Starting phenix.real_space_refine on Mon Sep 14 03:36:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25vj_80404/09_2026/25vj_80404.cif Found real_map, /net/cci-nas-00/data/ceres_data/25vj_80404/09_2026/25vj_80404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25vj_80404/09_2026/25vj_80404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25vj_80404/09_2026/25vj_80404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25vj_80404/09_2026/25vj_80404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25vj_80404/09_2026/25vj_80404.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16830 2.51 5 N 4761 2.21 5 O 5214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26916 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 809 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'TRANS': 108} Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2721 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2721 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain: "C" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2721 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain: "E" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 809 Classifications: {'peptide': 110} Link IDs: {'TRANS': 109} Chain: "F" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2721 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain: "G" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2721 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain: "H" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2721 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain: "I" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 809 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'TRANS': 108} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2721 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain: "K" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2721 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain: "L" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2721 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Time building chain proxies: 6.24, per 1000 atoms: 0.23 Number of scatterers: 26916 At special positions: 0 Unit cell: (135.196, 137.974, 230.574, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5214 8.00 N 4761 7.00 C 16830 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: 2.15 Conformation dependent library (CDL) restraints added in 1.2 seconds 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6438 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 49 sheets defined 24.6% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'D' and resid 919 through 953 removed outlier: 3.969A pdb=" N GLY D 932 " --> pdb=" O SER D 928 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 953 " --> pdb=" O ARG D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 1028 removed outlier: 3.867A pdb=" N MET D 959 " --> pdb=" O GLY D 955 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG D1015 " --> pdb=" O ALA D1011 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN D1016 " --> pdb=" O THR D1012 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA D1017 " --> pdb=" O SER D1013 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER D1028 " --> pdb=" O GLN D1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 77 through 93 removed outlier: 4.104A pdb=" N ASN A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.668A pdb=" N GLY A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'B' and resid 82 through 99 Processing helix chain 'B' and resid 100 through 105 removed outlier: 6.775A pdb=" N TRP B 103 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.745A pdb=" N GLY B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.504A pdb=" N ASN B 229 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 230 " --> pdb=" O GLN B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'C' and resid 24 through 29 removed outlier: 4.211A pdb=" N ASN C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 99 removed outlier: 3.928A pdb=" N ASN C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR C 96 " --> pdb=" O GLN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.518A pdb=" N ASN C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 Processing helix chain 'E' and resid 920 through 953 removed outlier: 3.952A pdb=" N GLY E 932 " --> pdb=" O SER E 928 " (cutoff:3.500A) Processing helix chain 'E' and resid 955 through 1027 removed outlier: 3.514A pdb=" N MET E 959 " --> pdb=" O GLY E 955 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG E1015 " --> pdb=" O ALA E1011 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN E1016 " --> pdb=" O THR E1012 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA E1017 " --> pdb=" O SER E1013 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.515A pdb=" N ASN F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 93 removed outlier: 4.216A pdb=" N ASN F 90 " --> pdb=" O PHE F 86 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 99 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 108 through 117 removed outlier: 3.617A pdb=" N GLY F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 128 Processing helix chain 'F' and resid 130 through 139 Processing helix chain 'G' and resid 82 through 99 Processing helix chain 'G' and resid 100 through 105 removed outlier: 6.768A pdb=" N TRP G 103 " --> pdb=" O ILE G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 117 removed outlier: 3.742A pdb=" N GLY G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 130 through 139 Processing helix chain 'G' and resid 226 through 230 Processing helix chain 'H' and resid 24 through 29 removed outlier: 4.177A pdb=" N ASN H 28 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 99 removed outlier: 3.948A pdb=" N ASN H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA H 95 " --> pdb=" O ASN H 91 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N THR H 96 " --> pdb=" O GLN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 108 through 116 Processing helix chain 'H' and resid 119 through 127 Processing helix chain 'H' and resid 130 through 139 Processing helix chain 'I' and resid 920 through 953 removed outlier: 3.948A pdb=" N GLY I 932 " --> pdb=" O SER I 928 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP I 953 " --> pdb=" O ARG I 949 " (cutoff:3.500A) Processing helix chain 'I' and resid 955 through 1027 removed outlier: 3.856A pdb=" N MET I 959 " --> pdb=" O GLY I 955 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG I1015 " --> pdb=" O ALA I1011 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN I1016 " --> pdb=" O THR I1012 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA I1017 " --> pdb=" O SER I1013 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 77 through 93 removed outlier: 4.194A pdb=" N ASN J 90 " --> pdb=" O PHE J 86 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN J 91 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 99 Processing helix chain 'J' and resid 101 through 105 Processing helix chain 'J' and resid 108 through 117 removed outlier: 3.615A pdb=" N GLY J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 128 Processing helix chain 'J' and resid 130 through 139 Processing helix chain 'K' and resid 82 through 99 Processing helix chain 'K' and resid 100 through 105 removed outlier: 6.780A pdb=" N TRP K 103 " --> pdb=" O ILE K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 117 removed outlier: 3.565A pdb=" N GLY K 117 " --> pdb=" O GLN K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 128 Processing helix chain 'K' and resid 130 through 139 Processing helix chain 'K' and resid 226 through 230 Processing helix chain 'L' and resid 24 through 29 removed outlier: 4.205A pdb=" N ASN L 28 " --> pdb=" O ASP L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 removed outlier: 3.966A pdb=" N ASN L 81 " --> pdb=" O GLY L 77 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA L 95 " --> pdb=" O ASN L 91 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR L 96 " --> pdb=" O GLN L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 105 Processing helix chain 'L' and resid 108 through 116 Processing helix chain 'L' and resid 119 through 127 Processing helix chain 'L' and resid 130 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 4.963A pdb=" N SER A 66 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A 11 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER A 55 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 154 removed outlier: 6.071A pdb=" N MET A 153 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 214 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 217 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 154 removed outlier: 6.071A pdb=" N MET A 153 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 252 removed outlier: 3.652A pdb=" N THR A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA6, first strand: chain 'A' and resid 291 through 292 removed outlier: 6.917A pdb=" N LEU A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL A 333 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER A 339 " --> pdb=" O MET A 331 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.644A pdb=" N VAL B 9 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL B 53 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL B 48 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER B 55 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 155 