: 0.8310 (t0) REVERT: J 197 ASP cc_start: 0.9728 (m-30) cc_final: 0.9279 (m-30) outliers start: 28 outliers final: 16 residues processed: 316 average time/residue: 0.1269 time to fit residues: 59.0180 Evaluate side-chains 317 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 293 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 177 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [22, 168, 77, 72, 154, 129, 90, 54, 151, 175, 134] chunk 22 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 0.0870 chunk 134 optimal weight: 4.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 131 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** 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 = 0.2781 r_free = 0.2781 target = 0.049700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.038382 restraints weight = 48850.275| |-----------------------------------------------------------------------------| r_work (start): 0.2462 rms_B_bonded: 4.32 r_work: 0.2277 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15330 Z= 0.134 Angle : 0.508 8.956 20790 Z= 0.268 Chirality : 0.042 0.159 2380 Planarity : 0.003 0.028 2650 Dihedral : 7.729 56.134 2493 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.72 % Allowed : 23.76 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 1870 helix: 2.37 (0.19), residues: 790 sheet: 2.03 (0.23), residues: 460 loop : -0.57 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 151 TYR 0.015 0.001 TYR A 87 PHE 0.010 0.001 PHE J 97 HIS 0.002 0.000 HIS J 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (15300) covalent geometry : angle 0.50751 / 0.27 (20790) hydrogen bonds : bond 0.03187 / 2.12 ( 652) hydrogen bonds : angle 4.28696 / 3.00 ( 1821) metal coordination : bond 0.00405 / 0.28 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8954 (p) REVERT: A 70 MET cc_start: 0.8939 (mmm) cc_final: 0.8564 (mmm) REVERT: A 86 MET cc_start: 0.9215 (tmm) cc_final: 0.8734 (tmm) REVERT: A 131 GLN cc_start: 0.9082 (tp40) cc_final: 0.8247 (tp40) REVERT: A 176 THR cc_start: 0.9647 (m) cc_final: 0.9288 (t) REVERT: A 197 ASP cc_start: 0.9656 (t0) cc_final: 0.9297 (m-30) REVERT: B 68 ASN cc_start: 0.8958 (m110) cc_final: 0.8736 (m110) REVERT: B 70 MET cc_start: 0.8809 (mmm) cc_final: 0.8501 (mmm) REVERT: B 86 MET cc_start: 0.9435 (tmm) cc_final: 0.9101 (tmm) REVERT: B 131 GLN cc_start: 0.8582 (tt0) cc_final: 0.8036 (tt0) REVERT: B 176 THR cc_start: 0.9610 (m) cc_final: 0.9156 (t) REVERT: B 197 ASP cc_start: 0.9416 (m-30) cc_final: 0.9135 (m-30) REVERT: C 76 ASP cc_start: 0.9422 (OUTLIER) cc_final: 0.9141 (t0) REVERT: C 86 MET cc_start: 0.9448 (tmm) cc_final: 0.9002 (tmm) REVERT: C 131 GLN cc_start: 0.8926 (pp30) cc_final: 0.8294 (pp30) REVERT: C 145 MET cc_start: 0.9401 (tpp) cc_final: 0.8807 (tpp) REVERT: C 171 LYS cc_start: 0.9638 (mmtt) cc_final: 0.8902 (mmmt) REVERT: C 176 THR cc_start: 0.9610 (m) cc_final: 0.8983 (p) REVERT: C 188 ASN cc_start: 0.9034 (t0) cc_final: 0.8617 (t0) REVERT: D 18 GLN cc_start: 0.8634 (tt0) cc_final: 0.8222 (tp40) REVERT: D 69 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9035 (p) REVERT: D 131 GLN cc_start: 0.9160 (pt0) cc_final: 0.8922 (pp30) REVERT: D 171 LYS cc_start: 0.9754 (mmtt) cc_final: 0.9080 (mmmt) REVERT: D 176 THR cc_start: 0.9719 (m) cc_final: 0.9163 (t) REVERT: E 68 ASN cc_start: 0.8771 (m110) cc_final: 0.8422 (m110) REVERT: E 69 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9026 (p) REVERT: E 70 MET cc_start: 0.9099 (mmm) cc_final: 0.8694 (mmm) REVERT: E 86 MET cc_start: 0.9439 (tmm) cc_final: 0.9221 (tmm) REVERT: E 131 GLN cc_start: 0.8595 (tt0) cc_final: 0.8124 (tt0) REVERT: E 147 LYS cc_start: 0.9399 (tppp) cc_final: 0.9074 (tppp) REVERT: E 171 LYS cc_start: 0.9685 (mmtt) cc_final: 0.9031 (mmmt) REVERT: E 176 THR cc_start: 0.9592 (m) cc_final: 0.9083 (t) REVERT: F 145 MET cc_start: 0.9176 (tpp) cc_final: 0.8805 (tpp) REVERT: F 160 GLU cc_start: 0.9298 (tt0) cc_final: 0.9069 (tt0) REVERT: F 171 LYS cc_start: 0.9722 (mmtt) cc_final: 0.9068 (mmmt) REVERT: F 176 THR cc_start: 0.9646 (m) cc_final: 0.9059 (t) REVERT: F 197 ASP cc_start: 0.9519 (m-30) cc_final: 0.9140 (m-30) REVERT: G 86 MET cc_start: 0.9266 (tmm) cc_final: 0.8966 (tmm) REVERT: G 100 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8445 (p) REVERT: G 131 GLN cc_start: 0.8844 (mt0) cc_final: 0.8355 (tt0) REVERT: G 145 MET cc_start: 0.9142 (tpp) cc_final: 0.8798 (tpp) REVERT: G 171 LYS cc_start: 0.9636 (mmtt) cc_final: 0.8895 (mmmt) REVERT: G 176 THR cc_start: 0.9554 (m) cc_final: 0.9043 (t) REVERT: G 188 ASN cc_start: 0.8650 (t0) cc_final: 0.8251 (t0) REVERT: G 197 ASP cc_start: 0.9531 (m-30) cc_final: 0.9233 (m-30) REVERT: H 70 MET cc_start: 0.9142 (mmm) cc_final: 0.8797 (mmm) REVERT: H 86 MET cc_start: 0.9629 (ttp) cc_final: 0.8944 (tmm) REVERT: H 131 GLN cc_start: 0.9069 (mt0) cc_final: 0.8570 (tt0) REVERT: H 145 MET cc_start: 0.9407 (tpp) cc_final: 0.8719 (tpp) REVERT: H 167 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8151 (ttp80) REVERT: H 171 LYS cc_start: 0.9648 (mmtt) cc_final: 0.8961 (mmmt) REVERT: H 176 THR cc_start: 0.9677 (m) cc_final: 0.9221 (t) REVERT: H 197 ASP cc_start: 0.9457 (m-30) cc_final: 0.8968 (m-30) REVERT: I 30 TYR cc_start: 0.9411 (m-80) cc_final: 0.9177 (m-80) REVERT: I 70 MET cc_start: 0.9053 (mmm) cc_final: 0.8609 (mmm) REVERT: I 131 GLN cc_start: 0.8881 (mt0) cc_final: 0.8424 (tt0) REVERT: I 171 LYS cc_start: 0.9698 (mmtt) cc_final: 0.9043 (mmmt) REVERT: I 176 THR cc_start: 0.9663 (m) cc_final: 0.9082 (t) REVERT: I 197 ASP cc_start: 0.9520 (m-30) cc_final: 0.9242 (m-30) REVERT: J 86 MET cc_start: 0.9269 (tmm) cc_final: 0.8820 (tmm) REVERT: J 100 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8449 (p) REVERT: J 131 GLN cc_start: 0.8768 (mt0) cc_final: 0.8307 (tt0) REVERT: J 176 THR cc_start: 0.9575 (m) cc_final: 0.9293 (t) REVERT: J 188 ASN cc_start: 0.8725 (t0) cc_final: 0.8423 (t0) REVERT: J 197 ASP cc_start: 0.9729 (m-30) cc_final: 0.9277 (m-30) outliers start: 27 outliers final: 16 residues processed: 320 average time/residue: 0.1220 time to fit residues: 57.2760 Evaluate side-chains 326 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 177 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [17, 