Starting phenix.real_space_refine on Sun Aug 24 17:47:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hee_34689/08_2025/8hee_34689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hee_34689/08_2025/8hee_34689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hee_34689/08_2025/8hee_34689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hee_34689/08_2025/8hee_34689.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hee_34689/08_2025/8hee_34689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hee_34689/08_2025/8hee_34689.map" } resolution = 3.2 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= 0.004 sd= 0.111 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 85 5.16 5 C 14015 2.51 5 N 3785 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21905 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "B" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "C" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "E" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "F" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "L" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "I" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "J" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "K" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Time building chain proxies: 5.85, per 1000 atoms: 0.27 Number of scatterers: 21905 At special positions: 0 Unit cell: (62.4, 178.88, 178.88, 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 85 16.00 O 4020 8.00 N 3785 7.00 C 14015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 50 sheets defined 13.2% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 removed outlier: 4.540A pdb=" N HIS A 29 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 30 " --> pdb=" O ARG A 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 30' Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.743A pdb=" N MET A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.838A pdb=" N SER A 99 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.687A pdb=" N HIS B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.772A pdb=" N TYR B 138 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 140 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR B 141 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 143 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 51 removed outlier: 3.764A pdb=" N VAL C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'D' and resid 27 through 30 removed outlier: 3.602A pdb=" N THR D 30 " --> pdb=" O ARG D 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 31 through 36 removed outlier: 3.962A pdb=" N MET D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.669A pdb=" N SER D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 30 removed outlier: 3.563A pdb=" N THR E 30 " --> pdb=" O ARG E 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 27 through 30' Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.967A pdb=" N MET E 36 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 94 through 100 removed outlier: 3.764A pdb=" N SER E 99 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 31 through 36 removed outlier: 3.944A pdb=" N MET F 36 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 56 removed outlier: 3.741A pdb=" N THR F 56 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 68 Processing helix chain 'F' and resid 94 through 100 removed outlier: 3.778A pdb=" N SER F 99 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 30 removed outlier: 3.823A pdb=" N THR G 30 " --> pdb=" O ARG G 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 27 through 30' Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 52 through 56 removed outlier: 3.520A pdb=" N THR G 56 " --> pdb=" O LEU G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 68 Processing helix chain 'G' and resid 94 through 100 removed outlier: 3.657A pdb=" N SER G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 51 removed outlier: 3.773A pdb=" N VAL L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 89 through 96 Processing helix chain 'L' and resid 138 through 143 removed outlier: 3.751A pdb=" N HIS L 142 " --> pdb=" O ARG L 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 51 removed outlier: 3.534A pdb=" N VAL M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 138 through 143 removed outlier: 3.965A pdb=" N HIS M 142 " --> pdb=" O ARG M 139 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS M 143 " --> pdb=" O ALA M 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 51 removed outlier: 3.607A pdb=" N VAL N 47 " --> pdb=" O ASN N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 96 Processing helix chain 'N' and resid 138 through 143 removed outlier: 3.680A pdb=" N HIS N 142 " --> pdb=" O ARG N 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 51 removed outlier: 3.578A pdb=" N VAL O 47 " --> pdb=" O ASN O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 96 Processing helix chain 'O' and resid 138 through 143 removed outlier: 3.761A pdb=" N HIS O 142 " --> pdb=" O ARG O 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 97 removed outlier: 3.686A pdb=" N HIS H 93 " --> pdb=" O GLY H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 143 removed outlier: 3.772A pdb=" N TYR H 138 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 140 " --> pdb=" O LYS H 137 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR H 141 " --> pdb=" O TYR H 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE H 143 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 97 removed outlier: 3.686A pdb=" N HIS I 93 " --> pdb=" O GLY I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 143 removed outlier: 3.772A pdb=" N TYR I 138 " --> pdb=" O ARG I 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU I 140 " --> pdb=" O LYS I 137 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR I 141 " --> pdb=" O TYR I 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE I 143 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 97 removed outlier: 3.687A pdb=" N HIS J 93 " --> pdb=" O GLY J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 143 removed outlier: 3.773A pdb=" N TYR J 138 " --> pdb=" O ARG J 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU J 140 " --> pdb=" O LYS J 137 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR J 141 " --> pdb=" O TYR J 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 97 removed outlier: 3.687A pdb=" N HIS K 93 " --> pdb=" O GLY K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 143 removed outlier: 3.772A pdb=" N TYR K 138 " --> pdb=" O ARG K 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU K 140 " --> pdb=" O LYS K 137 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR K 141 " --> pdb=" O TYR K 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE K 143 " --> pdb=" O LEU K 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.788A pdb=" N ASP A 171 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 81 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 175 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 79 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 177 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU A 77 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET A 179 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP A 75 " --> pdb=" O MET A 179 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG A 181 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A 73 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU A 183 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR A 71 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR A 185 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA A 69 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP O 23 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.513A pdb=" N TYR A 72 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA A 69 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR A 185 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR A 71 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU A 183 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A 73 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG A 181 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP A 75 " --> pdb=" O MET A 179 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET A 179 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU A 77 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 177 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 79 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 175 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 81 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 171 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 184 " --> pdb=" O PHE O 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE O 41 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP B 106 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS B 207 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY B 104 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 213 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 98 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 198 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 197 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN B 68 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 199 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 66 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 203 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP B 106 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS B 207 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY B 104 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 213 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 98 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 82 removed outlier: 6.118A pdb=" N CYS B 120 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY B 118 " --> pdb=" O PRO B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 removed outlier: 7.413A pdb=" N VAL L 5 " --> pdb=" O PRO C 4 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA C 6 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS L 7 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL M 5 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA L 6 " --> pdb=" O VAL M 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS M 7 " --> pdb=" O ALA L 6 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL N 5 " --> pdb=" O PRO M 4 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ALA M 6 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS N 7 " --> pdb=" O ALA M 6 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL O 5 " --> pdb=" O PRO N 4 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ALA N 6 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS O 7 " --> pdb=" O ALA N 6 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 3 " --> pdb=" O PRO O 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 41 removed outlier: 4.453A pdb=" N LEU D 184 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA D 69 " --> pdb=" O PRO D 187 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 72 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 78 removed outlier: 6.994A pdb=" N LEU C 73 " --> pdb=" O GLN C 189 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLN C 189 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 75 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG C 120 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 121 " --> pdb=" O TRP C 148 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP C 148 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 123 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE C 144 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'D' and resid 40 through 41 removed outlier: 3.930A pdb=" N ASP D 171 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG D 81 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU D 175 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D 79 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 177 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU D 77 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 48 through 51 removed outlier: 4.158A pdb=" N GLY D 165 " --> pdb=" O ILE D 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 40 through 41 removed outlier: 4.003A pdb=" N ASP E 171 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG E 81 " --> pdb=" O SER E 173 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 175 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL E 79 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL E 177 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU E 77 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP L 23 " --> pdb=" O ARG E 114 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA E 116 " --> pdb=" O ASP L 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=AB8, first strand: chain 'E' and resid 126 through 127 removed outlier: 6.202A pdb=" N ALA E 69 " --> pdb=" O PRO E 187 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU E 184 " --> pdb=" O PHE L 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.872A pdb=" N ASP F 171 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG F 81 " --> pdb=" O SER F 173 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU F 175 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL F 79 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL F 177 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU F 77 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP M 23 " --> pdb=" O ARG F 114 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 116 " --> pdb=" O ASP M 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 48 through 50 Processing sheet with id=AC2, first strand: chain 'F' and resid 126 through 127 removed outlier: 6.274A pdb=" N ALA F 69 " --> pdb=" O PRO F 187 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU F 184 " --> pdb=" O PHE M 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 39 through 41 removed outlier: 6.029A pdb=" N ILE G 172 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU G 83 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU G 174 " --> pdb=" O ARG G 81 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP N 23 " --> pdb=" O ARG G 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 48 through 50 Processing sheet with id=AC5, first strand: chain 'G' and resid 126 through 127 removed outlier: 6.224A pdb=" N ALA G 69 " --> pdb=" O PRO G 187 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU G 184 " --> pdb=" O PHE N 41 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'L' and resid 73 through 78 removed outlier: 6.695A pdb=" N LEU L 73 " --> pdb=" O GLN L 189 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLN L 189 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA L 75 " --> pdb=" O ILE L 187 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP L 184 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG L 120 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR L 121 " --> pdb=" O TRP L 148 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP L 148 " --> pdb=" O TYR L 121 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE L 144 " --> pdb=" O TYR L 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 169 through 170 Processing sheet with id=AD1, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AD2, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AD3, first strand: chain 'M' and resid 73 through 79 removed outlier: 7.004A pdb=" N LEU M 73 " --> pdb=" O GLN M 189 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLN M 189 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA M 75 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY M 183 " --> pdb=" O VAL M 79 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP M 184 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG M 120 " --> pdb=" O ILE M 190 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE M 144 " --> pdb=" O TYR M 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 169 through 170 Processing sheet with id=AD5, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'N' and resid 73 through 78 removed outlier: 6.717A pdb=" N LEU N 73 " --> pdb=" O GLN N 189 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLN N 189 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA N 75 " --> pdb=" O ILE N 187 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG N 120 " --> pdb=" O ILE N 190 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR N 121 " --> pdb=" O TRP N 148 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP N 148 " --> pdb=" O TYR N 121 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE N 144 " --> pdb=" O TYR N 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 169 through 170 Processing sheet with id=AD9, first strand: chain 'O' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'O' and resid 73 through 79 removed outlier: 7.021A pdb=" N LEU O 73 " --> pdb=" O GLN O 189 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLN O 189 " --> pdb=" O LEU O 73 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA O 75 " --> pdb=" O ILE O 187 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY O 183 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG O 120 " --> pdb=" O ILE O 190 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR O 121 " --> pdb=" O TRP O 148 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TRP O 148 " --> pdb=" O TYR O 121 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE O 144 " --> pdb=" O TYR O 125 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 100 through 101 Processing sheet with id=AE3, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.226A pdb=" N ASP H 106 " --> pdb=" O PRO H 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS H 207 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY H 104 " --> pdb=" O HIS H 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU H 213 " --> pdb=" O PHE H 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE H 98 " --> pdb=" O GLU H 213 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS H 198 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE H 197 " --> pdb=" O ASN H 68 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN H 68 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL H 199 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 66 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE H 203 " --> pdb=" O PHE H 62 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.226A pdb=" N ASP H 106 " --> pdb=" O PRO H 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS H 207 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY H 104 " --> pdb=" O HIS H 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU H 213 " --> pdb=" O PHE H 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE H 98 " --> pdb=" O GLU H 213 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 78 through 82 removed outlier: 6.117A pdb=" N CYS H 120 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY H 118 " --> pdb=" O PRO H 186 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.226A pdb=" N ASP I 106 " --> pdb=" O PRO I 205 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS I 207 " --> pdb=" O GLY I 104 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY I 104 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU I 213 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE I 98 " --> pdb=" O GLU I 213 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS I 198 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE I 197 " --> pdb=" O ASN I 68 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN I 68 " --> pdb=" O ILE I 197 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL I 199 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU I 66 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE I 203 " --> pdb=" O PHE I 62 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.226A pdb=" N ASP I 106 " --> pdb=" O PRO I 205 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS I 207 " --> pdb=" O GLY I 104 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY I 104 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU I 213 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE I 98 " --> pdb=" O GLU I 213 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 78 through 82 removed outlier: 6.118A pdb=" N CYS I 120 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY I 118 " --> pdb=" O PRO I 186 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP J 106 " --> pdb=" O PRO J 205 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS J 207 " --> pdb=" O GLY J 104 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY J 104 " --> pdb=" O HIS J 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU J 213 " --> pdb=" O PHE J 98 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE J 98 " --> pdb=" O GLU J 213 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS J 198 " --> pdb=" O VAL J 112 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE J 197 " --> pdb=" O ASN J 68 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN J 68 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL J 199 " --> pdb=" O LEU J 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 66 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE J 203 " --> pdb=" O PHE J 62 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP J 106 " --> pdb=" O PRO J 205 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS J 207 " --> pdb=" O GLY J 104 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY J 104 " --> pdb=" O HIS J 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU J 213 " --> pdb=" O PHE J 98 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE J 98 " --> pdb=" O GLU J 213 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 78 through 82 removed outlier: 6.118A pdb=" N CYS J 120 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY J 118 " --> pdb=" O PRO J 186 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP K 106 " --> pdb=" O PRO K 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS K 207 " --> pdb=" O GLY K 104 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY K 104 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU K 213 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE K 98 " --> pdb=" O GLU K 213 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS K 198 " --> pdb=" O VAL K 112 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE K 197 " --> pdb=" O ASN K 68 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN K 68 " --> pdb=" O ILE K 197 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL K 199 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU K 66 " --> pdb=" O VAL K 199 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 203 " --> pdb=" O PHE K 62 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP K 106 " --> pdb=" O PRO K 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS K 207 " --> pdb=" O GLY K 104 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY K 104 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU K 213 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE K 98 " --> pdb=" O GLU K 213 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 78 through 82 removed outlier: 6.118A pdb=" N CYS K 120 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY K 118 " --> pdb=" O PRO K 186 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1569 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: 4.64 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.08: 1 1.08 - 1.27: 3500 1.27 - 1.45: 6519 1.45 - 1.63: 12365 1.63 - 1.82: 135 Bond restraints: 22520 Sorted by residual: bond pdb=" CB PRO D 208 " pdb=" CG PRO D 208 " ideal model delta sigma weight residual 1.492 0.899 0.593 5.00e-02 4.00e+02 1.41e+02 bond pdb=" CG PRO D 208 " pdb=" CD PRO D 208 " ideal model delta sigma weight residual 1.503 1.341 0.162 3.40e-02 8.65e+02 2.28e+01 bond pdb=" CA PRO D 208 " pdb=" CB PRO D 208 " ideal model delta sigma weight residual 1.533 1.578 -0.045 1.42e-02 4.96e+03 9.92e+00 bond pdb=" CB VAL B 210 " pdb=" CG1 VAL B 210 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.03e+00 bond pdb=" CB VAL H 210 " pdb=" CG1 VAL H 210 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.99e+00 ... (remaining 22515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 30717 14.77 - 29.53: 0 29.53 - 44.30: 2 44.30 - 59.07: 0 59.07 - 73.83: 1 Bond angle restraints: 30720 Sorted by residual: angle pdb=" CB PRO D 208 " pdb=" CG PRO D 208 " pdb=" CD PRO D 208 " ideal model delta sigma weight residual 106.10 179.93 -73.83 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO D 208 " pdb=" CD PRO D 208 " pdb=" CG PRO D 208 " ideal model delta sigma weight residual 103.20 71.81 31.39 1.50e+00 4.44e-01 4.38e+02 angle pdb=" CA PRO D 208 " pdb=" CB PRO D 208 " pdb=" CG PRO D 208 " ideal model delta sigma weight residual 104.50 69.76 34.74 1.90e+00 2.77e-01 3.34e+02 angle pdb=" CA PRO D 208 " pdb=" N PRO D 208 " pdb=" CD PRO D 208 " ideal model delta sigma weight residual 112.00 98.37 13.63 1.40e+00 5.10e-01 9.48e+01 angle pdb=" N PRO D 208 " pdb=" CA PRO D 208 " pdb=" CB PRO D 208 " ideal model delta sigma weight residual 103.25 95.15 8.10 1.05e+00 9.07e-01 5.94e+01 ... (remaining 30715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11614 17.94 - 35.88: 1380 35.88 - 53.82: 281 53.82 - 71.76: 31 71.76 - 89.71: 24 Dihedral angle restraints: 13330 sinusoidal: 5210 harmonic: 8120 Sorted by residual: dihedral pdb=" CA LEU C 212 " pdb=" C LEU C 212 " pdb=" N ARG C 213 " pdb=" CA ARG C 213 " ideal model delta harmonic sigma weight residual 180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU L 212 " pdb=" C LEU L 212 " pdb=" N ARG L 213 " pdb=" CA ARG L 213 " ideal model delta harmonic sigma weight residual 180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA SER A 74 " pdb=" C SER A 74 " pdb=" N ASP A 75 " pdb=" CA ASP A 75 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 13327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2379 0.042 - 0.083: 734 0.083 - 0.125: 273 0.125 - 0.167: 19 0.167 - 0.208: 5 Chirality restraints: 3410 Sorted by residual: chirality pdb=" CB VAL M 123 " pdb=" CA VAL M 123 " pdb=" CG1 VAL M 123 " pdb=" CG2 VAL M 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA VAL M 123 " pdb=" N VAL M 123 " pdb=" C VAL M 123 " pdb=" CB VAL M 123 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE M 187 " pdb=" CA ILE M 187 " pdb=" CG1 ILE M 187 " pdb=" CG2 ILE M 187 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 3407 not shown) Planarity restraints: 3960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 207 " 0.078 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO D 208 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO D 208 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 208 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 200 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C TYR H 200 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR H 200 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA H 201 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR K 200 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR K 200 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR K 200 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA K 201 " -0.021 2.00e-02 2.50e+03 ... (remaining 3957 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 122 2.42 - 3.04: 12917 3.04 - 3.66: 32458 3.66 - 4.28: 49285 4.28 - 4.90: 85783 Nonbonded interactions: 180565 Sorted by model distance: nonbonded pdb=" OD1 ASN M 88 " pdb=" NH1 ARG J 135 " model vdw 1.796 3.120 nonbonded pdb=" OH TYR E 71 " pdb=" OE2 GLU I 128 " model vdw 2.047 3.040 nonbonded pdb=" OD1 ASN L 88 " pdb=" NH1 ARG I 135 " model vdw 2.055 3.120 nonbonded pdb=" O ARG C 213 " pdb=" ND1 HIS D 29 " model vdw 2.072 3.120 nonbonded pdb=" ND1 HIS A 29 " pdb=" O ARG O 213 " model vdw 2.088 3.120 ... (remaining 180560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.570 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: 0.040 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.900 Find NCS groups from input model: 0.580 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.006 0.593 22520 Z= 0.199 Angle : 0.881 73.834 30720 Z= 0.461 Chirality : 0.046 0.208 3410 Planarity : 0.006 0.108 3960 Dihedral : 15.875 89.705 8110 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.64 % Allowed : 23.95 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.16), residues: 2735 helix: -2.34 (0.31), residues: 245 sheet: -0.24 (0.20), residues: 750 loop : -0.92 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 26 TYR 0.057 0.002 TYR L 168 PHE 0.029 0.002 PHE H 98 TRP 0.016 0.001 TRP O 148 HIS 0.005 0.001 HIS G 201 Details of bonding type rmsd covalent geometry : bond 0.00563 (22520) covalent geometry : angle 0.88077 (30720) hydrogen bonds : bond 0.25875 ( 595) hydrogen bonds : angle 9.06579 ( 1569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 415 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7300 (ptm160) cc_final: 0.6872 (mtt-85) REVERT: F 81 ARG cc_start: 0.8119 (ttp-170) cc_final: 0.7866 (ttp-170) REVERT: H 61 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.5717 (m-10) REVERT: H 65 HIS cc_start: 0.6520 (t70) cc_final: 0.6300 (t70) REVERT: H 167 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7512 (mtp180) REVERT: H 170 GLN cc_start: 0.7316 (mt0) cc_final: 0.7090 (mt0) REVERT: I 63 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5824 (mmtm) REVERT: I 168 TYR cc_start: 0.7517 (m-80) cc_final: 0.7302 (m-80) REVERT: J 107 VAL cc_start: 0.8085 (m) cc_final: 0.7836 (t) REVERT: J 170 GLN cc_start: 0.7976 (mt0) cc_final: 0.7527 (mt0) outliers start: 15 outliers final: 5 residues processed: 421 average time/residue: 0.1766 time to fit residues: 112.9621 Evaluate side-chains 346 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 339 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain I residue 63 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 HIS B 139 GLN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 HIS M 106 ASN M 189 GLN H 166 ASN ** H 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 ASN J 139 GLN K 77 