removed outlier: 6.284A pdb=" N MET B 153 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 247 through 252 removed outlier: 4.014A pdb=" N THR B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 291 through 292 Processing sheet with id=AB2, first strand: chain 'B' and resid 291 through 292 removed outlier: 7.181A pdb=" N LEU B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL B 333 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER B 339 " --> pdb=" O MET B 331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 68 removed outlier: 5.374A pdb=" N SER C 66 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL C 11 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL C 53 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL C 48 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER C 55 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 154 removed outlier: 6.031A pdb=" N MET C 153 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 247 through 252 removed outlier: 3.540A pdb=" N THR C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 291 through 292 Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 292 removed outlier: 7.098A pdb=" N LEU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL C 333 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER C 339 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET C 331 " --> pdb=" O SER C 339 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 65 through 68 removed outlier: 4.973A pdb=" N SER F 66 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL F 11 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL F 53 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL F 48 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER F 55 " --> pdb=" O THR F 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 153 through 154 removed outlier: 6.091A pdb=" N MET F 153 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F 214 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN F 217 " --> pdb=" O ALA F 214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 153 through 154 removed outlier: 6.091A pdb=" N MET F 153 " --> pdb=" O ALA F 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 247 through 252 removed outlier: 3.783A pdb=" N THR F 265 " --> pdb=" O TYR F 261 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 291 through 292 Processing sheet with id=AC4, first strand: chain 'F' and resid 291 through 292 removed outlier: 6.958A pdb=" N LEU F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL F 333 " --> pdb=" O LEU F 337 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER F 339 " --> pdb=" O MET F 331 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER F 329 " --> pdb=" O TYR F 341 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 65 through 68 removed outlier: 5.664A pdb=" N VAL G 9 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS G 57 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE G 45 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 153 through 155 removed outlier: 6.338A pdb=" N MET G 153 " --> pdb=" O ALA G 168 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 247 through 252 removed outlier: 4.042A pdb=" N THR G 265 " --> pdb=" O TYR G 261 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 291 through 292 Processing sheet with id=AC9, first strand: chain 'G' and resid 291 through 292 removed outlier: 7.161A pdb=" N LEU G 337 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL G 333 " --> pdb=" O LEU G 337 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER G 339 " --> pdb=" O MET G 331 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 65 through 68 removed outlier: 5.377A pdb=" N SER H 66 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL H 11 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER H 55 " --> pdb=" O THR H 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 153 through 154 removed outlier: 6.293A pdb=" N MET H 153 " --> pdb=" O ALA H 168 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 247 through 252 removed outlier: 3.906A pdb=" N THR H 265 " --> pdb=" O TYR H 261 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 291 through 292 Processing sheet with id=AD5, first strand: chain 'H' and resid 291 through 292 removed outlier: 7.108A pdb=" N LEU H 337 " --> pdb=" O VAL H 333 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL H 333 " --> pdb=" O LEU H 337 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER H 339 " --> pdb=" O MET H 331 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET H 331 " --> pdb=" O SER H 339 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 65 through 68 removed outlier: 4.946A pdb=" N SER J 66 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL J 11 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER J 55 " --> pdb=" O THR J 46 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 153 through 154 removed outlier: 6.065A pdb=" N MET J 153 " --> pdb=" O ALA J 168 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA J 214 " --> pdb=" O ASN J 217 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN J 217 " --> pdb=" O ALA J 214 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 153 through 154 removed outlier: 6.065A pdb=" N MET J 153 " --> pdb=" O ALA J 168 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 247 through 252 removed outlier: 3.708A pdb=" N THR J 265 " --> pdb=" O TYR J 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 291 through 292 Processing sheet with id=AE2, first strand: chain 'J' and resid 291 through 292 removed outlier: 6.879A pdb=" N LEU J 337 " --> pdb=" O VAL J 333 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL J 333 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER J 339 " --> pdb=" O MET J 331 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER J 329 " --> pdb=" O TYR J 341 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 65 through 68 removed outlier: 5.641A pdb=" N VAL K 9 " --> pdb=" O GLY K 67 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL K 53 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL K 48 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER K 55 " --> pdb=" O THR K 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 153 through 155 removed outlier: 6.292A pdb=" N MET K 153 " --> pdb=" O ALA K 168 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 247 through 252 removed outlier: 3.969A pdb=" N THR K 265 " --> pdb=" O TYR K 261 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 291 through 292 Processing sheet with id=AE7, first strand: chain 'K' and resid 291 through 292 removed outlier: 7.216A pdb=" N LEU K 337 " --> pdb=" O VAL K 333 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL K 333 " --> pdb=" O LEU K 337 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER K 339 " --> pdb=" O MET K 331 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 65 through 68 removed outlier: 5.338A pdb=" N SER L 66 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL L 11 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL L 53 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL L 48 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER L 55 " --> pdb=" O THR L 46 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 153 through 155 removed outlier: 6.057A pdb=" N MET L 153 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN L 217 " --> pdb=" O ALA L 214 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 153 through 155 removed outlier: 6.057A pdb=" N MET L 153 " --> pdb=" O ALA L 168 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 247 through 252 removed outlier: 3.719A pdb=" N THR L 265 " --> pdb=" O TYR L 261 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 291 through 292 Processing sheet with id=AF4, first strand: chain 'L' and resid 291 through 292 removed outlier: 7.100A pdb=" N LEU L 337 " --> pdb=" O VAL L 333 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL L 333 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER L 339 " --> pdb=" O MET L 331 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET L 331 " --> pdb=" O SER L 339 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.78 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9033 1.34 - 1.46: 6938 1.46 - 1.58: 11422 1.58 - 1.70: 0 1.70 - 1.82: 213 Bond restraints: 27606 Sorted by residual: bond pdb=" CA MET H 116 " pdb=" C MET H 116 " ideal model delta sigma weight residual 1.523 1.492 0.032 1.80e-02 3.09e+03 3.09e+00 bond pdb=" CG1 ILE K 267 " pdb=" CD1 ILE K 267 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" CG1 ILE G 267 " pdb=" CD1 ILE G 267 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.16e+00 bond pdb=" CG LEU C 166 " pdb=" CD1 LEU C 166 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.36e+00 bond pdb=" CG1 ILE B 267 " pdb=" CD1 ILE B 267 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.34e+00 ... (remaining 27601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 37324 2.34 - 4.68: 379 4.68 - 7.02: 29 7.02 - 9.36: 12 9.36 - 11.70: 5 Bond angle restraints: 37749 Sorted by residual: angle pdb=" CG ARG K 317 " pdb=" CD ARG K 317 " pdb=" NE ARG K 317 " ideal model delta sigma weight residual 112.00 121.77 -9.77 2.20e+00 2.07e-01 1.97e+01 angle pdb=" C ASP H 115 " pdb=" N MET H 116 " pdb=" CA MET H 116 " ideal model delta sigma weight residual 122.31 114.37 7.94 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CA GLU J 16 " pdb=" CB GLU J 16 " pdb=" CG