Starting phenix.real_space_refine on Wed Jun 18 19:38:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x6o_33024/06_2025/7x6o_33024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x6o_33024/06_2025/7x6o_33024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x6o_33024/06_2025/7x6o_33024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x6o_33024/06_2025/7x6o_33024.map" model { file = "/net/cci-nas-00/data/ceres_data/7x6o_33024/06_2025/7x6o_33024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x6o_33024/06_2025/7x6o_33024.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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 96 5.16 5 C 13581 2.51 5 N 3678 2.21 5 O 4254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21609 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "B" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "C" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "I" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "K" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "H" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "J" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Time building chain proxies: 13.20, per 1000 atoms: 0.61 Number of scatterers: 21609 At special positions: 0 Unit cell: (185.838, 176.612, 142.344, 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 96 16.00 O 4254 8.00 N 3678 7.00 C 13581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 107 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 285 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 146 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 313 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 102 " - pdb=" SG CYS I 107 " distance=2.03 Simple disulfide: pdb=" SG CYS I 157 " - pdb=" SG CYS I 213 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 285 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 100 " - pdb=" SG CYS F 146 " distance=2.03 Simple disulfide: pdb=" SG CYS F 289 " - pdb=" SG CYS F 313 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 102 " - pdb=" SG CYS J 107 " distance=2.03 Simple disulfide: pdb=" SG CYS J 157 " - pdb=" SG CYS J 213 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 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: 5.06 Conformation dependent library (CDL) restraints added in 3.2 seconds 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5142 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 60 sheets defined 15.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.610A pdb=" N LEU A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.830A pdb=" N GLU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.675A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.510A pdb=" N GLN A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 53 removed outlier: 3.541A pdb=" N ILE B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 124 removed outlier: 3.941A pdb=" N LEU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.620A pdb=" N VAL B 152 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.799A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR C 91 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.963A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.643A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 183 through 187 removed outlier: 3.818A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 187' Processing helix chain 'D' and resid 212 through 214 No H-bonds generated for 'chain 'D' and resid 212 through 214' Processing helix chain 'E' and resid 66 through 72 removed outlier: 3.606A pdb=" N LEU E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 removed outlier: 3.777A pdb=" N GLU E 78 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 removed outlier: 3.667A pdb=" N LEU E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 removed outlier: 3.540A pdb=" N GLN E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 53 Processing helix chain 'G' and resid 74 through 124 removed outlier: 3.790A pdb=" N LEU G 80 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 96 " --> pdb=" O TRP G 92 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.643A pdb=" N VAL G 152 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 153 " --> pdb=" O MET G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 167 removed outlier: 3.628A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G 166 " --> pdb=" O TYR G 162 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.788A pdb=" N THR I 91 " --> pdb=" O ASP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.671A pdb=" N LEU K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 121 through 126' Processing helix chain 'K' and resid 183 through 189 removed outlier: 3.799A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS K 188 " --> pdb=" O ALA K 184 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 183 through 189' Processing helix chain 'K' and resid 212 through 214 No H-bonds generated for 'chain 'K' and resid 212 through 214' Processing helix chain 'F' and resid 66 through 72 removed outlier: 3.623A pdb=" N LEU F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 78 removed outlier: 3.729A pdb=" N GLU F 78 " --> pdb=" O PRO F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 115 removed outlier: 3.669A pdb=" N LEU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 removed outlier: 3.532A pdb=" N GLN F 199 " --> pdb=" O THR F 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 53 Processing helix chain 'H' and resid 74 through 124 removed outlier: 3.804A pdb=" N LEU H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY H 87 " --> pdb=" O LYS H 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA H 96 " --> pdb=" O TRP H 92 