Starting phenix.real_space_refine on Wed Jun 18 22:16:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hee_34689/06_2025/8hee_34689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hee_34689/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hee_34689/06_2025/8hee_34689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hee_34689/06_2025/8hee_34689.map" model { file = "/net/cci-nas-00/data/ceres_data/8hee_34689/06_2025/8hee_34689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hee_34689/06_2025/8hee_34689.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.79, per 1000 atoms: 0.54 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: 4.35 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.83 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: 6.34 Time building geometry restraints manager: 5.31 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: 0.06 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: 1.440 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 44.360 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (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 TRP 0.016 0.001 TRP O 148 HIS 0.005 0.001 HIS G 201 PHE 0.029 0.002 PHE H 98 TYR 0.057 0.002 TYR L 168 ARG 0.007 0.001 ARG F 26 Details of bonding type rmsd hydrogen bonds : bond 0.25875 ( 595) hydrogen bonds : angle 9.06579 ( 1569) covalent geometry : bond 0.00563 (22520) covalent geometry : angle 0.88077 (30720) *********************** 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 : 2.114 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: 0.3485 time to fit residues: 221.6827 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 : 2.458 ------------------------------------------------------------------------------- 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 227 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 157 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** 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 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 93 HIS I 166 ASN J 139 GLN K 77 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.195448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.151036 restraints weight = 26825.311| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.96 r_work: 0.3612 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 22520 Z= 0.163 Angle : 0.615 7.395 30720 Z= 0.323 Chirality : 0.046 0.171 3410 Planarity : 0.005 0.059 3960 Dihedral : 5.309 53.824 3058 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.52 % Allowed : 21.78 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.16), residues: 2735 helix: -1.10 (0.45), residues: 155 sheet: -0.38 (0.19), residues: 765 loop : -1.07 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 69 HIS 0.008 0.001 HIS I 93 PHE 0.016 0.002 PHE C 77 TYR 0.015 0.002 TYR H 91 ARG 0.005 0.001 ARG I 151 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 595) hydrogen bonds : angle 6.42498 ( 1569) covalent geometry : bond 0.00392 (22520) covalent geometry : angle 0.61459 (30720) *********************** 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 438 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 355 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7430 (ptm160) cc_final: 0.6975 (mtt-85) REVERT: C 80 SER cc_start: 0.5355 (OUTLIER) cc_final: 0.4961 (p) REVERT: D 130 TYR cc_start: 0.9242 (t80) cc_final: 0.8861 (t80) REVERT: M 106 ASN cc_start: 0.8157 (m-40) cc_final: 0.7913 (m110) REVERT: N 21 THR cc_start: 0.8974 (p) cc_final: 0.8767 (p) REVERT: N 122 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6595 (ttp) REVERT: N 216 ILE cc_start: 0.8648 (pt) cc_final: 0.8406 (pt) REVERT: H 65 HIS cc_start: 0.6732 (t70) cc_final: 0.6374 (t70) REVERT: H 103 ASN cc_start: 0.8460 (p0) cc_final: 0.8175 (p0) REVERT: H 152 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8018 (p) REVERT: H 167 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.7600 (mtp180) REVERT: H 168 TYR cc_start: 0.8531 (m-80) cc_final: 0.8292 (m-80) REVERT: I 168 TYR cc_start: 0.7829 (m-80) cc_final: 0.7491 (m-80) REVERT: J 79 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7402 (mm-30) REVERT: J 213 GLU cc_start: -0.1270 (OUTLIER) cc_final: -0.1886 (tt0) REVERT: K 100 TYR cc_start: 0.6862 (m-80) cc_final: 0.6040 (m-80) outliers start: 83 outliers final: 49 residues processed: 408 average time/residue: 0.3372 time to fit residues: 212.2126 Evaluate side-chains 377 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 2.389 ------------------------------------------------------------------------------- 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 126 LEU 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 80 SER Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain D residue 76 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 203 GLN 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 115 LEU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 183 GLU 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 157 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 N residue 199 THR 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 80 LYS Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 213 GLU 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 90 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 152 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 139 optimal weight: 0.0040 chunk 170 optimal weight: 5.9990 chunk 186 optimal weight: 0.0040 chunk 226 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 235 optimal weight: 7.9990 chunk 246 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 32 