GLU J 16 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " pdb=" CG GLU A 16 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CA GLU F 16 " pdb=" CB GLU F 16 " pdb=" CG GLU F 16 " ideal model delta sigma weight residual 114.10 121.92 -7.82 2.00e+00 2.50e-01 1.53e+01 ... (remaining 37744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 13764 17.74 - 35.48: 1530 35.48 - 53.23: 413 53.23 - 70.97: 84 70.97 - 88.71: 28 Dihedral angle restraints: 15819 sinusoidal: 5643 harmonic: 10176 Sorted by residual: dihedral pdb=" CA GLY C 351 " pdb=" C GLY C 351 " pdb=" N MET C 352 " pdb=" CA MET C 352 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA GLY L 351 " pdb=" C GLY L 351 " pdb=" N MET L 352 " pdb=" CA MET L 352 " ideal model delta harmonic sigma weight residual -180.00 -158.50 -21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA MET K 280 " pdb=" C MET K 280 " pdb=" N ALA K 281 " pdb=" CA ALA K 281 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 15816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2902 0.041 - 0.083: 840 0.083 - 0.124: 302 0.124 - 0.166: 30 0.166 - 0.207: 3 Chirality restraints: 4077 Sorted by residual: chirality pdb=" CA ILE B 267 " pdb=" N ILE B 267 " pdb=" C ILE B 267 " pdb=" CB ILE B 267 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE K 267 " pdb=" N ILE K 267 " pdb=" C ILE K 267 " pdb=" CB ILE K 267 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE G 267 " pdb=" N ILE G 267 " pdb=" C ILE G 267 " pdb=" CB ILE G 267 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 4074 not shown) Planarity restraints: 4974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN H 191 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO H 192 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO H 192 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO H 192 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 362 " 0.030 2.00e-02 2.50e+03 2.61e-02 1.71e+01 pdb=" CG TRP C 362 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP C 362 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 362 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 362 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 362 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 362 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 362 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 362 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 362 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 191 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO C 192 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 192 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 192 " 0.036 5.00e-02 4.00e+02 ... (remaining 4971 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1060 2.69 - 3.25: 26829 3.25 - 3.80: 47340 3.80 - 4.35: 59685 4.35 - 4.90: 101459 Nonbonded interactions: 236373 Sorted by model distance: nonbonded pdb=" OD1 ASN A 314 " pdb=" OG SER C 329 " model vdw 2.142 3.040 nonbonded pdb=" OH TYR F 200 " pdb=" OE1 GLN H 198 " model vdw 2.182 3.040 nonbonded pdb=" OG1 THR L 130 " pdb=" OD1 ASN L 133 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR J 200 " pdb=" OE1 GLN L 198 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR C 130 " pdb=" OD1 ASN C 133 " model vdw 2.195 3.040 ... (remaining 236368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 13.210 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.270 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27606 Z= 0.159 Angle : 0.600 11.696 37749 Z= 0.316 Chirality : 0.044 0.207 4077 Planarity : 0.004 0.115 4974 Dihedral : 16.562 88.711 9381 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 3.51 % Allowed : 28.14 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3564 helix: 2.71 (0.18), residues: 744 sheet: -0.32 (0.17), residues: 825 loop : -1.46 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D1021 TYR 0.038 0.001 TYR H 341 PHE 0.022 0.001 PHE B 305 TRP 0.072 0.002 TRP C 362 HIS 0.005 0.001 HIS G 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (27606) covalent geometry : angle 0.59966 / 0.32 (37749) hydrogen bonds : bond 0.12642 / 8.65 ( 1247) hydrogen bonds : angle 6.07047 / 4.47 ( 3561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 196 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1008 GLU cc_start: 0.7212 (pp20) cc_final: 0.6912 (pp20) REVERT: E 982 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: G 305 PHE cc_start: 0.5897 (m-80) cc_final: 0.5626 (m-80) REVERT: H 16 GLU cc_start: 0.8164 (pm20) cc_final: 0.7694 (pm20) REVERT: H 201 GLN cc_start: 0.7364 (tt0) cc_final: 0.6694 (tt0) REVERT: K 230 LEU cc_start: 0.6033 (tm) cc_final: 0.5738 (tp) REVERT: L 201 GLN cc_start: 0.7405 (tt0) cc_final: 0.6794 (tt0) REVERT: L 362 TRP cc_start: 0.7929 (p-90) cc_final: 0.7635 (p-90) outliers start: 96 outliers final: 86 residues processed: 282 average time/residue: 0.1583 time to fit residues: 74.2660 Evaluate side-chains 275 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 188 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 1018 THR Chi-restraints excluded: chain D residue 1025 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain E residue 945 LEU Chi-restraints excluded: chain E residue 950 ASP Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 1018 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 145 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 76 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 248 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain I residue 1025 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 259 VAL Chi-restraints excluded: chain J residue 343 TYR Chi-restraints excluded: chain K residue 151 ASN Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 148 TRP Chi-restraints excluded: chain L residue 153 MET Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 193 ASP Chi-restraints excluded: chain L residue 222 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN A 241 ASN A 248 GLN B 90 ASN ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN F 188 GLN G 90 ASN I 937 GLN J 188 GLN K 90 ASN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.145205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.099211 restraints weight = 58313.789| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.36 r_work: 0.3240 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27606 Z= 0.125 Angle : 0.545 7.880 37749 Z= 0.288 Chirality : 0.043 0.191 4077 Planarity : 0.004 0.082 4974 Dihedral : 7.055 58.559 4040 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 4.76 % Allowed : 25.47 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3564 helix: 2.76 (0.18), residues: 759 sheet: -0.66 (0.16), residues: 909 loop : -1.45 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1021 TYR 0.026 0.001 TYR C 341 PHE 0.009 0.001 PHE F 255 TRP 0.023 0.001 TRP C 362 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (27606) covalent geometry : angle 0.54465 / 0.29 (37749) hydrogen bonds : bond 0.03920 / 2.70 ( 1247) hydrogen bonds : angle 5.04177 / 3.69 ( 3561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 224 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 982 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: A 198 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6522 (tm-30) REVERT: A 225 TYR cc_start: 0.8567 (m-80) cc_final: 0.8289 (m-80) REVERT: A 280 MET cc_start: 0.5132 (ppp) cc_final: 0.4814 (ppp) REVERT: A 352 MET cc_start: 0.2802 (mpt) cc_final: 0.1909 (mmt) REVERT: B 145 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: B 280 MET cc_start: 0.6982 (pp-130) cc_final: 0.6700 (pp-130) REVERT: B 343 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.4586 (m-80) REVERT: C 312 MET cc_start: 0.1801 (mmt) cc_final: -0.0464 (ttt) REVERT: E 982 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: F 198 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6826 (tm-30) REVERT: F 291 TYR cc_start: 0.2454 (OUTLIER) cc_final: 0.1351 (m-80) REVERT: F 352 MET cc_start: 0.3176 (mpt) cc_final: 0.2249 (mmt) REVERT: G 146 MET cc_start: 0.7726 (ttp) cc_final: 0.7299 (ttp) REVERT: G 305 PHE cc_start: 0.6015 (m-80) cc_final: 0.5680 (m-80) REVERT: G 343 TYR cc_start: 0.5434 (OUTLIER) cc_final: 0.3887 (m-80) REVERT: H 87 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8518 (mtm180) REVERT: H 201 GLN cc_start: 0.7774 (tt0) cc_final: 0.7213 (tt0) REVERT: I 929 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: I 944 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8716 (tm) REVERT: I 982 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: J 198 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: J 291 TYR cc_start: 0.2686 (OUTLIER) cc_final: 0.1917 (m-80) REVERT: J 331 MET cc_start: 0.4507 (pmm) cc_final: 0.4262 (pmm) REVERT: J 352 MET cc_start: 0.1960 (pmm) cc_final: 0.0898 (ptp) REVERT: K 16 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7939 (mm-30) REVERT: K 230 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.5424 (tp) REVERT: K 280 MET cc_start: 0.6838 (pp-130) cc_final: 0.6442 (pp-130) REVERT: K 317 ARG cc_start: 0.3188 (OUTLIER) cc_final: 0.2976 (mtp85) REVERT: K 343 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.3631 (m-80) REVERT: L 116 MET cc_start: 0.9027 (ttp) cc_final: 0.8729 (mtp) REVERT: L 201 GLN cc_start: 0.7770 (tt0) cc_final: 0.7292 (tt0) REVERT: L 362 TRP cc_start: 0.7783 (p-90) cc_final: 0.7518 (p-90) outliers start: 130 outliers final: 85 residues