135, 128, 157, 95, 19, 105, 79, 57, 97, 109] chunk 17 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.050002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.038817 restraints weight = 48894.486| |-----------------------------------------------------------------------------| r_work (start): 0.2474 rms_B_bonded: 4.32 r_work: 0.2291 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15330 Z= 0.119 Angle : 0.500 6.835 20790 Z= 0.266 Chirality : 0.042 0.156 2380 Planarity : 0.003 0.028 2650 Dihedral : 7.521 56.063 2493 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.46 % Allowed : 24.46 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.19), residues: 1870 helix: 2.41 (0.19), residues: 790 sheet: 2.05 (0.23), residues: 460 loop : -0.54 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 151 TYR 0.012 0.001 TYR A 87 PHE 0.009 0.001 PHE G 97 HIS 0.002 0.000 HIS J 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (15300) covalent geometry : angle 0.49973 / 0.27 (20790) hydrogen bonds : bond 0.03137 / 2.07 ( 652) hydrogen bonds : angle 4.22115 / 2.96 ( 1821) metal coordination : bond 0.00332 / 0.23 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 312 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9050 (mm-30) REVERT: A 27 GLU cc_start: 0.9506 (tp30) cc_final: 0.9102 (tp30) REVERT: A 54 GLU cc_start: 0.9349 (tt0) cc_final: 0.9128 (tm-30) REVERT: A 69 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8973 (p) REVERT: A 70 MET cc_start: 0.8940 (mmm) cc_final: 0.8561 (mmm) REVERT: A 77 GLU cc_start: 0.8943 (mp0) cc_final: 0.8638 (mp0) REVERT: A 83 GLU cc_start: 0.9597 (mm-30) cc_final: 0.8980 (mp0) REVERT: A 86 MET cc_start: 0.9225 (tmm) cc_final: 0.8742 (tmm) REVERT: A 131 GLN cc_start: 0.9032 (tp40) cc_final: 0.8068 (tp40) REVERT: A 176 THR cc_start: 0.9641 (m) cc_final: 0.9290 (t) REVERT: A 197 ASP cc_start: 0.9657 (t0) cc_final: 0.9296 (m-30) REVERT: B 68 ASN cc_start: 0.8874 (m110) cc_final: 0.8665 (m110) REVERT: B 70 MET cc_start: 0.8827 (mmm) cc_final: 0.8543 (mmm) REVERT: B 86 MET cc_start: 0.9440 (tmm) cc_final: 0.9127 (tmm) REVERT: B 131 GLN cc_start: 0.8562 (tt0) cc_final: 0.8209 (tt0) REVERT: B 176 THR cc_start: 0.9613 (m) cc_final: 0.9206 (t) REVERT: B 197 ASP cc_start: 0.9423 (m-30) cc_final: 0.9140 (m-30) REVERT: C 76 ASP cc_start: 0.9409 (OUTLIER) cc_final: 0.9136 (t0) REVERT: C 86 MET cc_start: 0.9433 (tmm) cc_final: 0.8989 (tmm) REVERT: C 131 GLN cc_start: 0.8898 (pp30) cc_final: 0.8312 (pp30) REVERT: C 145 MET cc_start: 0.9399 (tpp) cc_final: 0.8796 (tpp) REVERT: C 171 LYS cc_start: 0.9639 (mmtt) cc_final: 0.8910 (mmmt) REVERT: C 176 THR cc_start: 0.9602 (m) cc_final: 0.8974 (p) REVERT: C 188 ASN cc_start: 0.9021 (t0) cc_final: 0.8547 (t0) REVERT: D 18 GLN cc_start: 0.8632 (tt0) cc_final: 0.8218 (tp40) REVERT: D 69 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9038 (p) REVERT: D 171 LYS cc_start: 0.9743 (mmtt) cc_final: 0.9071 (mmmt) REVERT: D 176 THR cc_start: 0.9705 (m) cc_final: 0.9143 (t) REVERT: E 55 MET cc_start: 0.8758 (mtm) cc_final: 0.8445 (mtm) REVERT: E 68 ASN cc_start: 