optimal weight: 0.0980 chunk 244 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 overall best weight: 0.9806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 HIS ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 HIS L 31 ASN L 85 HIS M 189 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.198087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.152817 restraints weight = 26993.192| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.97 r_work: 0.3616 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22520 Z= 0.130 Angle : 0.559 5.971 30720 Z= 0.291 Chirality : 0.044 0.156 3410 Planarity : 0.005 0.050 3960 Dihedral : 4.851 50.567 3044 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.40 % Allowed : 22.76 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2735 helix: -1.06 (0.40), residues: 190 sheet: -0.40 (0.19), residues: 775 loop : -0.95 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 184 HIS 0.007 0.001 HIS I 77 PHE 0.013 0.001 PHE C 77 TYR 0.013 0.001 TYR A 107 ARG 0.003 0.000 ARG K 151 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 595) hydrogen bonds : angle 5.85375 ( 1569) covalent geometry : bond 0.00308 (22520) covalent geometry : angle 0.55915 (30720) *********************** 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 423 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 343 time to evaluate : 2.325 Fit side-chains revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7616 (ptm160) cc_final: 0.7062 (mtt-85) REVERT: D 130 TYR cc_start: 0.9254 (t80) cc_final: 0.8954 (t80) REVERT: F 119 TYR cc_start: 0.7653 (t80) cc_final: 0.6977 (t80) REVERT: M 61 LYS cc_start: 0.8321 (mttm) cc_final: 0.7488 (pttm) REVERT: N 216 ILE cc_start: 0.8620 (pt) cc_final: 0.8364 (pt) REVERT: H 65 HIS cc_start: 0.6657 (t70) cc_final: 0.5821 (t70) REVERT: H 103 ASN cc_start: 0.8445 (p0) cc_final: 0.8181 (p0) REVERT: H 152 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.8047 (p) REVERT: H 167 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.7587 (mtp180) REVERT: H 168 TYR cc_start: 0.8587 (m-80) cc_final: 0.8344 (m-80) REVERT: J 61 PHE cc_start: 0.7267 (m-10) cc_final: 0.6762 (m-10) REVERT: J 207 HIS cc_start: 0.7942 (m90) cc_final: 0.7689 (m90) REVERT: J 213 GLU cc_start: -0.0730 (OUTLIER) cc_final: -0.1455 (tt0) REVERT: K 100 TYR cc_start: 0.6860 (m-80) cc_final: 0.6550 (m-80) outliers start: 80 outliers final: 54 residues processed: 396 average time/residue: 0.3221 time to fit residues: 199.7559 Evaluate side-chains 367 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 311 time to evaluate : 2.223 ------------------------------------------------------------------------------- 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 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 76 LEU 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 115 LEU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain L residue 74 LEU 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 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 3 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 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 133 THR Chi-restraints excluded: chain H residue 152 THR 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 I residue 155 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain J residue 90 VAL 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 90 VAL Chi-restraints excluded: chain K residue 101 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 183 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 204 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 222 optimal weight: 30.0000 chunk 6 optimal weight: 6.9990 chunk 235 optimal weight: 0.0770 chunk 223 optimal weight: 1.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 HIS ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN M 189 GLN O 221 GLN H 157 HIS ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.195892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.151862 restraints weight = 27025.507| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.73 r_work: 0.3630 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2156 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= 0.126 Angle : 0.551 6.768 30720 Z= 0.286 Chirality : 0.044 0.163 3410 Planarity : 0.004 0.045 3960 Dihedral : 4.765 50.091 3044 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.78 % Allowed : 22.63 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.16), residues: 2735 helix: -1.02 (0.40), residues: 190 sheet: -0.34 (0.19), residues: 775 loop : -0.89 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 184 HIS 0.012 0.001 HIS H 65 PHE 0.016 0.001 PHE C 41 TYR 0.012 0.001 TYR F 72 ARG 0.003 0.000 ARG D 181 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 595) hydrogen bonds : angle 5.59703 ( 1569) covalent geometry : bond 0.00304 (22520) covalent geometry : angle 0.55149 (30720) *********************** 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 418 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 329 time to evaluate : 2.335 Fit side-chains revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7587 (ptm160) cc_final: 0.7048 (mtt-85) REVERT: D 130 TYR cc_start: 0.9246 (t80) cc_final: 0.8910 (t80) REVERT: E 117 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8135 (mt) REVERT: F 119 TYR cc_start: 0.7675 (t80) cc_final: 0.6907 (t80) REVERT: G 45 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7999 (m) REVERT: M 26 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.6252 (m-80) REVERT: M 61 LYS cc_start: 0.8356 (mttm) cc_final: 0.7517 (pttm) REVERT: M 76 LYS cc_start: 