processed: 325 average time/residue: 0.1599 time to fit residues: 86.0865 Evaluate side-chains 314 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 212 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 982 GLU Chi-restraints excluded: chain D residue 984 GLU Chi-restraints excluded: chain D residue 1018 THR Chi-restraints excluded: chain D residue 1025 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain E residue 950 ASP Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1025 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 145 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 343 TYR Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain H residue 76 HIS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 929 GLU Chi-restraints excluded: chain I residue 944 LEU Chi-restraints excluded: chain I residue 950 ASP Chi-restraints excluded: chain I residue 976 GLU Chi-restraints excluded: chain I residue 982 GLU Chi-restraints excluded: chain I residue 1025 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 198 GLN Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 291 TYR Chi-restraints excluded: chain J residue 343 TYR Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 317 ARG Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 343 TYR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 352 MET Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 148 TRP Chi-restraints excluded: chain L residue 153 MET Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain L residue 248 GLN Chi-restraints excluded: chain L residue 341 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 344 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 294 optimal weight: 0.1980 chunk 296 optimal weight: 4.9990 chunk 317 optimal weight: 20.0000 chunk 338 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 937 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN F 248 GLN G 248 GLN ** J 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 GLN K 248 GLN ** L 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.143726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.090711 restraints weight = 58320.367| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.71 r_work: 0.3199 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27606 Z= 0.195 Angle : 0.566 7.910 37749 Z= 0.301 Chirality : 0.044 0.197 4077 Planarity : 0.004 0.067 4974 Dihedral : 6.667 57.828 3989 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 6.04 % Allowed : 23.56 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 3564 helix: 2.38 (0.18), residues: 768 sheet: -0.57 (0.17), residues: 864 loop : -1.56 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1015 TYR 0.018 0.002 TYR L 341 PHE 0.017 0.001 PHE J 305 TRP 0.015 0.002 TRP C 362 HIS 0.006 0.001 HIS G 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (27606) covalent geometry : angle 0.56563 / 0.30 (37749) hydrogen bonds : bond 0.04371 / 3.04 ( 1247) hydrogen bonds : angle 5.00428 / 3.64 ( 3561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 215 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 982 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: A 198 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: A 225 TYR cc_start: 0.8741 (m-80) cc_final: 0.8364 (m-80) REVERT: A 280 MET cc_start: 0.5415 (ppp) cc_final: 0.5184 (ppp) REVERT: A 352 MET cc_start: 0.2844 (mpt) cc_final: 0.1949 (mmt) REVERT: B 16 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: B 57 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8395 (ttpt) REVERT: B 145 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: B 148 TRP cc_start: 0.7956 (OUTLIER) cc_final: 0.7615 (m-90) REVERT: B 280 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6777 (pp-130) REVERT: B 312 MET cc_start: 0.4807 (mmm) cc_final: 0.2856 (ttt) REVERT: B 343 TYR cc_start: 0.5506 (OUTLIER) cc_final: 0.4785 (m-80) REVERT: C 148 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.6496 (m-90) REVERT: C 362 TRP cc_start: 0.7904 (p-90) cc_final: 0.7664 (p-90) REVERT: E 982 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: E 1003 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7608 (ttt180) REVERT: F 75 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8068 (mp) REVERT: F 198 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: F 291 TYR cc_start: 0.3215 (OUTLIER) cc_final: 0.2378 (m-80) REVERT: F 331 MET cc_start: 0.4617 (pmm) cc_final: 0.4413 (pmm) REVERT: F 352 MET cc_start: 0.2984 (mpt) cc_final: 0.2261 (mtp) REVERT: G 146 MET cc_start: 0.7943 (ttp) cc_final: 0.7700 (ttp) REVERT: G 305 PHE cc_start: 0.5868 (m-80) cc_final: 0.5582 (m-80) REVERT: G 343 TYR cc_start: 0.5582 (OUTLIER) cc_final: 0.4992 (m-80) REVERT: H 87 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8513 (ttp-170) REVERT: H 201 GLN cc_start: 0.8059 (tt0) cc_final: 0.7535 (tt0) REVERT: H 327 TRP cc_start: 0.5478 (p90) cc_final: 0.5129 (p90) REVERT: H 352 MET cc_start: 0.3716 (mtp) cc_final: 0.3388 (mtm) REVERT: H 362 TRP cc_start: 0.7877 (p-90) cc_final: 0.7675 (p-90) REVERT: I 929 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: I 944 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8793 (tm) REVERT: I 982 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: J 291 TYR cc_start: 0.2813 (OUTLIER) cc_final: 0.2150 (m-80) REVERT: J 352 MET cc_start: 0.2286 (pmm) cc_final: 0.1367 (ptp) REVERT: K 16 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8045 (mm-30) REVERT: K 230 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5644 (tp) REVERT: K 280 MET cc_start: 0.6843 (pp-130) cc_final: 0.6304 (pp-130) REVERT: K 343 TYR cc_start: 0.5281 (OUTLIER) cc_final: 0.3766 (m-80) REVERT: L 201 GLN cc_start: 0.8053 (tt0) cc_final: 0.7501 (tt0) REVERT: L 316 MET cc_start: 0.5485 (mmt) cc_final: 0.4969 (tpp) REVERT: L 362 TRP cc_start: 0.7820 (p-90) cc_final: 0.7518 (p-90) outliers start: 165 outliers final: 105 residues processed: 346 average time/residue: 0.1575 time to fit residues: 89.5657 Evaluate side-chains 328 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 201 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 982 GLU Chi-restraints excluded: chain D residue 984 GLU Chi-restraints excluded: chain D residue 1018 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain E residue 950 ASP Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1003 ARG Chi-restraints excluded: chain E residue 1025 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 343 TYR Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain H residue 76 HIS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 148 TRP Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 341 TYR Chi-restraints excluded: chain I residue 929 GLU Chi-restraints excluded: chain I residue 944 LEU Chi-restraints excluded: chain I residue 950 ASP Chi-restraints excluded: chain I residue 976 GLU Chi-restraints excluded: chain I residue 982 GLU Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 1007 VAL Chi-restraints excluded: chain I residue 1018 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 291 TYR Chi-restraints excluded: chain J residue 343 TYR Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 92 GLN Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 219 SER Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 268 CYS Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 343 TYR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 352 MET Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 148 TRP Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain L residue 248 GLN Chi-restraints excluded: chain L residue 341 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 211 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 184 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 265 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN L 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.144398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.099097 restraints weight = 57746.334| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.50 r_work: 0.3212 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27606 Z= 0.134 Angle : 0.523 7.119 37749 Z= 0.278 Chirality : 0.043 0.188 4077 Planarity : 0.004 0.058 4974 Dihedral : 6.092 57.185 3970 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 5.60 % Allowed : 23.12 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 3564 helix: 2.48 (0.18), residues: 783 sheet: -0.60 (0.17), residues: 864 loop : -1.51 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 325 TYR 0.017 0.001 TYR L 341 PHE 0.013 0.001 PHE J 305 TRP 0.012 0.001 TRP C 362 HIS 0.003 0.001 HIS G 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (27606) covalent geometry : angle 0.52299 / 0.28 (37749) hydrogen bonds : bond 0.03815 / 2.64 ( 1247) hydrogen bonds : angle 4.83524 / 3.52 ( 3561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 232 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 982 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: D 1008 GLU cc_start: 0.7336 (pt0) cc_final: 0.7096 (pt0) REVERT: D 1021 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7795 (mmm-85) REVERT: A 198 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6710 (tm-30) REVERT: A 224 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8520 (mp10) REVERT: A 280 MET cc_start: 0.5189 (ppp) cc_final: 0.4905 (ppp) REVERT: A 352 MET cc_start: 0.3007 (mpt) cc_final: 0.2159 (mmt) REVERT: B 16 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: B 145 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8171 (mt0) REVERT: B 280 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6545 (pp-130) REVERT: B 312 MET cc_start: 0.4833 (mmm) cc_final: 0.2850 (ttt) REVERT: B 343 TYR cc_start: 0.5518 (OUTLIER) cc_final: 0.4038 (m-80) REVERT: C 362 TRP cc_start: 0.7939 (p-90) cc_final: 0.7716 (p-90) REVERT: E 982 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: F 75 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7822 (mp) REVERT: F 198 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: F 224 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: F 280 MET cc_start: 0.4977 (ppp) cc_final: 0.4771 (ppp) REVERT: F 291 TYR cc_start: 0.3341 (OUTLIER) cc_final: 0.2393 (m-80) REVERT: F 352 MET cc_start: 0.2962 (mpt) cc_final: 0.2257 (mtp) REVERT: G 57 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8546 (ttpt) REVERT: G 280 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6464 (pp-130) REVERT: G 305 PHE cc_start: 0.5965 (m-80) cc_final: 0.5620 (m-80) REVERT: G 343 TYR cc_start: 0.5809 (OUTLIER) cc_final: 0.5183 (m-80) REVERT: H 87 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8371 (ttp-170) REVERT: H 115 ASP cc_start: 0.8215 (m-30) cc_final: 0.7907 (m-30) REVERT: H 148 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.7618 (m-90) REVERT: H 201 GLN cc_start: 0.7843 (tt0) cc_final: 0.7338 (tt0) REVERT: H 263 ASP cc_start: 0.7542 (p0) cc_final: 0.7203 (p0) REVERT: H 352 MET cc_start: 0.3918 (mtp) cc_final: 0.3617 (mtt) REVERT: I 944 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8721 (tm) REVERT: I 982 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: J 198 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6847 (tm-30) REVERT: J 291 TYR cc_start: 0.3068 (OUTLIER) cc_final: 0.2441 (m-80) REVERT: J 352 MET cc_start: 0.2407 (pmm) cc_final: 0.1562 (ptp) REVERT: K 16 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7975 (mm-30) REVERT: K 230 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5503 (tp) REVERT: K 280 MET cc_start: 0.6953 (pp-130) cc_final: 0.6136 (pp-130) REVERT: K 343 TYR cc_start: 0.5228 (OUTLIER) cc_final: 0.3605 (m-80) REVERT: L 201 GLN cc_start: 0.7861 (tt0) cc_final: 0.7320 (tt0) REVERT: L 224 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.5582 (mp10) REVERT: L 362 TRP cc_start: 0.7756 (p-90) cc_final: 0.7487 (p-90) outliers start: 153 outliers final: 102 residues processed: 356 average time/residue: 0.1642 time to fit residues: 95.5660 Evaluate side-chains 335 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 209 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 928 SER Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 982 GLU Chi-restraints excluded: chain D residue 1003 ARG Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain E residue 950 ASP Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1003 ARG Chi-restraints excluded: chain E residue 1025 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 224 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 145 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 343 TYR Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain H residue 76 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 148 TRP Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 944 LEU Chi-restraints excluded: chain I residue 950 ASP Chi-restraints excluded: chain I residue 976 GLU Chi-restraints excluded: chain I residue 982 GLU Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 1004 ILE Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 198 GLN Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 291 TYR Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 343 TYR Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 145 GLN Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 343 TYR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 148 TRP Chi-restraints excluded: chain L residue 153 MET Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain L residue 224 GLN Chi-restraints excluded: chain L residue 248 GLN Chi-restraints excluded: chain L residue 341 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 38 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 302 optimal weight: 0.0670 chunk 183 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 344 optimal weight: 0.9990 chunk 348 optimal weight: 6.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN F 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.144184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098647 restraints weight = 57654.798| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.62 r_work: 0.3192 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27606 Z= 0.148 Angle : 0.528 6.459 37749 Z= 0.280 Chirality : 0.043 0.204 4077 Planarity : 0.004 0.049 4974 Dihedral : 6.043 56.434 3968 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.78 % Allowed : 23.09 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 3564 helix: 2.50 (0.18), residues: 783 sheet: -0.60 (0.17), residues: 864 loop : -1.49 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 260 TYR 0.019 0.001 TYR C 341 PHE 0.012 0.001 PHE J 305 TRP 0.036 0.002 TRP H 362 HIS 0.004 0.001 HIS G 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (27606) covalent geometry : angle 0.52796 / 0.28 (37749) hydrogen bonds : bond 0.03862 / 2.67 ( 1247) hydrogen bonds : angle 4.84622 / 3.52 ( 3561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 214 time to evaluate : 0.882 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: D 982 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: A 26 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8765 (pp) REVERT: A 198 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: A 224 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8399 (mp10) REVERT: A 280 MET cc_start: 0.5248 (ppp) cc_final: 0.4987 (ppp) REVERT: A 352 MET cc_start: 0.2988 (mpt) cc_final: 0.2150 (mmt) REVERT: B 16 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: B 145 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: B 148 TRP cc_start: 0.7882 (m-90) cc_final: 0.7552 (m-90) REVERT: B 228 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6731 (m-80) REVERT: B 280 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6526 (pp-130) REVERT: B 343 TYR cc_start: 0.5160 (OUTLIER) cc_final: 0.4538 (m-80) REVERT: C 362 TRP cc_start: 0.7953 (p-90) cc_final: 0.7699 (p-90) REVERT: E 982 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: F 75 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7879 (mp) REVERT: F 198 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6844 (tm-30) REVERT: F 225 TYR cc_start: 0.8176 (m-80) cc_final: 0.7818 (m-80) REVERT: F 291 TYR cc_start: 0.3509 (OUTLIER) cc_final: 0.2625 (m-80) REVERT: F 352 MET cc_start: 0.3014 (mpt) cc_final: 0.2352 (mtp) REVERT: G 57 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8566 (ttpt) REVERT: G 280 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6517 (pp-130) REVERT: G 305 PHE cc_start: 0.5798 (m-80) cc_final: 0.5508 (m-80) REVERT: H 87 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8302 (ttp-170) REVERT: H 148 TRP cc_start: 0.8382 (OUTLIER) cc_final: 0.7596 (m-90) REVERT: H 201 GLN cc_start: 0.7863 (tt0) cc_final: 0.7348 (tt0) REVERT: H 352 MET cc_start: 0.3869 (mtp) cc_final: 0.3579 (mtt) REVERT: H 362 TRP cc_start: 0.7762 (p-90) cc_final: 0.7357 (p-90) REVERT: I 944 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8687 (tm) REVERT: I 982 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: J 198 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6844 (tm-30) REVERT: J 225 TYR cc_start: 0.8380 (m-80) cc_final: 0.7984 (m-80) REVERT: J 291 TYR cc_start: 0.3255 (OUTLIER) cc_final: 0.2635 (m-80) REVERT: J 352 MET cc_start: 0.2369 (pmm) cc_final: 0.1581 (ptp) REVERT: K 16 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7904 (mm-30) REVERT: K 230 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5226 (tp) REVERT: K 280 MET cc_start: 0.6971 (pp-130) cc_final: 0.6105 (pp-130) REVERT: K 343 TYR cc_start: 0.5194 (OUTLIER) cc_final: 0.3902 (m-80) REVERT: L 201 GLN cc_start: 0.7881 (tt0) cc_final: 0.7260 (tt0) REVERT: L 362 TRP cc_start: 0.7778 (p-90) cc_final: 0.7483 (p-90) outliers start: 158 outliers final: 111 residues processed: 342 average time/residue: 0.1613 time to fit residues: 90.3837 Evaluate side-chains 338 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 204 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 982 GLU Chi-restraints excluded: chain D residue 984 GLU Chi-restraints excluded: chain D residue 1003 ARG Chi-restraints excluded: chain D residue 1025 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain E residue 948 THR Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1003 ARG Chi-restraints excluded: chain E residue 1025 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 219 SER Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 76 HIS Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 145 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain H residue 76 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 148 TRP Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 944 LEU Chi-restraints excluded: chain I residue 950 ASP Chi-restraints excluded: chain I residue 976 GLU Chi-restraints excluded: chain I residue 982 GLU Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 1004 ILE Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 198 