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 removed outlier: 3.648A pdb=" N VAL H 152 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS H 153 " --> pdb=" O MET H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 167 removed outlier: 3.773A pdb=" N TYR H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU H 165 " --> pdb=" O LYS H 161 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA H 166 " --> pdb=" O TYR H 162 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.791A pdb=" N THR J 91 " --> pdb=" O ASP J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 175 No H-bonds generated for 'chain 'J' and resid 173 through 175' Processing helix chain 'J' and resid 204 through 206 No H-bonds generated for 'chain 'J' and resid 204 through 206' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.965A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.623A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 121 through 126' Processing helix chain 'L' and resid 183 through 187 removed outlier: 3.804A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 removed outlier: 3.509A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 14 " --> pdb=" O HIS B 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 139 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.453A pdb=" N LEU A 51 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR A 287 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LYS A 53 " --> pdb=" O THR A 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 61 removed outlier: 7.699A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.514A pdb=" N ALA A 266 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 186 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.514A pdb=" N ALA A 266 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 171 through 176 removed outlier: 3.514A pdb=" N ALA A 254 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 175 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 211 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 294 through 296 removed outlier: 3.651A pdb=" N THR A 291 " --> pdb=" O GLY A 294 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 296 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 289 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR B 64 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.878A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.928A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 127 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 12 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.928A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 127 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 12 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 97 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG C 98 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY C 116 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 137 through 140 removed outlier: 3.641A pdb=" N SER C 197 " --> pdb=" O CYS C 157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 193 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 198 " --> pdb=" O HIS C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 137 through 140 removed outlier: 3.641A pdb=" N SER C 197 " --> pdb=" O CYS C 157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 193 " --> pdb=" O ASP C 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 167 through 171 removed outlier: 3.746A pdb=" N TYR C 211 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.513A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.454A pdb=" N VAL D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 49 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.639A pdb=" N ASN D 137 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D 138 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 145 through 150 removed outlier: 3.641A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 149 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR D 192 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 32 through 36 removed outlier: 3.528A pdb=" N GLY G 33 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS E 14 " --> pdb=" O HIS G 25 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU G 139 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.559A pdb=" N LEU E 51 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N CYS E 285 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 60 through 61 removed outlier: 7.683A pdb=" N LEU E 60 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.586A pdb=" N ALA E 266 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU E 186 " --> pdb=" O PRO E 261 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.586A pdb=" N ALA E 266 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 171 through 176 removed outlier: 3.619A pdb=" N TYR E 175 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 211 " --> pdb=" O LYS E 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 294 through 296 removed outlier: 3.531A pdb=" N THR E 291 " --> pdb=" O GLY E 294 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 296 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS E 289 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 310 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR G 64 " --> pdb=" O GLY E 311 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.868A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.842A pdb=" N GLY I 10 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR I 127 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 12 " --> pdb=" O THR I 127 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.842A pdb=" N GLY I 10 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR I 127 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 12 " --> pdb=" O THR I 127 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I 97 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG I 98 " --> pdb=" O ASP I 118 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY I 116 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.609A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL I 198 " --> pdb=" O HIS I 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.609A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 167 through 171 removed outlier: 3.793A pdb=" N TYR I 211 " --> pdb=" O VAL I 228 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.637A pdb=" N SER K 65 " --> pdb=" O THR K 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.535A pdb=" N VAL K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR K 49 " --> pdb=" O ARG K 53 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.642A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN K 138 " --> pdb=" O TYR K 173 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 145 through 150 removed outlier: 3.607A pdb=" N LYS K 145 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS K 149 " --> pdb=" O ALA K 193 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR K 192 " --> pdb=" O PHE K 209 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS K 207 " --> pdb=" O CYS K 194 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL K 205 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 32 through 36 removed outlier: 3.534A pdb=" N GLY H 33 " --> pdb=" O HIS H 26 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS F 14 " --> pdb=" O HIS H 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 139 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AE7, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AE8, first strand: chain 'F' and resid 43 through 44 removed outlier: 3.535A pdb=" N GLU F 44 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 51 through 54 removed outlier: 7.479A pdb=" N LEU F 51 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR F 287 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LYS F 53 " --> pdb=" O THR F 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 60 through 61 removed outlier: 7.689A pdb=" N LEU F 60 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.545A pdb=" N ALA F 266 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU F 186 " --> pdb=" O PRO F 261 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.545A pdb=" N ALA F 266 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 171 through 176 removed outlier: 3.507A pdb=" N ALA F 254 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR F 175 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 211 " --> pdb=" O LYS F 218 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 294 through 296 removed outlier: 3.638A pdb=" N THR F 291 " --> pdb=" O GLY F 294 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE F 296 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS F 289 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 310 " --> pdb=" O GLN F 290 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR H 64 " --> pdb=" O GLY F 311 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.840A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.885A pdb=" N GLY J 10 " --> pdb=" O THR J 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR J 127 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 12 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR J 124 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.885A pdb=" N GLY J 10 " --> pdb=" O THR J 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR J 127 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 12 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR J 124 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA J 97 " --> pdb=" O ASN J 35 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG J 98 " --> pdb=" O ASP J 118 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLY J 116 " --> pdb=" O ARG J 100 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 137 through 140 removed outlier: 3.642A pdb=" N SER J 197 " --> pdb=" O CYS J 157 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR J 193 " --> pdb=" O ASP J 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL J 198 " --> pdb=" O HIS J 181 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 137 through 140 removed outlier: 3.642A pdb=" N SER J 197 " --> pdb=" O CYS J 157 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR J 193 " --> pdb=" O ASP J 161 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 167 through 171 removed outlier: 3.745A pdb=" N TYR J 211 " --> pdb=" O VAL J 228 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.548A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.499A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR L 49 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.655A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.645A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS L 149 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 1950 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: 7.71 Time building geometry restraints manager: 6.