0.6972 (tmtt) cc_final: 0.6694 (tmtt) REVERT: N 216 ILE cc_start: 0.8598 (pt) cc_final: 0.8307 (pt) REVERT: H 103 ASN cc_start: 0.8470 (p0) cc_final: 0.8217 (p0) REVERT: H 152 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8025 (p) REVERT: H 167 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.7584 (mtp180) REVERT: H 168 TYR cc_start: 0.8585 (m-80) cc_final: 0.8330 (m-80) REVERT: J 207 HIS cc_start: 0.7846 (m90) cc_final: 0.7578 (m90) REVERT: J 213 GLU cc_start: -0.0316 (OUTLIER) cc_final: -0.1103 (tt0) outliers start: 89 outliers final: 63 residues processed: 388 average time/residue: 0.3208 time to fit residues: 195.4522 Evaluate side-chains 380 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 312 time to evaluate : 2.565 ------------------------------------------------------------------------------- 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 A residue 171 ASP Chi-restraints excluded: chain A residue 174 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 46 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 183 GLU 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 117 LEU 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 78 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 143 CYS 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 L residue 204 VAL Chi-restraints excluded: chain M residue 26 TYR 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 3 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 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 152 THR 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 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 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 101 MET Chi-restraints excluded: chain K residue 157 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 109 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS M 88 ASN ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 HIS H 114 ASN H 170 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS I 157 HIS J 170 GLN K 139 GLN K 170 GLN K 209 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.181891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138527 restraints weight = 27538.934| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.56 r_work: 0.3455 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.077 22520 Z= 0.447 Angle : 0.833 9.935 30720 Z= 0.433 Chirality : 0.055 0.236 3410 Planarity : 0.007 0.060 3960 Dihedral : 5.993 50.849 3044 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.01 % Favored : 91.92 % Rotamer: Outliers : 5.22 % Allowed : 22.55 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.15), residues: 2735 helix: -2.11 (0.33), residues: 215 sheet: -0.47 (0.19), residues: 750 loop : -1.30 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP N 184 HIS 0.013 0.002 HIS G 29 PHE 0.038 0.004 PHE M 210 TYR 0.032 0.003 TYR M 26 ARG 0.012 0.001 ARG O 72 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 595) hydrogen bonds : angle 6.23579 ( 1569) covalent geometry : bond 0.01072 (22520) covalent geometry : angle 0.83289 (30720) *********************** 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 442 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 319 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7794 (ptm160) cc_final: 0.7202 (mtt-85) REVERT: D 41 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8352 (tttm) REVERT: D 175 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.7999 (tp) REVERT: E 117 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8279 (mt) REVERT: F 202 LYS cc_start: 0.6953 (mmtm) cc_final: 0.6549 (mmtm) REVERT: G 45 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8009 (m) REVERT: M 35 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7420 (t) REVERT: M 61 LYS cc_start: 0.8588 (mttm) cc_final: 0.8309 (mttt) REVERT: M 121 TYR cc_start: 0.6364 (m-80) cc_final: 0.6116 (m-80) REVERT: N 122 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6895 (ttp) REVERT: H 103 ASN cc_start: 0.8447 (p0) cc_final: 0.8206 (p0) REVERT: H 152 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8238 (p) REVERT: H 167 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.7780 (mtp180) REVERT: H 168 TYR cc_start: 0.8939 (m-80) cc_final: 0.8683 (m-80) REVERT: I 61 PHE cc_start: 0.7759 (m-10) cc_final: 0.7523 (m-10) REVERT: I 136 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8517 (mt-10) REVERT: J 213 GLU cc_start: -0.0525 (OUTLIER) cc_final: -0.1599 (tt0) outliers start: 123 outliers final: 84 residues processed: 409 average time/residue: 0.3528 time to fit residues: 225.6383 Evaluate side-chains 388 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 297 time to evaluate : 2.217 ------------------------------------------------------------------------------- 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 107 VAL Chi-restraints excluded: chain B residue 142 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 200 LEU 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 206 ILE Chi-restraints excluded: chain E residue 35 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 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 174 GLU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 193 VAL 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 144 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 220 THR 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 175 VAL 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 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 MET Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 173 SER 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 