0.8867 (m110) cc_final: 0.8576 (m110) REVERT: E 69 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9027 (p) REVERT: E 70 MET cc_start: 0.9100 (mmm) cc_final: 0.8687 (mmm) REVERT: E 86 MET cc_start: 0.9441 (tmm) cc_final: 0.9209 (tmm) REVERT: E 131 GLN cc_start: 0.8539 (tt0) cc_final: 0.8063 (tt0) REVERT: E 147 LYS cc_start: 0.9377 (tppp) cc_final: 0.9059 (tppp) REVERT: E 171 LYS cc_start: 0.9681 (mmtt) cc_final: 0.9009 (mmmt) REVERT: E 176 THR cc_start: 0.9590 (m) cc_final: 0.9087 (t) REVERT: F 145 MET cc_start: 0.9191 (tpp) cc_final: 0.8818 (tpp) REVERT: F 160 GLU cc_start: 0.9255 (tt0) cc_final: 0.9048 (tt0) REVERT: F 171 LYS cc_start: 0.9709 (mmtt) cc_final: 0.9025 (mmmt) REVERT: F 176 THR cc_start: 0.9638 (m) cc_final: 0.9077 (t) REVERT: F 197 ASP cc_start: 0.9522 (m-30) cc_final: 0.9143 (m-30) REVERT: G 86 MET cc_start: 0.9445 (tmm) cc_final: 0.9073 (tmm) REVERT: G 100 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8454 (p) REVERT: G 124 ASP cc_start: 0.9414 (t0) cc_final: 0.9187 (t0) REVERT: G 131 GLN cc_start: 0.8873 (mt0) cc_final: 0.8395 (tt0) REVERT: G 145 MET cc_start: 0.9240 (tpp) cc_final: 0.8895 (tpp) REVERT: G 171 LYS cc_start: 0.9628 (mmtt) cc_final: 0.8890 (mmmt) REVERT: G 176 THR cc_start: 0.9548 (m) cc_final: 0.9039 (t) REVERT: G 197 ASP cc_start: 0.9533 (m-30) cc_final: 0.9232 (m-30) REVERT: H 70 MET cc_start: 0.9088 (mmm) cc_final: 0.8734 (mmm) REVERT: H 86 MET cc_start: 0.9635 (ttp) cc_final: 0.8954 (tmm) REVERT: H 131 GLN cc_start: 0.9008 (mt0) cc_final: 0.8548 (tt0) REVERT: H 171 LYS cc_start: 0.9640 (mmtt) cc_final: 0.8953 (mmmt) REVERT: H 176 THR cc_start: 0.9675 (m) cc_final: 0.9219 (t) REVERT: H 197 ASP cc_start: 0.9456 (m-30) cc_final: 0.8961 (m-30) REVERT: I 30 TYR cc_start: 0.9402 (m-80) cc_final: 0.9166 (m-80) REVERT: I 70 MET cc_start: 0.9066 (mmm) cc_final: 0.8633 (mmm) REVERT: I 131 GLN cc_start: 0.8828 (mt0) cc_final: 0.8387 (tt0) REVERT: I 171 LYS cc_start: 0.9672 (mmtt) cc_final: 0.9029 (mmmt) REVERT: I 176 THR cc_start: 0.9664 (m) cc_final: 0.9080 (t) REVERT: I 197 ASP cc_start: 0.9535 (m-30) cc_final: 0.9261 (m-30) REVERT: J 86 MET cc_start: 0.9267 (tmm) cc_final: 0.8809 (tmm) REVERT: J 100 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8588 (p) REVERT: J 131 GLN cc_start: 0.8802 (mt0) cc_final: 0.8245 (tt0) REVERT: J 160 GLU cc_start: 0.9038 (tt0) cc_final: 0.8566 (tp30) REVERT: J 176 THR cc_start: 0.9564 (m) cc_final: 0.9298 (t) REVERT: J 188 ASN cc_start: 0.8699 (t0) cc_final: 0.8396 (t0) REVERT: J 197 ASP cc_start: 0.9726 (m-30) cc_final: 0.9269 (m-30) outliers start: 23 outliers final: 15 residues processed: 325 average time/residue: 0.1221 time to fit residues: 58.7581 Evaluate side-chains 322 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 301 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [166, 30, 162, 25, 81, 124, 163, 118, 95, 75, 58] chunk 166 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.049558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.038297 restraints weight = 49162.168| |-----------------------------------------------------------------------------| r_work (start): 0.2464 rms_B_bonded: 4.32 r_work: 0.2282 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15330 Z= 0.154 Angle : 0.526 6.937 20790 Z= 0.277 Chirality : 0.043 0.155 2380 Planarity : 0.003 0.027 2650 Dihedral : 7.415 57.231 2491 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.59 % Allowed : 24.90 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.19), residues: 1870 helix: 2.41 (0.19), residues: 790 sheet: 2.02 (0.23), residues: 460 loop : -0.56 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.016 0.001 TYR A 87 PHE 0.009 0.001 PHE J 97 HIS 0.003 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (15300) covalent geometry : angle 0.52578 / 0.28 (20790) hydrogen bonds : bond 0.03278 / 2.19 ( 652) hydrogen bonds : angle 4.25863 / 2.98 ( 1821) metal coordination : bond 0.00476 / 0.33 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 297 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8936 (p) REVERT: A 70 MET cc_start: 0.8888 (mmm) cc_final: 0.8500 (mmm) REVERT: A 86 MET cc_start: 0.9226 (tmm) cc_final: 0.8727 (tmm) REVERT: A 131 GLN cc_start: 0.9044 (tp40) cc_final: 0.8058 (tp40) REVERT: A 176 THR cc_start: 0.9628 (m) cc_final: 0.9278 (t) REVERT: A 197 ASP cc_start: 0.9662 (t0) cc_final: 0.9297 (m-30) REVERT: B 68 ASN cc_start: 0.8846 (m110) cc_final: 0.8585 (m110) REVERT: B 70 MET cc_start: 0.8832 (mmm) cc_final: 0.8537 (mmm) REVERT: B 86 MET cc_start: 0.9449 (tmm) cc_final: 0.9135 (tmm) REVERT: B 131 GLN cc_start: 0.8592 (tt0) cc_final: 0.8020 (tt0) REVERT: B 176 THR cc_start: 0.9594 (m) cc_final: 0.9181 (t) REVERT: B 197 ASP cc_start: 0.9428 (m-30) cc_final: 0.9137 (m-30) REVERT: C 76 ASP cc_start: 0.9422 (OUTLIER) cc_final: 0.9152 (t0) REVERT: C 86 MET cc_start: 0.9463 (tmm) cc_final: 0.9028 (tmm) REVERT: C 131 GLN cc_start: 0.8913 (pp30) cc_final: 0.8315 (pp30) REVERT: C 171 LYS cc_start: 0.9612 (mmtt) cc_final: 0.8998 (mmmt) REVERT: C 176 THR cc_start: 0.9571 (m) cc_final: 0.8941 (p) REVERT: D 18 GLN cc_start: 0.8610 (tt0) cc_final: 0.8220 (tp40) REVERT: D 69 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.8977 (p) REVERT: D 171 LYS cc_start: 0.9717 (mmtt) cc_final: 0.9049 (mmmt) REVERT: D 176 THR cc_start: 0.9698 (m) cc_final: 0.9156 (t) REVERT: E 55 MET cc_start: 0.8729 (mtm) cc_final: 0.8409 (mtm) REVERT: E 68 ASN cc_start: 0.8800 (m110) cc_final: 0.8467 (m110) REVERT: E 69 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.8988 (p) REVERT: E 70 MET cc_start: 0.9051 (mmm) cc_final: 0.8610 (mmm) REVERT: E 86 MET cc_start: 0.9413 (tmm) cc_final: 0.9031 (tmm) REVERT: E 131 GLN cc_start: 0.8524 (tt0) cc_final: 0.8006 (tt0) REVERT: E 147 LYS cc_start: 0.9360 (tppp) cc_final: 0.9050 (tppp) REVERT: E 171 LYS cc_start: 0.9665 (mmtt) cc_final: 0.8993 (mmmt) REVERT: E 176 THR cc_start: 0.9561 (m) cc_final: 0.9059 (t) REVERT: F 145 MET cc_start: 0.9225 (tpp) cc_final: 0.8800 (tpp) REVERT: F 160 GLU cc_start: 0.9220 (tt0) cc_final: 0.9006 (tt0) REVERT: F 171 LYS cc_start: 0.9696 (mmtt) cc_final: 0.9049 (mmmt) REVERT: F 176 THR cc_start: 0.9625 (m) cc_final: 0.9062 (t) REVERT: F 197 ASP cc_start: 