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.193058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.147634 restraints weight = 27397.201| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.76 r_work: 0.3556 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 22520 Z= 0.241 Angle : 0.677 7.683 30720 Z= 0.356 Chirality : 0.048 0.162 3410 Planarity : 0.006 0.063 3960 Dihedral : 5.594 53.781 3058 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.08 % Allowed : 22.12 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.16), residues: 2735 helix: -1.24 (0.44), residues: 155 sheet: -0.44 (0.19), residues: 735 loop : -1.24 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 151 TYR 0.020 0.002 TYR M 26 PHE 0.021 0.002 PHE M 210 TRP 0.020 0.002 TRP M 184 HIS 0.008 0.001 HIS I 77 Details of bonding type rmsd covalent geometry : bond 0.00577 (22520) covalent geometry : angle 0.67698 (30720) hydrogen bonds : bond 0.04381 ( 595) hydrogen bonds : angle 6.46701 ( 1569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 348 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7596 (ptm160) cc_final: 0.7082 (mtt-85) REVERT: B 94 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6539 (mm) REVERT: D 179 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8186 (mtt) REVERT: G 201 HIS cc_start: 0.6320 (t-170) cc_final: 0.5821 (t-170) REVERT: G 203 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: M 61 LYS cc_start: 0.8518 (mttm) cc_final: 0.8227 (mttt) REVERT: N 21 THR cc_start: 0.8981 (p) cc_final: 0.8708 (p) REVERT: N 122 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6729 (ttp) REVERT: O 156 PHE cc_start: 0.7676 (t80) cc_final: 0.7284 (t80) REVERT: H 65 HIS cc_start: 0.6787 (t70) cc_final: 0.6409 (t70) REVERT: H 103 ASN cc_start: 0.8504 (p0) cc_final: 0.8220 (p0) REVERT: H 167 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.7664 (mtp180) REVERT: H 168 TYR cc_start: 0.8666 (m-80) cc_final: 0.8425 (m-80) REVERT: I 154 MET cc_start: 0.5680 (tpp) cc_final: 0.5480 (tpp) REVERT: J 79 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7414 (mm-30) REVERT: J 91 TYR cc_start: 0.7547 (t80) cc_final: 0.7192 (t80) REVERT: J 213 GLU cc_start: -0.1184 (OUTLIER) cc_final: -0.1777 (tt0) REVERT: K 100 TYR cc_start: 0.7214 (m-80) cc_final: 0.6477 (m-80) outliers start: 96 outliers final: 51 residues processed: 411 average time/residue: 0.1621 time to fit residues: 104.2980 Evaluate side-chains 373 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 317 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 MET Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 215 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 234 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN M 106 ASN M 189 GLN ** H 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.196623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153036 restraints weight = 27221.793| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.84 r_work: 0.3604 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22520 Z= 0.123 Angle : 0.568 5.797 30720 Z= 0.296 Chirality : 0.044 0.155 3410 Planarity : 0.005 0.051 3960 Dihedral : 4.984 50.839 3044 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.03 % Favored : 93.93 % Rotamer: Outliers : 3.23 % Allowed : 22.85 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.16), residues: 2735 helix: -1.15 (0.39), residues: 190 sheet: -0.38 (0.19), residues: 765 loop : -1.07 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 72 TYR 0.013 0.001 TYR I 91 PHE 0.014 0.001 PHE N 41 TRP 0.014 0.001 TRP M 184 HIS 0.008 0.001 HIS I 157 Details of bonding type rmsd covalent geometry : bond 0.00290 (22520) covalent geometry : angle 0.56810 (30720) hydrogen bonds : bond 0.03646 ( 595) hydrogen bonds : angle 5.95449 ( 1569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 345 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7604 (ptm160) cc_final: 0.7020 (mtt-85) REVERT: D 130 TYR cc_start: 0.9241 (t80) cc_final: 0.8855 (t80) REVERT: F 119 TYR cc_start: 0.7827 (t80) cc_final: 0.7050 (t80) REVERT: G 45 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7973 (m) REVERT: G 201 HIS cc_start: 0.6203 (t-170) cc_final: 0.5611 (t-170) REVERT: G 203 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7475 (mt0) REVERT: L 211 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7788 (tt0) REVERT: M 61 LYS cc_start: 0.8397 (mttm) cc_final: 0.8018 (mttt) REVERT: M 106 ASN cc_start: 0.8164 (m-40) cc_final: 0.7959 (m110) REVERT: N 216 ILE cc_start: 0.8647 (pt) cc_final: 0.8394 (pt) REVERT: H 65 HIS cc_start: 0.6774 (t70) cc_final: 0.5808 (t70) REVERT: H 103 ASN cc_start: 0.8466 (p0) cc_final: 0.8199 (p0) REVERT: H 167 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.7596 (mtp180) REVERT: H 168 TYR cc_start: 0.8632 (m-80) cc_final: 0.8369 (m-80) REVERT: H 198 LYS cc_start: 0.6340 (mttm) cc_final: 0.6113 (mmmt) REVERT: H 209 HIS cc_start: 0.7307 (m-70) cc_final: 0.7101 (m170) REVERT: J 61 PHE cc_start: 0.7356 (m-10) cc_final: 0.6843 (m-10) REVERT: J 79 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7350 (mm-30) REVERT: J 91 TYR cc_start: 0.7528 (t80) cc_final: 0.7154 (t80) REVERT: J 207 HIS cc_start: 0.7966 (m90) cc_final: 0.7705 (m90) REVERT: J 213 GLU cc_start: -0.0841 (OUTLIER) cc_final: -0.1560 (tt0) REVERT: K 100 TYR cc_start: 0.6970 (m-80) cc_final: 0.6727 (m-80) outliers start: 76 outliers final: 51 residues processed: 394 average time/residue: 0.1632 time to fit residues: 100.3765 Evaluate side-chains 366 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 82 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN M 88 ASN H 157 HIS H 170 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS I 117 ASN K 139 GLN K 209 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.193022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.148218 restraints weight = 27335.989| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.77 r_work: 0.3558 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22520 Z= 0.177 Angle : 0.595 6.496 30720 Z= 0.309 Chirality : 0.045 0.183 3410 Planarity : 0.005 0.045 3960 Dihedral : 5.063 50.031 3044 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.71 % Allowed : 21.91 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.16), residues: 2735 helix: -1.26 (0.44), residues: 155 sheet: -0.44 (0.18), residues: 780 loop : -0.99 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 213 TYR 0.030 0.002 TYR L 168 PHE 0.019 0.002 PHE C 41 TRP 0.011 0.001 TRP O 184 HIS 0.006 0.001 HIS G 29 Details of bonding type rmsd covalent geometry : bond 0.00428 (22520) covalent geometry : angle 0.59499 (30720) hydrogen bonds : bond 0.03550 ( 595) hydrogen bonds : angle 5.70138 ( 1569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 326 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7644 (ptm160) cc_final: 0.7103 (mtt-85) REVERT: B 94 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6687 (mm) REVERT: C 211 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: E 117 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8134 (mt) REVERT: G 45 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7976 (m) REVERT: G 201 HIS cc_start: 0.6001 (t-170) cc_final: 0.5603 (t-170) REVERT: G 203 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: L 34 ARG cc_start: 0.7894 (ptp90) cc_final: 0.7552 (ptp90) REVERT: M 26 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.6028 (m-80) REVERT: M 61 LYS cc_start: 0.8491 (mttm) cc_final: 0.8139 (mttt) REVERT: M 147 GLU cc_start: 0.7284 (pm20) cc_final: 0.6901 (pp20) REVERT: N 122 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6487 (ttp) REVERT: N 216 ILE cc_start: 0.8623 (pt) cc_final: 0.8404 (pt) REVERT: H 103 ASN cc_start: 0.8497 (p0) cc_final: 0.8273 (p0) REVERT: H 167 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.7680 (mtp180) REVERT: H 168 TYR cc_start: 0.8713 (m-80) cc_final: 0.8475 (m-80) REVERT: I 61 PHE cc_start: 0.7739 (m-10) cc_final: 0.7496 (m-10) REVERT: J 91 TYR cc_start: 0.7772 (t80) cc_final: 0.7529 (t80) REVERT: J 207 HIS cc_start: 0.8002 (m90) cc_final: 0.7698 (m90) REVERT: J 213 GLU cc_start: -0.0513 (OUTLIER) cc_final: -0.1361 (tt0) outliers start: 111 outliers final: 71 residues processed: 403 average time/residue: 0.1568 time to fit residues: 100.4964 Evaluate side-chains 384 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 305 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 MET Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 157 HIS Chi-restraints excluded: chain K residue 206 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 HIS F 28 HIS ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 HIS H 170 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS K 207 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.193089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.149336 restraints weight = 26722.808| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.97 r_work: 0.3589 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22520 Z= 0.129 Angle : 0.557 7.374 30720 Z= 0.289 Chirality : 0.043 0.156 3410 Planarity : 0.005 0.043 3960 Dihedral : 4.861 47.993 3044 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.03 % Allowed : 22.42 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.16), residues: 2735 helix: -1.11 (0.39), residues: 190 sheet: -0.39 (0.19), residues: 785 loop : -0.92 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 72 TYR 0.025 0.001 TYR L 168 PHE 0.016 0.001 PHE C 41 TRP 0.007 0.001 TRP O 184 HIS 0.005 0.001 HIS I 77 Details of bonding type rmsd covalent geometry : bond 0.00311 (22520) covalent geometry : angle 0.55721 (30720) hydrogen bonds : bond 0.03188 ( 595) hydrogen bonds : angle 5.49296 ( 1569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 325 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6714 (mm) REVERT: C 211 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: D 130 TYR cc_start: 0.9237 (t80) cc_final: 0.8813 (t80) REVERT: D 175 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8093 (tp) REVERT: E 117 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8149 (mt) REVERT: F 81 ARG cc_start: 0.8300 (ttp-170) cc_final: 0.8078 (ttp-110) REVERT: F 202 LYS cc_start: 0.7015 (mmtm) cc_final: 0.6590 (mmtm) REVERT: G 45 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7995 (m) REVERT: G 201 HIS cc_start: 0.6249 (t-170) cc_final: 0.5600 (t-170) REVERT: G 203 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7479 (mt0) REVERT: L 34 ARG cc_start: 0.7866 (ptp90) cc_final: 0.7533 (ptp90) REVERT: L 78 ASP cc_start: 0.6061 (OUTLIER) cc_final: 0.5670 (t0) REVERT: M 26 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.6363 (m-80) REVERT: M 61 LYS cc_start: 0.8454 (mttm) cc_final: 0.8137 (mttt) REVERT: M 147 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6922 (pp20) REVERT: N 122 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6484 (ttp) REVERT: N 216 ILE cc_start: 0.8615 (pt) cc_final: 0.8335 (pt) REVERT: O 76 LYS cc_start: 0.7447 (mtpt) cc_final: 0.6977 (ttpt) REVERT: H 103 ASN cc_start: 0.8428 (p0) cc_final: 0.8168 (p0) REVERT: H 167 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.7614 (mtp180) REVERT: H 168 TYR cc_start: 0.8711 (m-80) cc_final: 0.8472 (m-80) REVERT: J 91 TYR cc_start: 0.7699 (t80) cc_final: 0.7470 (t80) REVERT: J 207 HIS cc_start: 0.7981 (m90) cc_final: 0.7671 (m90) REVERT: J 213 GLU cc_start: -0.0440 (OUTLIER) cc_final: -0.1325 (tt0) outliers start: 95 outliers final: 66 residues processed: 388 average time/residue: 0.1576 time to fit residues: 96.3928 Evaluate side-chains 385 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 308 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 MET Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 MET Chi-restraints excluded: chain K residue 157 HIS Chi-restraints excluded: chain K residue 206 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 2 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 124 optimal weight: 0.1980 chunk 127 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN O 145 HIS O 221 GLN H 170 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.195017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.150775 restraints weight = 27140.717| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.72 r_work: 0.3595 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22520 Z= 0.125 Angle : 0.549 7.111 30720 Z= 0.284 Chirality : 0.043 0.243 3410 Planarity : 0.004 0.044 3960 Dihedral : 4.751 46.974 3044 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.95 % Allowed : 22.42 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.16), residues: 2735 helix: -1.01 (0.40), residues: 190 sheet: -0.34 (0.18), residues: 785 loop : -0.86 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 181 TYR 0.019 0.001 TYR L 168 PHE 0.017 0.001 PHE C 41 TRP 0.008 0.001 TRP N 148 HIS 0.005 0.001 HIS I 77 Details of bonding type rmsd covalent geometry : bond 0.00302 (22520) covalent geometry : angle 0.54853 (30720) hydrogen bonds : bond 0.03048 ( 595) hydrogen bonds : angle 5.33470 ( 1569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 324 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6732 (mm) REVERT: B 108 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7725 (mp0) REVERT: B 163 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8001 (pp) REVERT: C 148 TRP cc_start: 0.7280 (p-90) cc_final: 0.6950 (p-90) REVERT: C 211 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: D 130 TYR cc_start: 0.9243 (t80) cc_final: 0.8818 (t80) REVERT: D 175 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8109 (tp) REVERT: E 117 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8145 (mt) REVERT: F 81 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.8043 (ttp-110) REVERT: F 119 TYR cc_start: 0.7963 (t80) cc_final: 0.7121 (t80) REVERT: F 202 LYS cc_start: 0.6890 (mmtm) cc_final: 0.6576 (mmtm) REVERT: G 45 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.8021 (m) REVERT: L 34 ARG cc_start: 0.7874 (ptp90) cc_final: 0.7578 (ptp90) REVERT: M 26 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.6559 (m-80) REVERT: M 147 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6971 (pp20) REVERT: N 122 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6504 (ttp) REVERT: N 216 ILE cc_start: 0.8585 (pt) cc_final: 0.8298 (pt) REVERT: H 103 ASN cc_start: 0.8446 (p0) cc_final: 0.8171 (p0) REVERT: H 167 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.7630 (mtp180) REVERT: H 168 TYR cc_start: 0.8731 (m-80) cc_final: 0.8491 (m-80) REVERT: J 207 HIS cc_start: 0.7920 (m90) cc_final: 0.7614 (m90) REVERT: J 213 GLU cc_start: -0.0506 (OUTLIER) cc_final: -0.1339 (tt0) REVERT: K 163 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8143 (pp) outliers start: 93 outliers final: 69 residues processed: 386 average time/residue: 0.1572 time to fit residues: 95.4907 Evaluate side-chains 388 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 308 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 MET Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 208 LYS Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 MET Chi-restraints excluded: chain K residue 157 