GLN Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 291 TYR Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 343 TYR Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 92 GLN Chi-restraints excluded: chain K residue 145 GLN Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 343 TYR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 352 MET Chi-restraints excluded: chain K residue 355 SER Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 148 TRP Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain L residue 248 GLN Chi-restraints excluded: chain L residue 341 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 87 optimal weight: 1.9990 chunk 150 optimal weight: 0.0030 chunk 69 optimal weight: 0.1980 chunk 278 optimal weight: 9.9990 chunk 194 optimal weight: 0.0270 chunk 143 optimal weight: 2.9990 chunk 114 optimal weight: 0.0020 chunk 206 optimal weight: 0.4980 chunk 303 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.1456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS C 203 ASN I1024 GLN K 186 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.148801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101584 restraints weight = 57633.633| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.17 r_work: 0.3269 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27606 Z= 0.094 Angle : 0.501 6.678 37749 Z= 0.265 Chirality : 0.043 0.210 4077 Planarity : 0.004 0.044 4974 Dihedral : 5.595 53.616 3964 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.13 % Allowed : 24.48 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3564 helix: 2.75 (0.18), residues: 789 sheet: -0.68 (0.16), residues: 915 loop : -1.30 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 260 TYR 0.023 0.001 TYR A 225 PHE 0.019 0.001 PHE F 305 TRP 0.024 0.001 TRP H 362 HIS 0.003 0.001 HIS L 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (27606) covalent geometry : angle 0.50143 / 0.27 (37749) hydrogen bonds : bond 0.03201 / 2.19 ( 1247) hydrogen bonds : angle 4.64222 / 3.38 ( 3561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 231 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 982 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: D 1021 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7823 (mmm-85) REVERT: A 26 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8733 (pp) REVERT: A 198 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: A 280 MET cc_start: 0.5079 (ppp) cc_final: 0.4787 (ppp) REVERT: A 352 MET cc_start: 0.2765 (mpt) cc_final: 0.2209 (mmt) REVERT: B 145 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: B 228 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6592 (m-80) REVERT: B 280 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6566 (pp-130) REVERT: B 343 TYR cc_start: 0.5280 (OUTLIER) cc_final: 0.4802 (m-80) REVERT: C 362 TRP cc_start: 0.7901 (p-90) cc_final: 0.7695 (p-90) REVERT: E 982 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: F 75 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7631 (mp) REVERT: F 198 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: F 291 TYR cc_start: 0.3564 (OUTLIER) cc_final: 0.2594 (m-80) REVERT: F 331 MET cc_start: 0.4423 (pmm) cc_final: 0.4159 (pmm) REVERT: F 352 MET cc_start: 0.3197 (mpt) cc_final: 0.2575 (mtp) REVERT: G 280 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6392 (pp-130) REVERT: G 316 MET cc_start: 0.2587 (OUTLIER) cc_final: 0.2328 (mpp) REVERT: H 76 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7627 (m90) REVERT: H 115 ASP cc_start: 0.8051 (m-30) cc_final: 0.7776 (m-30) REVERT: H 201 GLN cc_start: 0.7687 (tt0) cc_final: 0.7197 (tt0) REVERT: H 263 ASP cc_start: 0.7525 (p0) cc_final: 0.7139 (p0) REVERT: H 352 MET cc_start: 0.3713 (mtp) cc_final: 0.3489 (mtt) REVERT: I 982 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: J 198 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: J 246 ILE cc_start: 0.6820 (mt) cc_final: 0.6573 (mt) REVERT: J 291 TYR cc_start: 0.3302 (OUTLIER) cc_final: 0.2623 (m-80) REVERT: J 352 MET cc_start: 0.2574 (pmm) cc_final: 0.1775 (ptp) REVERT: K 16 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7939 (mm-30) REVERT: K 230 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5325 (tp) REVERT: K 280 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.5904 (pp-130) REVERT: K 343 TYR cc_start: 0.5317 (OUTLIER) cc_final: 0.3774 (m-80) REVERT: L 87 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8803 (ttp-170) REVERT: L 362 TRP cc_start: 0.7754 (p-90) cc_final: 0.7451 (p-90) outliers start: 113 outliers final: 73 residues processed: 313 average time/residue: 0.1656 time to fit residues: 84.8278 Evaluate side-chains 304 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 210 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 982 GLU Chi-restraints excluded: chain D residue 1003 ARG Chi-restraints excluded: chain D residue 1025 LEU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1025 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 145 GLN Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain H residue 76 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 976 GLU Chi-restraints excluded: chain I residue 982 GLU Chi-restraints excluded: chain I residue 1004 ILE Chi-restraints excluded: chain I residue 1024 GLN Chi-restraints excluded: chain I residue 1025 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 198 GLN Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 291 TYR Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 343 TYR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 280 MET Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 343 TYR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 148 TRP Chi-restraints excluded: chain L residue 248 GLN Chi-restraints excluded: chain L residue 341 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 101 optimal weight: 4.9990 chunk 293 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 356 optimal weight: 6.9990 chunk 219 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.144359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098417 restraints weight = 57678.328| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.72 r_work: 0.3190 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27606 Z= 0.180 Angle : 0.550 6.559 37749 Z= 0.292 Chirality : 0.044 0.196 4077 Planarity : 0.004 0.045 4974 Dihedral : 5.708 56.125 3944 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.98 % Allowed : 23.71 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3564 helix: 2.46 (0.18), residues: 786 sheet: -0.52 (0.17), residues: 828 loop : -1.49 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 307 TYR 0.019 0.001 TYR A 225 PHE 0.014 0.001 PHE F 305 TRP 0.033 0.002 TRP G 221 HIS 0.005 0.001 HIS G 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (27606) covalent geometry : angle 0.55027 / 0.29 (37749) hydrogen bonds : bond 0.03999 / 2.77 ( 1247) hydrogen bonds : angle 4.79259 / 3.48 ( 3561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 211 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 982 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: A 26 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8753 (pp) REVERT: A 280 MET cc_start: 0.5172 (ppp) cc_final: 0.4849 (ppp) REVERT: A 352 MET cc_start: 0.2960 (mpt) cc_final: 0.2299 (mmt) REVERT: B 16 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: B 116 MET cc_start: 0.8702 (mtp) cc_final: 0.8502 (mtp) REVERT: B 145 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: B 228 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: B 280 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6451 (pp-130) REVERT: B 343 TYR cc_start: 0.5239 (OUTLIER) cc_final: 0.4874 (m-80) REVERT: C 201 GLN cc_start: 0.7889 (tt0) cc_final: 0.7655 (tp40) REVERT: C 224 GLN cc_start: 0.6047 (OUTLIER) cc_final: 0.5497 (mp10) REVERT: C 362 TRP cc_start: 0.7949 (p-90) cc_final: 0.7733 (p-90) REVERT: E 982 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: F 198 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6807 (tm-30) REVERT: F 291 TYR cc_start: 0.3493 (OUTLIER) cc_final: 0.2537 (m-80) REVERT: F 352 MET cc_start: 0.3247 (mpt) cc_final: 0.2654 (mtt) REVERT: G 280 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6333 (pp-130) REVERT: G 305 PHE cc_start: 0.5762 (m-80) cc_final: 0.5456 (m-80) REVERT: G 316 MET cc_start: 0.2588 (mpp) cc_final: 0.2342 (mpp) REVERT: H 87 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8369 (ttp-170) REVERT: H 148 TRP cc_start: 0.8487 (OUTLIER) cc_final: 0.7186 (m-90) REVERT: H 201 GLN cc_start: 0.7845 (tt0) cc_final: 0.7262 (tt0) REVERT: H 224 GLN cc_start: 0.6180 (OUTLIER) cc_final: 0.5510 (mp10) REVERT: H 352 MET cc_start: 0.3681 (mtp) cc_final: 0.3452 (mtt) REVERT: I 944 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8793 (tm) REVERT: I 982 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: J 198 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: J 291 TYR cc_start: 0.3357 (OUTLIER) cc_final: 0.2724 (m-80) REVERT: J 352 MET cc_start: 0.2704 (pmm) cc_final: 0.1969 (ptm) REVERT: K 16 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7849 (mm-30) REVERT: K 280 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.5719 (pp-130) REVERT: K 343 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.4156 (m-80) REVERT: L 201 GLN cc_start: 0.7876 (tt0) cc_final: 0.7280 (tt0) outliers start: 136 outliers final: 100 residues processed: 313 average time/residue: 0.1617 