157 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 152 THR 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 121 LEU 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 90 VAL Chi-restraints excluded: chain K residue 101 MET Chi-restraints excluded: chain K residue 182 MET 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 134 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 267 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 139 GLN B 202 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 145 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN M 106 ASN O 145 HIS H 114 ASN H 170 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS I 117 ASN K 207 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.190012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145537 restraints weight = 27299.294| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.71 r_work: 0.3528 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22520 Z= 0.176 Angle : 0.612 8.990 30720 Z= 0.319 Chirality : 0.045 0.156 3410 Planarity : 0.005 0.045 3960 Dihedral : 5.314 48.223 3044 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.08 % Allowed : 23.78 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 2735 helix: -1.42 (0.42), residues: 155 sheet: -0.33 (0.19), residues: 715 loop : -1.21 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 184 HIS 0.005 0.001 HIS G 29 PHE 0.019 0.002 PHE L 77 TYR 0.019 0.002 TYR J 91 ARG 0.005 0.000 ARG I 102 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 595) hydrogen bonds : angle 5.75215 ( 1569) covalent geometry : bond 0.00421 (22520) covalent geometry : angle 0.61215 (30720) *********************** 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: 96 poor density : 321 time to evaluate : 2.367 Fit side-chains revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8356 (tttm) REVERT: D 130 TYR cc_start: 0.9242 (t80) cc_final: 0.8874 (t80) REVERT: E 117 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8179 (mt) REVERT: F 202 LYS cc_start: 0.6862 (mmtm) cc_final: 0.6552 (mmtm) REVERT: G 45 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7974 (m) REVERT: G 201 HIS cc_start: 0.6473 (t-170) cc_final: 0.6159 (t-170) REVERT: L 78 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6568 (t0) REVERT: L 211 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7731 (tt0) REVERT: M 26 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.6688 (m-80) REVERT: M 61 LYS cc_start: 0.8521 (mttm) cc_final: 0.8238 (mttt) REVERT: M 121 TYR cc_start: 0.6534 (m-80) cc_final: 0.6257 (m-80) REVERT: M 147 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6960 (pp20) REVERT: N 216 ILE cc_start: 0.8637 (pt) cc_final: 0.8427 (pt) REVERT: H 73 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6975 (ptpp) REVERT: H 103 ASN cc_start: 0.8415 (p0) cc_final: 0.8159 (p0) REVERT: H 152 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8285 (p) REVERT: H 167 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.7797 (mtp180) REVERT: H 168 TYR cc_start: 0.8903 (m-80) cc_final: 0.8636 (m-80) REVERT: I 136 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8415 (mt-10) REVERT: J 213 GLU cc_start: -0.0547 (OUTLIER) cc_final: -0.1769 (tt0) outliers start: 96 outliers final: 69 residues processed: 388 average time/residue: 0.3249 time to fit residues: 196.1882 Evaluate side-chains 378 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 301 time to evaluate : 2.454 ------------------------------------------------------------------------------- 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 207 HIS 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 D residue 80 VAL 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 174 GLU 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 105 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 78 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 144 ILE 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 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 173 SER Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 35 THR 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 73 LYS Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 152 THR 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 195 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 133 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 101 MET Chi-restraints excluded: chain K residue 157 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 182 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 151 optimal weight: 0.3980 chunk 166 optimal weight: 0.5980 chunk 200 optimal weight: 0.0870 chunk 132 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.3760 ------------------------------------------------------------------------------- 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** B 202 ASN ** C 36 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** G 201 HIS M 106 ASN H 114 ASN H 170 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 170 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.188014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145075 restraints weight = 26876.324| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.60 r_work: 0.3556 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3153 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= 0.153 Angle : 0.588 7.832 30720 Z= 0.305 Chirality : 0.044 0.255 3410 Planarity : 0.005 0.057 3960 Dihedral : 5.106 46.807 3044 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.20 % Allowed : 24.03 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2735 helix: -1.30 (0.43), residues: 