HIS Chi-restraints excluded: chain K residue 163 LEU Chi-restraints excluded: chain K residue 206 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 32 optimal weight: 0.7980 chunk 103 optimal weight: 0.0970 chunk 244 optimal weight: 20.0000 chunk 237 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS J 202 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.194516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151067 restraints weight = 26812.139| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.90 r_work: 0.3625 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22520 Z= 0.110 Angle : 0.547 7.969 30720 Z= 0.282 Chirality : 0.043 0.234 3410 Planarity : 0.004 0.044 3960 Dihedral : 4.626 46.061 3044 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.82 % Allowed : 23.48 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.16), residues: 2735 helix: -0.92 (0.40), residues: 190 sheet: -0.14 (0.19), residues: 775 loop : -0.83 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 135 TYR 0.018 0.001 TYR J 91 PHE 0.015 0.001 PHE C 41 TRP 0.008 0.001 TRP M 184 HIS 0.005 0.001 HIS G 201 Details of bonding type rmsd covalent geometry : bond 0.00266 (22520) covalent geometry : angle 0.54741 (30720) hydrogen bonds : bond 0.02940 ( 595) hydrogen bonds : angle 5.23200 ( 1569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 315 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7687 (m-10) cc_final: 0.7417 (m-10) REVERT: B 108 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7644 (mp0) REVERT: B 163 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7966 (pp) REVERT: C 211 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: D 130 TYR cc_start: 0.9251 (t80) cc_final: 0.8988 (t80) REVERT: E 117 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8149 (mt) REVERT: F 81 ARG cc_start: 0.8267 (ttp-170) cc_final: 0.8044 (ttp-110) REVERT: F 119 TYR cc_start: 0.7933 (t80) cc_final: 0.7184 (t80) REVERT: F 123 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7436 (m-70) REVERT: F 202 LYS cc_start: 0.6855 (mmtm) cc_final: 0.6524 (mmtm) REVERT: G 45 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.8036 (m) REVERT: L 34 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7497 (ptp90) REVERT: M 26 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: M 61 LYS cc_start: 0.8473 (mttm) cc_final: 0.8056 (mttt) REVERT: M 147 GLU cc_start: 0.7223 (pm20) cc_final: 0.6901 (pp20) REVERT: N 216 ILE cc_start: 0.8531 (pt) cc_final: 0.8256 (pt) REVERT: H 103 ASN cc_start: 0.8458 (p0) cc_final: 0.8195 (p0) REVERT: H 154 MET cc_start: 0.7318 (mmp) cc_final: 0.6223 (ptm) REVERT: H 167 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.7620 (mtp180) REVERT: H 168 TYR cc_start: 0.8696 (m-80) cc_final: 0.8469 (m-80) REVERT: I 106 ASP cc_start: 0.7082 (p0) cc_final: 0.6799 (p0) REVERT: K 163 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8222 (pp) outliers start: 90 outliers final: 62 residues processed: 377 average time/residue: 0.1623 time to fit residues: 95.8059 Evaluate side-chains 375 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 306 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 MET Chi-restraints excluded: chain K residue 157 HIS Chi-restraints excluded: chain K residue 163 LEU Chi-restraints excluded: chain K residue 206 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 120 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 263 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 HIS H 114 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS J 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.192088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.148314 restraints weight = 26693.136| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.94 r_work: 0.3592 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22520 Z= 0.141 Angle : 0.570 7.913 30720 Z= 0.291 Chirality : 0.044 0.200 3410 Planarity : 0.004 0.044 3960 Dihedral : 4.581 21.210 3040 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.78 % Allowed : 23.52 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.16), residues: 2735 helix: -0.99 (0.40), residues: 190 sheet: -0.11 (0.19), residues: 770 loop : -0.79 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 34 TYR 0.013 0.001 TYR L 168 PHE 0.016 0.001 PHE C 41 TRP 0.007 0.001 TRP N 184 HIS 0.004 0.001 HIS I 77 Details of bonding type rmsd covalent geometry : bond 0.00341 (22520) covalent geometry : angle 0.56986 (30720) hydrogen bonds : bond 0.03036 ( 595) hydrogen bonds : angle 5.21598 ( 1569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 314 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7818 (mp0) REVERT: B 163 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7975 (pp) REVERT: C 211 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6991 (tm-30) REVERT: D 130 TYR cc_start: 0.9240 (t80) cc_final: 0.8978 (t80) REVERT: D 175 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8166 (tp) REVERT: E 117 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8179 (mt) REVERT: F 81 ARG cc_start: 0.8263 (ttp-170) cc_final: 0.8029 (ttp-110) REVERT: F 119 TYR cc_start: 0.7997 (t80) cc_final: 0.7302 (t80) REVERT: F 123 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7504 (m-70) REVERT: F 202 LYS cc_start: 0.6876 (mmtm) cc_final: 0.6569 (mmtm) REVERT: G 45 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.8011 (m) REVERT: L 34 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7621 (ptp90) REVERT: M 26 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: M 61 LYS cc_start: 0.8531 (mttm) cc_final: 0.8150 (mttm) REVERT: N 216 ILE cc_start: 0.8585 (pt) cc_final: 0.8302 (pt) REVERT: H 103 ASN cc_start: 0.8458 (p0) cc_final: 0.8189 (p0) REVERT: H 154 MET cc_start: 0.7423 (mmp) cc_final: 0.6336 (ptm) REVERT: H 167 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.7654 (mtp180) REVERT: H 168 TYR cc_start: 0.8754 (m-80) cc_final: 0.8502 (m-80) REVERT: K 163 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8137 (pp) REVERT: K 196 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7332 (tm-30) outliers start: 89 outliers final: 71 residues processed: 374 average time/residue: 0.1647 time to fit residues: 96.5261 Evaluate side-chains 392 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 313 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 208 LYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 MET Chi-restraints excluded: chain K residue 157 HIS Chi-restraints excluded: chain K residue 163 LEU Chi-restraints excluded: chain K residue 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 172 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 118 optimal weight: 0.0040 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 chunk 40 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 209 optimal weight: 0.0980 chunk 156 optimal weight: 5.