time to fit residues: 83.5811 Evaluate side-chains 322 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 201 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 982 GLU Chi-restraints excluded: chain D residue 984 GLU Chi-restraints excluded: chain D residue 1003 ARG Chi-restraints excluded: chain D residue 1025 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain E residue 948 THR Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1025 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain H residue 76 HIS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 148 TRP Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 224 GLN Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 944 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 950 ASP Chi-restraints excluded: chain I residue 976 GLU Chi-restraints excluded: chain I residue 982 GLU Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 1023 ASP Chi-restraints excluded: chain I residue 1025 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 198 GLN Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 291 TYR Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 343 TYR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 145 GLN Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain K residue 280 MET Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 343 TYR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 352 MET Chi-restraints excluded: chain K residue 355 SER Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 148 TRP Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain L residue 248 GLN Chi-restraints excluded: chain L residue 341 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 260 optimal weight: 0.7980 chunk 339 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 330 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 314 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN ** H 248 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 = 0.4222 r_free = 0.4222 target = 0.146472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.101309 restraints weight = 57648.530| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.65 r_work: 0.3202 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27606 Z= 0.130 Angle : 0.523 7.291 37749 Z= 0.276 Chirality : 0.043 0.200 4077 Planarity : 0.004 0.044 4974 Dihedral : 5.604 55.531 3944 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.54 % Allowed : 24.22 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3564 helix: 2.54 (0.18), residues: 783 sheet: -0.49 (0.17), residues: 843 loop : -1.42 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1021 TYR 0.017 0.001 TYR L 341 PHE 0.013 0.001 PHE F 305 TRP 0.047 0.001 TRP L 362 HIS 0.003 0.001 HIS G 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (27606) covalent geometry : angle 0.52336 / 0.28 (37749) hydrogen bonds : bond 0.03657 / 2.53 ( 1247) hydrogen bonds : angle 4.72055 / 3.43 ( 3561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 210 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 982 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 26 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8766 (pp) REVERT: A 198 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6703 (tm-30) REVERT: A 280 MET cc_start: 0.5100 (ppp) cc_final: 0.4765 (ppp) REVERT: A 352 MET cc_start: 0.2922 (mpt) cc_final: 0.2440 (mmt) REVERT: B 16 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: B 145 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: B 228 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6519 (m-80) REVERT: B 280 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6509 (pp-130) REVERT: B 343 TYR cc_start: 0.5371 (OUTLIER) cc_final: 0.4952 (m-80) REVERT: E 982 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: F 198 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: F 291 TYR cc_start: 0.3616 (OUTLIER) cc_final: 0.2642 (m-80) REVERT: F 352 MET cc_start: 0.3289 (mpt) cc_final: 0.2719 (mtt) REVERT: G 115 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: G 280 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6415 (pp-130) REVERT: G 305 PHE cc_start: 0.5691 (m-80) cc_final: 0.5330 (m-80) REVERT: G 316 MET cc_start: 0.2951 (mpp) cc_final: 0.2706 (mpp) REVERT: H 87 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8365 (ttp-170) REVERT: H 148 TRP cc_start: 0.8366 (OUTLIER) cc_final: 0.7075 (m-90) REVERT: H 201 GLN cc_start: 0.7800 (tt0) cc_final: 0.7267 (tt0) REVERT: H 352 MET cc_start: 0.3635 (mtp) cc_final: 0.3406 (mtt) REVERT: I 982 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: J 198 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: J 246 ILE cc_start: 0.6889 (mt) cc_final: 0.6661 (mt) REVERT: J 291 TYR cc_start: 0.3353 (OUTLIER) cc_final: 0.2748 (m-80) REVERT: J 352 MET cc_start: 0.2716 (pmm) cc_final: 0.2025 (ptm) REVERT: K 16 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7923 (mm-30) REVERT: K 280 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.5857 (pp-130) REVERT: K 343 TYR cc_start: 0.5538 (OUTLIER) cc_final: 0.4292 (m-80) REVERT: L 201 GLN cc_start: 0.7890 (tt0) cc_final: 0.7350 (tt0) outliers start: 124 outliers final: 92 residues processed: 304 average time/residue: 0.1578 time to fit residues: 79.0074 Evaluate side-chains 312 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 200 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 982 GLU Chi-restraints excluded: chain D residue 984 GLU Chi-restraints excluded: chain D residue 1003 ARG Chi-restraints excluded: chain D residue 1025 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain E residue 948 THR Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1025 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain H residue 76 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 148 TRP Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 976 GLU Chi-restraints excluded: chain I residue 982 GLU Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 1025 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 198 GLN Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 263 ASP Chi-restraints excluded: chain J residue 291 TYR Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 343 TYR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain K residue 280 MET Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 343 TYR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 355 SER Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 148 TRP Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain L residue 248 GLN Chi-restraints excluded: chain L residue 341 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 66 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 346 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** F 224 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 = 0.4216 r_free = 0.4216 target = 0.146010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094423 restraints weight = 57606.672| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.13 r_work: 0.3199 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27606 Z= 0.152 Angle : 0.537 7.918 37749 Z= 0.284 Chirality : 0.044 0.198 4077 Planarity : 0.004 0.045 4974 Dihedral : 5.653 55.510 3944 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.29 % Rotamer: Outliers : 4.98 % Allowed : 23.67 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3564 helix: 2.47 (0.18), residues: 786 sheet: -0.52 (0.17), residues: 849 loop : -1.46 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1021 TYR 0.017 0.001 TYR L 341 PHE 0.011 0.001 PHE F 305 TRP 0.065 0.002 TRP C 362 HIS 0.004 0.001 HIS G 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (27606) covalent geometry : angle 0.53696 / 0.28 (37749) hydrogen bonds : bond 0.03775 / 2.61 ( 1247) hydrogen bonds : angle 4.75230 / 3.45 ( 3561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 202 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 982 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: A 26 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8755 (pp) REVERT: A 198 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: A 225 TYR cc_start: 0.8427 (m-80) cc_final: 0.8132 (m-80) REVERT: A 280 MET cc_start: 0.5136 (ppp) cc_final: 0.4798 (ppp) REVERT: B 16 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: B 145 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: B 228 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: B 280 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6606 (pp-130) REVERT: B 312 MET cc_start: 0.4720 (mmm) cc_final: 0.2712 (ttt) REVERT: B 343 TYR cc_start: 0.5399 (OUTLIER) cc_final: 0.5030 (m-80) REVERT: C 224 GLN cc_start: 0.6200 (OUTLIER) cc_final: 0.5615 (mp10) REVERT: E 982 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: F 198 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6784 (tm-30) REVERT: F 291 TYR cc_start: 0.3620 (OUTLIER) cc_final: 0.2707 (m-80) REVERT: F 352 MET cc_start: 0.3245 (mpt) cc_final: 0.2707 (mtt) REVERT: G 115 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: G 213 LYS cc_start: 0.6813 (tttp) cc_final: 0.6420 (tttt) REVERT: G 228 PHE cc_start: 0.6686 (m-10) cc_final: 0.6469 (m-10) REVERT: G 280 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6431 (pp-130) REVERT: G 305 PHE cc_start: 0.5542 (m-80) cc_final: 0.5189 (m-80) REVERT: G 316 MET cc_start: 0.3026 (mpp) cc_final: 0.2795 (mpp) REVERT: H 87 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8349 (ttp-170) REVERT: H 148 TRP