0.9531 (m-30) cc_final: 0.9157 (m-30) REVERT: G 86 MET cc_start: 0.9397 (tmm) cc_final: 0.8999 (tmm) REVERT: G 100 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8415 (p) REVERT: G 131 GLN cc_start: 0.8865 (mt0) cc_final: 0.8313 (tt0) REVERT: G 145 MET cc_start: 0.9255 (tpp) cc_final: 0.8907 (tpp) REVERT: G 171 LYS cc_start: 0.9610 (mmtt) cc_final: 0.8874 (mmmt) REVERT: G 176 THR cc_start: 0.9516 (m) cc_final: 0.8991 (t) REVERT: G 197 ASP cc_start: 0.9539 (m-30) cc_final: 0.9239 (m-30) REVERT: H 70 MET cc_start: 0.9061 (mmm) cc_final: 0.8705 (mmm) REVERT: H 86 MET cc_start: 0.9628 (ttp) cc_final: 0.8915 (tmm) REVERT: H 171 LYS cc_start: 0.9615 (mmtt) cc_final: 0.8933 (mmmt) REVERT: H 176 THR cc_start: 0.9652 (m) cc_final: 0.9204 (t) REVERT: H 197 ASP cc_start: 0.9468 (m-30) cc_final: 0.8981 (m-30) REVERT: I 30 TYR cc_start: 0.9388 (m-80) cc_final: 0.9153 (m-80) REVERT: I 70 MET cc_start: 0.9041 (mmm) cc_final: 0.8599 (mmm) REVERT: I 131 GLN cc_start: 0.8874 (mt0) cc_final: 0.8387 (tt0) REVERT: I 171 LYS cc_start: 0.9652 (mmtt) cc_final: 0.9009 (mmmt) REVERT: I 176 THR cc_start: 0.9634 (m) cc_final: 0.9050 (t) REVERT: I 197 ASP cc_start: 0.9542 (m-30) cc_final: 0.9272 (m-30) REVERT: J 70 MET cc_start: 0.9093 (mmm) cc_final: 0.8792 (mmm) REVERT: J 86 MET cc_start: 0.9266 (tmm) cc_final: 0.8804 (tmm) REVERT: J 100 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8509 (p) REVERT: J 131 GLN cc_start: 0.8847 (mt0) cc_final: 0.8288 (tt0) REVERT: J 176 THR cc_start: 0.9546 (m) cc_final: 0.9266 (t) REVERT: J 188 ASN cc_start: 0.8657 (t0) cc_final: 0.8345 (t0) REVERT: J 197 ASP cc_start: 0.9731 (m-30) cc_final: 0.9278 (m-30) outliers start: 25 outliers final: 14 residues processed: 310 average time/residue: 0.1222 time to fit residues: 56.0448 Evaluate side-chains 315 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 295 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [78, 142, 77, 89, 114, 87, 133, 116, 110, 167, 160] chunk 78 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.037508 restraints weight = 48440.349| |-----------------------------------------------------------------------------| r_work (start): 0.2442 rms_B_bonded: 4.25 r_work: 0.2259 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15330 Z= 0.214 Angle : 0.567 6.792 20790 Z= 0.297 Chirality : 0.044 0.167 2380 Planarity : 0.003 0.026 2650 Dihedral : 7.511 59.309 2491 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.27 % Allowed : 25.54 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.19), residues: 1870 helix: 2.35 (0.19), residues: 790 sheet: 1.97 (0.23), residues: 460 loop : -0.58 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 167 TYR 0.018 0.001 TYR A 87 PHE 0.010 0.001 PHE A 97 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (15300) covalent geometry : angle 0.56654 / 0.30 (20790) hydrogen bonds : bond 0.03581 / 2.37 ( 652) hydrogen bonds : angle 4.33709 / 3.04 ( 1821) metal coordination : bond 0.00697 / 0.47 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2997.63 seconds wall clock time: 52 minutes 12.47 seconds (3132.47 seconds total)