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS J 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.193331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150155 restraints weight = 26825.346| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.88 r_work: 0.3613 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22520 Z= 0.119 Angle : 0.556 8.445 30720 Z= 0.285 Chirality : 0.043 0.173 3410 Planarity : 0.004 0.047 3960 Dihedral : 4.507 19.167 3040 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.65 % Allowed : 23.31 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.16), residues: 2735 helix: -0.93 (0.40), residues: 190 sheet: 0.01 (0.19), residues: 765 loop : -0.77 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 181 TYR 0.012 0.001 TYR F 72 PHE 0.016 0.001 PHE I 98 TRP 0.008 0.001 TRP M 184 HIS 0.006 0.001 HIS G 201 Details of bonding type rmsd covalent geometry : bond 0.00287 (22520) covalent geometry : angle 0.55610 (30720) hydrogen bonds : bond 0.02917 ( 595) hydrogen bonds : angle 5.12372 ( 1569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 316 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7771 (mp0) REVERT: B 163 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7947 (pp) REVERT: C 211 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: D 55 GLN cc_start: 0.8255 (tp40) cc_final: 0.7864 (tm-30) REVERT: D 130 TYR cc_start: 0.9240 (t80) cc_final: 0.8971 (t80) REVERT: D 175 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8217 (tp) REVERT: E 117 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8151 (mt) REVERT: E 195 VAL cc_start: 0.5917 (OUTLIER) cc_final: 0.5672 (t) REVERT: F 81 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.8001 (ttp-110) REVERT: F 119 TYR cc_start: 0.7913 (t80) cc_final: 0.7165 (t80) REVERT: F 123 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7436 (m-70) REVERT: F 202 LYS cc_start: 0.6810 (mmtm) cc_final: 0.6500 (mmtm) REVERT: G 45 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8100 (m) REVERT: L 34 ARG cc_start: 0.7852 (ptp90) cc_final: 0.7606 (ptp90) REVERT: L 126 VAL cc_start: 0.7716 (t) cc_final: 0.7408 (m) REVERT: M 26 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.6598 (m-80) REVERT: M 35 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7286 (t) REVERT: M 61 LYS cc_start: 0.8520 (mttm) cc_final: 0.8094 (mttm) REVERT: N 216 ILE cc_start: 0.8548 (pt) cc_final: 0.8252 (pt) REVERT: O 72 ARG cc_start: 0.6087 (mmp80) cc_final: 0.5871 (mmp80) REVERT: H 73 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6815 (ptpp) REVERT: H 103 ASN cc_start: 0.8482 (p0) cc_final: 0.8212 (p0) REVERT: H 154 MET cc_start: 0.7542 (mmp) cc_final: 0.6441 (ptm) REVERT: H 167 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.7637 (mtp180) REVERT: H 168 TYR cc_start: 0.8799 (m-80) cc_final: 0.8544 (m-80) REVERT: K 163 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8052 (pp) REVERT: K 196 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7198 (tm-30) outliers start: 86 outliers final: 68 residues processed: 376 average time/residue: 0.1654 time to fit residues: 96.9171 Evaluate side-chains 388 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 309 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 MET Chi-restraints excluded: chain K residue 157 HIS Chi-restraints excluded: chain K residue 163 LEU Chi-restraints excluded: chain K residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 237 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 241 optimal weight: 0.0040 chunk 202 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 176 optimal weight: 9.9990 chunk 231 optimal weight: 0.6980 overall best weight: 1.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 HIS H 114 ASN H 170 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.190875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.147848 restraints weight = 26816.059| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.70 r_work: 0.3573 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22520 Z= 0.145 Angle : 0.575 8.455 30720 Z= 0.294 Chirality : 0.044 0.177 3410 Planarity : 0.004 0.045 3960 Dihedral : 4.610 18.945 3040 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.52 % Allowed : 23.31 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.16), residues: 2735 helix: -1.11 (0.38), residues: 195 sheet: -0.04 (0.19), residues: 770 loop : -0.75 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 120 TYR 0.014 0.001 TYR J 91 PHE 0.017 0.001 PHE C 41 TRP 0.009 0.001 TRP M 184 HIS 0.005 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00353 (22520) covalent geometry : angle 0.57484 (30720) hydrogen bonds : bond 0.03037 ( 595) hydrogen bonds : angle 5.14145 ( 1569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 317 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7808 (mp0) REVERT: B 163 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7987 (pp) REVERT: C 211 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6925 (tm-30) REVERT: D 55 GLN cc_start: 0.8385 (tp40) cc_final: 0.7885 (tm-30) REVERT: D 130 TYR cc_start: 0.9248 (t80) cc_final: 0.8989 (t80) REVERT: D 175 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8186 (tp) REVERT: D 204 LYS cc_start: 0.8084 (ttmm) cc_final: 0.7483 (tttt) REVERT: E 117 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8178 (mt) REVERT: E 195 VAL cc_start: 0.5909 (OUTLIER) cc_final: 0.5647 (t) REVERT: F 119 TYR cc_start: 0.7994 (t80) cc_final: 0.7227 (t80) REVERT: F 123 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.7576 (m-70) REVERT: F 202 LYS cc_start: 0.6857 (mmtm) cc_final: 0.6543 (mmtm) REVERT: G 45 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.8003 (m) REVERT: L 34 ARG cc_start: 0.8005 (ptp90) cc_final: 0.7726 (ptp90) REVERT: L 126 VAL cc_start: 0.7844 (t) cc_final: 0.7532 (m) REVERT: M 26 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: M 35 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7603 (t) REVERT: M 61 LYS cc_start: 0.8557 (mttm) cc_final: 0.8254 (mttt) REVERT: N 216 ILE cc_start: 0.8564 (pt) cc_final: 0.8285 (pt) REVERT: O 72 ARG cc_start: 0.6297 (mmp80) cc_final: 0.6079 (mmp80) REVERT: H 73 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6831 (ptpp) REVERT: H 103 ASN cc_start: 0.8463 (p0) cc_final: 0.8250 (p0) REVERT: H 167 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.7698 (mtp180) REVERT: H 168 TYR cc_start: 0.8849 (m-80) cc_final: 0.8602 (m-80) REVERT: J 123 VAL cc_start: 0.7013 (OUTLIER) cc_final: 0.6754 (m) REVERT: K 163 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8164 (pp) outliers start: 83 outliers final: 67 residues processed: 374 average time/residue: 0.1601 time to fit residues: 94.1740 Evaluate side-chains 388 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 309 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 MET Chi-restraints excluded: chain K residue 157 HIS Chi-restraints excluded: chain K residue 163 LEU Chi-restraints excluded: chain K residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 198 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN G 201 HIS L 31 ASN H 65 HIS H 114 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS I 117 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.185969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142652 restraints weight = 27119.874| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.62 r_work: 0.3519 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22520 Z= 0.243 Angle : 0.672 9.517 30720 Z= 0.345 Chirality : 0.047 0.184 3410 Planarity : 0.005 0.052 3960 Dihedral : 5.135 21.008 3040 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.57 % Allowed : 23.86 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.16), residues: 2735 helix: -1.13 (0.42), residues: 155 sheet: -0.19 (0.19), residues: 765 loop : -0.84 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 67 TYR 0.022 0.002 TYR M 26 PHE 0.021 0.002 PHE C 41 TRP 0.023 0.002 TRP N 184 HIS 0.007 0.001 HIS G 29 Details of bonding type rmsd covalent geometry : bond 0.00591 (22520) covalent geometry : angle 0.67249 (30720) hydrogen bonds : bond 0.03681 ( 595) hydrogen bonds : angle 5.46537 ( 1569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5568.57 seconds wall clock time: 96 minutes 50.00 seconds (5810.00 seconds total)