cc_start: 0.8422 (OUTLIER) cc_final: 0.7113 (m-90) REVERT: H 201 GLN cc_start: 0.7821 (tt0) cc_final: 0.7250 (tt0) REVERT: H 352 MET cc_start: 0.3654 (mtp) cc_final: 0.3423 (mtt) REVERT: I 944 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8799 (tm) REVERT: I 961 ASP cc_start: 0.8045 (t70) cc_final: 0.7803 (t0) REVERT: I 982 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: J 198 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: J 225 TYR cc_start: 0.8159 (m-80) cc_final: 0.7917 (m-80) REVERT: J 291 TYR cc_start: 0.3304 (OUTLIER) cc_final: 0.3017 (t80) REVERT: J 352 MET cc_start: 0.2733 (pmm) cc_final: 0.2053 (ptm) REVERT: K 16 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7839 (mm-30) REVERT: K 280 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.5917 (pp-130) REVERT: K 343 TYR cc_start: 0.5543 (OUTLIER) cc_final: 0.4308 (m-80) REVERT: L 201 GLN cc_start: 0.7913 (tt0) cc_final: 0.7341 (tt0) outliers start: 136 outliers final: 103 residues processed: 308 average time/residue: 0.1487 time to fit residues: 76.4986 Evaluate side-chains 324 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 199 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 982 GLU Chi-restraints excluded: chain D residue 984 GLU Chi-restraints excluded: chain D residue 1003 ARG Chi-restraints excluded: chain D residue 1025 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain E residue 948 THR Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1025 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 219 SER Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain H residue 76 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 148 TRP Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 944 LEU Chi-restraints excluded: chain I residue 950 ASP Chi-restraints excluded: chain I residue 976 GLU Chi-restraints excluded: chain I residue 982 GLU Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 1025 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 198 GLN Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 263 ASP Chi-restraints excluded: chain J residue 291 TYR Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 343 TYR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 145 GLN Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain K residue 280 MET Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 343 TYR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 352 MET Chi-restraints excluded: chain K residue 355 SER Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 148 TRP Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain L residue 248 GLN Chi-restraints excluded: chain L residue 341 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 209 optimal weight: 0.6980 chunk 307 optimal weight: 0.9990 chunk 356 optimal weight: 8.9990 chunk 180 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 335 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 325 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN ** F 224 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 = 0.4224 r_free = 0.4224 target = 0.145497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092964 restraints weight = 57783.833| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.64 r_work: 0.3254 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27606 Z= 0.118 Angle : 0.532 8.474 37749 Z= 0.280 Chirality : 0.043 0.203 4077 Planarity : 0.004 0.045 4974 Dihedral : 5.554 55.190 3944 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 4.50 % Allowed : 24.22 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3564 helix: 2.58 (0.18), residues: 786 sheet: -0.48 (0.17), residues: 840 loop : -1.42 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 307 TYR 0.017 0.001 TYR L 341 PHE 0.012 0.001 PHE F 305 TRP 0.051 0.001 TRP L 362 HIS 0.002 0.001 HIS G 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (27606) covalent geometry : angle 0.53241 / 0.28 (37749) hydrogen bonds : bond 0.03510 / 2.42 ( 1247) hydrogen bonds : angle 4.67678 / 3.39 ( 3561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 203 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 982 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: A 26 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8754 (pp) REVERT: A 198 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: A 225 TYR cc_start: 0.8472 (m-80) cc_final: 0.8186 (m-80) REVERT: A 280 MET cc_start: 0.5039 (ppp) cc_final: 0.4661 (ppp) REVERT: B 16 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: B 145 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: B 228 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: B 280 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.6448 (pp-130) REVERT: B 312 MET cc_start: 0.4842 (mmm) cc_final: 0.2741 (ttt) REVERT: B 343 TYR cc_start: 0.5487 (OUTLIER) cc_final: 0.5009 (m-80) REVERT: E 982 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: F 198 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: F 291 TYR cc_start: 0.3704 (OUTLIER) cc_final: 0.2720 (m-80) REVERT: F 352 MET cc_start: 0.3306 (mpt) cc_final: 0.2844 (mtp) REVERT: G 115 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7876 (m-30) REVERT: G 213 LYS cc_start: 0.6839 (tttp) cc_final: 0.6463 (tttt) REVERT: G 280 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6394 (pp-130) REVERT: G 305 PHE cc_start: 0.5573 (m-80) cc_final: 0.5182 (m-80) REVERT: G 316 MET cc_start: 0.3099 (mpp) cc_final: 0.2861 (mpp) REVERT: H 87 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8465 (ttp-170) REVERT: H 148 TRP cc_start: 0.8379 (OUTLIER) cc_final: 0.7121 (m-90) REVERT: H 201 GLN cc_start: 0.7918 (tt0) cc_final: 0.7387 (tt0) REVERT: H 352 MET cc_start: 0.3652 (mtp) cc_final: 0.3414 (mtt) REVERT: I 944 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8831 (tm) REVERT: I 982 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: I 1024 GLN cc_start: 0.7358 (tm-30) cc_final: 0.6628 (pp30) REVERT: J 198 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: J 291 TYR cc_start: 0.3293 (OUTLIER) cc_final: 0.3007 (t80) REVERT: J 352 MET cc_start: 0.2800 (pmm) cc_final: 0.1927 (ptp) REVERT: K 16 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7950 (mm-30) REVERT: K 280 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.5659 (pp-130) REVERT: K 343 TYR cc_start: 0.5635 (OUTLIER) cc_final: 0.4291 (m-80) REVERT: L 87 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8906 (mtm180) REVERT: L 201 GLN cc_start: 0.7984 (tt0) cc_final: 0.7450 (tt0) REVERT: L 210 MET cc_start: 0.7699 (ttp) cc_final: 0.7400 (ttp) outliers start: 123 outliers final: 98 residues processed: 300 average time/residue: 0.1538 time to fit residues: 76.4653 Evaluate side-chains 318 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 198 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 982 GLU Chi-restraints excluded: chain D residue 984 GLU Chi-restraints excluded: chain D residue 1003 ARG Chi-restraints excluded: chain D residue 1025 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain E residue 948 THR Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1025 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain H residue 76 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 148 TRP Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 944 LEU Chi-restraints excluded: chain I residue 976 GLU Chi-restraints excluded: chain I residue 982 GLU Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 1025 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 198 GLN Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 263 ASP Chi-restraints excluded: chain J residue 291 TYR Chi-restraints excluded: chain J residue 312 MET Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 343 TYR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain K residue 280 MET Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 343 TYR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 352 MET Chi-restraints excluded: chain K residue 355 SER Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 148 TRP Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain L residue 248 GLN Chi-restraints excluded: chain L residue 341 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 121 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 344 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 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 = 0.4210 r_free = 0.4210 target = 0.145517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.092818 restraints weight = 57457.292| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.75 r_work: 0.3215 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27606 Z= 0.167 Angle : 0.553 8.380 37749 Z= 0.292 Chirality : 0.044 0.196 4077 Planarity : 0.004 0.045 4974 Dihedral : 5.699 56.101 3944 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.76 % Allowed : 23.93 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3564 helix: 2.47 (0.18), residues: 783 sheet: -0.51 (0.17), residues: 849 loop : -1.49 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 307 TYR 0.016 0.001 TYR L 341 PHE 0.010 0.001 PHE F 305 TRP 0.050 0.002 TRP L 362 HIS 0.004 0.001 HIS G 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (27606) covalent geometry : angle 0.55311 / 0.29 (37749) hydrogen bonds : bond 0.03897 / 2.70 ( 1247) hydrogen bonds : angle 4.77146 / 3.46 ( 3561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8046.62 seconds wall clock time: 138 minutes 21.86 seconds (8301.86 seconds total)