155 sheet: -0.32 (0.19), residues: 765 loop : -1.04 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 148 HIS 0.005 0.001 HIS H 209 PHE 0.017 0.001 PHE C 41 TYR 0.021 0.002 TYR L 30 ARG 0.008 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 595) hydrogen bonds : angle 5.53704 ( 1569) covalent geometry : bond 0.00370 (22520) covalent geometry : angle 0.58809 (30720) *********************** 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 421 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 322 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.8743 (tp) cc_final: 0.8466 (tp) REVERT: B 163 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8060 (pp) REVERT: D 41 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8354 (tttm) REVERT: D 130 TYR cc_start: 0.9253 (t80) cc_final: 0.8891 (t80) REVERT: E 117 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8126 (mt) REVERT: F 123 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.7717 (m-70) REVERT: F 202 LYS cc_start: 0.6942 (mmtm) cc_final: 0.6651 (mmtm) REVERT: G 45 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7978 (m) REVERT: L 78 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6690 (t0) REVERT: M 26 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: M 61 LYS cc_start: 0.8536 (mttm) cc_final: 0.8253 (mttt) REVERT: M 121 TYR cc_start: 0.6429 (m-80) cc_final: 0.6201 (m-80) REVERT: N 216 ILE cc_start: 0.8590 (pt) cc_final: 0.8327 (pt) REVERT: H 73 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6968 (ptpp) REVERT: H 103 ASN cc_start: 0.8404 (p0) cc_final: 0.8134 (p0) REVERT: H 167 ARG cc_start: 0.8582 (ttm-80) cc_final: 0.7764 (mtp180) REVERT: H 168 TYR cc_start: 0.8851 (m-80) cc_final: 0.8609 (m-80) REVERT: I 172 LYS cc_start: 0.7514 (mttt) cc_final: 0.6747 (mtmt) REVERT: J 91 TYR cc_start: 0.7806 (t80) cc_final: 0.7420 (t80) REVERT: J 213 GLU cc_start: -0.0556 (OUTLIER) cc_final: -0.1748 (tt0) outliers start: 99 outliers final: 68 residues processed: 390 average time/residue: 0.3311 time to fit residues: 201.7169 Evaluate side-chains 389 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 313 time to evaluate : 2.212 ------------------------------------------------------------------------------- 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 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 211 GLU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 183 GLU 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 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 78 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 47 VAL 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 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 185 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 35 THR 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 O residue 180 ASN Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 73 LYS 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 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 195 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 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 101 MET Chi-restraints excluded: chain K residue 157 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 198 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 77 optimal weight: 0.0870 chunk 175 optimal weight: 4.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.187523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144477 restraints weight = 27023.959| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.61 r_work: 0.3539 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22520 Z= 0.192 Angle : 0.619 7.754 30720 Z= 0.320 Chirality : 0.045 0.224 3410 Planarity : 0.005 0.044 3960 Dihedral : 5.181 46.174 3044 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.33 % Allowed : 23.69 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.16), residues: 2735 helix: -1.33 (0.43), residues: 155 sheet: -0.39 (0.19), residues: 775 loop : -1.00 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 184 HIS 0.005 0.001 HIS H 207 PHE 0.019 0.002 PHE C 41 TYR 0.019 0.002 TYR M 26 ARG 0.006 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 595) hydrogen bonds : angle 5.52471 ( 1569) covalent geometry : bond 0.00464 (22520) covalent geometry : angle 0.61942 (30720) *********************** 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 415 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 313 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.8774 (tp) cc_final: 0.8512 (tp) REVERT: B 163 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8193 (pp) REVERT: D 41 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8397 (tttm) REVERT: D 204 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7455 (tttt) REVERT: E 117 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8141 (mt) REVERT: F 123 HIS cc_start: 0.8465 (OUTLIER) cc_final: 0.7701 (m-70) REVERT: F 202 LYS cc_start: 0.6922 (mmtm) cc_final: 0.6633 (mmtm) REVERT: G 45 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7983 (m) REVERT: M 26 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.6826 (m-80) REVERT: M 61 LYS cc_start: 0.8580 (mttm) cc_final: 0.8273 (mttt) REVERT: M 121 TYR cc_start: 0.6359 (m-80) cc_final: 0.6136 (m-80) REVERT: N 216 ILE cc_start: 0.8591 (pt) cc_final: 0.8286 (pt) REVERT: H 73 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6947 (ptpp) REVERT: H 103 ASN cc_start: 0.8401 (p0) cc_final: 0.8150 (p0) REVERT: H 167 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.7742 (mtp180) REVERT: H 168 TYR cc_start: 0.8857 (m-80) cc_final: 0.8628 (m-80) REVERT: I 172 LYS cc_start: 0.7557 (mttt) cc_final: 0.6805 (mtmt) REVERT: J 91 TYR cc_start: 0.7839 (t80) cc_final: 0.7469 (t80) REVERT: J 136 GLU cc_start: 0.7755 (pm20) cc_final: 0.7421 (pm20) REVERT: J 213 GLU cc_start: -0.0396 (OUTLIER) cc_final: -0.1572 (tt0) outliers start: 102 outliers final: 81 residues processed: 384 average time/residue: 0.3224 time to fit residues: 195.1785 Evaluate side-chains 397 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 309 time to evaluate : 2.359 ------------------------------------------------------------------------------- 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 122 MET 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 80 VAL Chi-restraints excluded: chain D residue 183 GLU 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 117 LEU Chi-restraints excluded: chain E residue 174 GLU 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 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 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 143 CYS Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 102 SER 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 216 ILE 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 35 THR 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 O residue 180 ASN Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 73 LYS 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 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 195 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 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 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 149 SER Chi-restraints excluded: chain K residue 157 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 106 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 257 optimal weight: 0.0770 chunk 142 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 ASN H 170 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS K 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.193711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149848 restraints weight = 27049.592| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.75 r_work: 0.3583 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3429 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= 0.111 Angle : 0.565 9.089 30720 Z= 0.290 Chirality : 0.043 0.172 3410 Planarity : 0.005 0.045 3960 Dihedral : 4.833 44.244 3044 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.40 % Allowed : 24.33 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2735 helix: -1.09 (0.40), residues: 190 sheet: -0.21 (0.19), residues: 775 loop : -0.92 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 148 HIS 0.003 0.001 HIS I 77 PHE 0.016 0.001 PHE L 41 TYR 0.016 0.001 TYR K 100 ARG 0.006 0.000 ARG O 72 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 595) hydrogen bonds : angle 5.26062 ( 1569) covalent geometry : bond 0.00265 (22520) covalent geometry : angle 0.56512 (30720) *********************** 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 415 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 335 time to evaluate : 2.454 Fit side-chains revert: symmetry clash REVERT: B 108 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7882 (mp0) REVERT: B 163 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8137 (pp) REVERT: D 41 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8402 (tttm) REVERT: D 175 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8180 (tp) REVERT: D 204 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7658 (mtpp) REVERT: F 81 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.8042 (ttp-110) REVERT: F 123 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.7547 (m-70) REVERT: F 202 LYS cc_start: 0.6929 (mmtm) cc_final: 0.6613 (mmtm) REVERT: G 45 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8078 (m) REVERT: L 34 ARG cc_start: 0.8134 (ptp90) cc_final: 0.7847 (ptp90) REVERT: L 189 GLN cc_start: 0.7828 (tt0) cc_final: 0.7524 (tp-100) REVERT: M 26 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: M 61 LYS cc_start: 0.8538 (mttm) cc_final: 0.8222 (mttt) REVERT: M 121 TYR cc_start: 0.6387 (m-80) cc_final: 0.6165 (m-80) REVERT: N 216 ILE cc_start: 0.8501 (pt) cc_final: 0.8237 (pt) REVERT: H 103 ASN cc_start: 0.8391 (p0) cc_final: 0.8156 (p0) REVERT: H 154 MET cc_start: 0.7755 (mmp) cc_final: 0.6668 (ptm) REVERT: H 167 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.7736 (mtp180) REVERT: H 168 TYR cc_start: 0.8817 (m-80) cc_final: 0.8583 (m-80) REVERT: I 61 PHE cc_start: 0.7745 (m-10) cc_final: 0.7476 (m-10) REVERT: I 172 LYS cc_start: 0.7486 (mttt) cc_final: 0.6715 (mtmt) REVERT: J 91 TYR cc_start: 0.7728 (t80) cc_final: 0.7314 (t80) REVERT: K 149 SER cc_start: 0.7626 (OUTLIER) cc_final: 0.7406 (p) outliers start: 80 outliers final: 63 residues processed: 389 average time/residue: 0.3320 time to fit residues: 202.1978 Evaluate side-chains 387 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 318 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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 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 211 GLU Chi-restraints excluded: chain D residue 80 VAL 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 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 L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 143 CYS 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 102 SER Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 3 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 35 THR Chi-restraints excluded: chain O residue 64 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 O residue 180 ASN Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 80 LYS 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 121 LEU Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 133 THR 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 149 SER Chi-restraints excluded: chain K residue 157 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 20.0000 chunk 191 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 262 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 263 optimal weight: 0.3980 chunk 230 optimal weight: 1.9990 chunk 226 optimal weight: 0.0980 chunk 16 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN H 114 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS I 157 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.190377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.146323 restraints weight = 27537.474| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.71 r_work: 0.3545 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22520 Z= 0.171 Angle : 0.609 8.505 30720 Z= 0.311 Chirality : 0.045 0.188 3410 Planarity : 0.005 0.044 3960 Dihedral : 4.948 44.333 3042 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.31 % Allowed : 24.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2735 helix: -1.17 (0.39), residues: 190 sheet: -0.20 (0.19), residues: 765 loop : -0.92 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 184 HIS 0.006 0.001 HIS I 157 PHE 0.018 0.002 PHE C 41 TYR 0.016 0.002 TYR M 26 ARG 0.006 0.000 ARG E 178 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 595) hydrogen bonds : angle 5.30344 ( 1569) covalent geometry : bond 0.00416 (22520) covalent geometry : angle 0.60927 (30720) ********************** 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 399 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 321 time to evaluate : 2.708 Fit side-chains revert: symmetry clash REVERT: B 163 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8172 (pp) REVERT: D 41 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8413 (tttm) REVERT: D 119 TYR cc_start: 0.8814 (t80) cc_final: 0.8473 (t80) REVERT: D 175 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8150 (tp) REVERT: D 204 LYS cc_start: 0.8092 (ttmm) cc_final: 0.7465 (tttt) REVERT: E 117 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8137 (mt) REVERT: E 195 VAL cc_start: 0.5736 (OUTLIER) cc_final: 0.5420 (t) REVERT: F 81 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.8014 (ttp-110) REVERT: F 123 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.7671 (m-70) REVERT: F 202 LYS cc_start: 0.6912 (mmtm) cc_final: 0.6615 (mmtm) REVERT: G 45 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7990 (m) REVERT: L 34 ARG cc_start: 0.8187 (ptp90) cc_final: 0.7881 (ptp90) REVERT: L 148 TRP cc_start: 0.7666 (p-90) cc_final: 0.6963 (p-90) REVERT: M 26 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.6888 (m-80) REVERT: M 61 LYS cc_start: 0.8570 (mttm) cc_final: 0.8250 (mttt) REVERT: N 216 ILE cc_start: 0.8567 (pt) cc_final: 0.8294 (pt) REVERT: H 73 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6892 (ptpp) REVERT: H 103 ASN cc_start: 0.8409 (p0) cc_final: 0.8208 (p0) REVERT: H 154 MET cc_start: 0.7766 (mmp) cc_final: 0.6626 (ptm) REVERT: H 167 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.7739 (mtp180) REVERT: H 168 TYR cc_start: 0.8894 (m-80) cc_final: 0.8642 (m-80) REVERT: I 172 LYS cc_start: 0.7496 (mttt) cc_final: 0.6710 (mtmt) REVERT: J 91 TYR cc_start: 0.7836 (t80) cc_final: 0.7501 (t80) REVERT: J 123 VAL cc_start: 0.7174 (OUTLIER) cc_final: 0.6879 (m) outliers start: 78 outliers final: 62 residues processed: 372 average time/residue: 0.3643 time to fit residues: 212.1147 Evaluate side-chains 384 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 313 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU 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 115 LEU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 143 CYS 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 45 LEU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 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 185 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 64 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 180 ASN Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 73 LYS 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 80 LYS Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 126 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN L 88 ASN M 106 ASN H 114 ASN H 170 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS K 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.182966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138085 restraints weight = 26738.687| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.74 r_work: 0.3462 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22520 Z= 0.190 Angle : 0.632 8.424 30720 Z= 0.324 Chirality : 0.045 0.164 3410 Planarity : 0.005 0.045 3960 Dihedral : 5.102 44.326 3042 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.69 % Allowed : 23.99 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2735 helix: -1.31 (0.43), residues: 155 sheet: -0.29 (0.18), residues: 770 loop : -0.93 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 184 HIS 0.005 0.001 HIS H 65 PHE 0.018 0.002 PHE C 41 TYR 0.019 0.002 TYR M 26 ARG 0.005 0.000 ARG I 135 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 595) hydrogen bonds : angle 5.37814 ( 1569) covalent geometry : bond 0.00462 (22520) covalent geometry : angle 0.63224 (30720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10901.76 seconds wall clock time: 188 minutes 37.39 seconds (11317.39 seconds total)