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7002 1.34 - 1.46: 5243 1.46 - 1.58: 9730 1.58 - 1.70: 0 1.70 - 1.81: 123 Bond restraints: 22098 Sorted by residual: bond pdb=" N SER A 299 " pdb=" CA SER A 299 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.34e+00 bond pdb=" N SER E 299 " pdb=" CA SER E 299 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.24e+00 bond pdb=" N SER F 299 " pdb=" CA SER F 299 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.22e+00 bond pdb=" C THR F 298 " pdb=" N SER F 299 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.40e-02 5.10e+03 2.84e+00 bond pdb=" C THR E 298 " pdb=" N SER E 299 " ideal model delta sigma weight residual 1.329 1.352 -0.023 1.40e-02 5.10e+03 2.66e+00 ... (remaining 22093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 29839 2.69 - 5.37: 139 5.37 - 8.06: 10 8.06 - 10.75: 0 10.75 - 13.44: 3 Bond angle restraints: 29991 Sorted by residual: angle pdb=" C THR E 298 " pdb=" N SER E 299 " pdb=" CA SER E 299 " ideal model delta sigma weight residual 121.70 135.14 -13.44 1.80e+00 3.09e-01 5.57e+01 angle pdb=" C THR F 298 " pdb=" N SER F 299 " pdb=" CA SER F 299 " ideal model delta sigma weight residual 121.70 135.10 -13.40 1.80e+00 3.09e-01 5.54e+01 angle pdb=" C THR A 298 " pdb=" N SER A 299 " pdb=" CA SER A 299 " ideal model delta sigma weight residual 121.70 134.87 -13.17 1.80e+00 3.09e-01 5.36e+01 angle pdb=" N VAL G 66 " pdb=" CA VAL G 66 " pdb=" C VAL G 66 " ideal model delta sigma weight residual 111.81 108.61 3.20 8.60e-01 1.35e+00 1.38e+01 angle pdb=" N VAL B 66 " pdb=" CA VAL B 66 " pdb=" C VAL B 66 " ideal model delta sigma weight residual 111.81 108.73 3.08 8.60e-01 1.35e+00 1.28e+01 ... (remaining 29986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 12644 14.70 - 29.41: 414 29.41 - 44.11: 135 44.11 - 58.82: 16 58.82 - 73.52: 3 Dihedral angle restraints: 13212 sinusoidal: 5163 harmonic: 8049 Sorted by residual: dihedral pdb=" CA HIS G 72 " pdb=" C HIS G 72 " pdb=" N LEU G 73 " pdb=" CA LEU G 73 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N LEU B 73 " pdb=" CA LEU B 73 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA HIS H 72 " pdb=" C HIS H 72 " pdb=" N LEU H 73 " pdb=" CA LEU H 73 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 13209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2504 0.041 - 0.081: 504 0.081 - 0.122: 286 0.122 - 0.162: 18 0.162 - 0.203: 3 Chirality restraints: 3315 Sorted by residual: chirality pdb=" CA SER F 299 " pdb=" N SER F 299 " pdb=" C SER F 299 " pdb=" CB SER F 299 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA SER E 299 " pdb=" N SER E 299 " pdb=" C SER E 299 " pdb=" CB SER E 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA SER A 299 " pdb=" N SER A 299 " pdb=" C SER A 299 " pdb=" CB SER A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 3312 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN K 79 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO K 80 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 80 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO L 80 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO D 80 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " -0.026 5.00e-02 4.00e+02 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5723 2.81 - 3.33: 16250 3.33 - 3.85: 36637 3.85 - 4.38: 39644 4.38 - 4.90: 70741 Nonbonded interactions: 168995 Sorted by model distance: nonbonded pdb=" OG1 THR E 287 " pdb=" O ILE E 296 " model vdw 2.283 3.040 nonbonded pdb=" O LEU B 89 " pdb=" OG1 THR B 93 " model vdw 2.311 3.040 nonbonded pdb=" O CYS A 52 " pdb=" OH TYR A 88 " model vdw 2.312 3.040 nonbonded pdb=" O LEU H 89 " pdb=" OG1 THR H 93 " model vdw 2.314 3.040 nonbonded pdb=" O LEU G 89 " pdb=" OG1 THR G 93 " model vdw 2.319 3.040 ... (remaining 168990 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 51.630 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 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 : 0.002 0.040 22128 Z= 0.115 Angle : 0.487 13.437 30051 Z= 0.280 Chirality : 0.042 0.203 3315 Planarity : 0.005 0.049 3864 Dihedral : 8.088 73.519 7980 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.82 % Allowed : 3.31 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -3.07 (0.13), residues: 2757 helix: -4.02 (0.11), residues: 300 sheet: -1.37 (0.17), residues: 822 loop : -2.03 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 86 HIS 0.005 0.000 HIS H 72 PHE 0.013 0.001 PHE A 154 TYR 0.009 0.001 TYR F 88 ARG 0.002 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.31192 ( 676) hydrogen bonds : angle 10.82961 ( 1950) SS BOND : bond 0.00107 ( 30) SS BOND : angle 0.41683 ( 60) covalent geometry : bond 0.00211 (22098) covalent geometry : angle 0.48741 (29991) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 527 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7396 (mp) cc_final: 0.7109 (mt) REVERT: A 90 VAL cc_start: 0.5771 (t) cc_final: 0.5550 (t) REVERT: A 108 TYR cc_start: 0.7161 (t80) cc_final: 0.6655 (t80) REVERT: A 133 TRP cc_start: 0.5698 (m-90) cc_final: 0.5073 (m-90) REVERT: A 170 LYS cc_start: 0.7683 (tttt) cc_final: 0.7269 (mmtt) REVERT: A 175 TYR cc_start: 0.6765 (t80) cc_final: 0.6497 (t80) REVERT: A 231 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7693 (ttt-90) REVERT: A 233 GLN cc_start: 0.6637 (mm-40) cc_final: 0.6344 (mm-40) REVERT: A 293 LYS cc_start: 0.7106 (mttt) cc_final: 0.6827 (mttt) REVERT: B 81 ASN cc_start: 0.7457 (t0) cc_final: 0.7245 (t0) REVERT: B 103 GLU cc_start: 0.6434 (mm-30) cc_final: 0.6223 (mm-30) REVERT: B 110 TYR cc_start: 0.7094 (t80) cc_final: 0.6747 (t80) REVERT: B 149 MET cc_start: 0.5695 (mmt) cc_final: 0.5389 (mmm) REVERT: B 150 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7023 (mm-30) REVERT: B 152 VAL cc_start: 0.6773 (t) cc_final: 0.6451 (m) REVERT: B 153 LYS cc_start: 0.6736 (ttpt) cc_final: 0.6419 (ttpt) REVERT: C 25 SER cc_start: 0.6975 (p) cc_final: 0.6768 (m) REVERT: C 36 TRP cc_start: 0.5129 (m100) cc_final: 0.4845 (m100) REVERT: C 67 ARG cc_start: 0.6312 (mtm180) cc_final: 0.6073 (mtm180) REVERT: D 4 MET cc_start: 0.5388 (mmm) cc_final: 0.4729 (mmm) REVERT: D 36 TYR cc_start: 0.4375 (m-80) cc_final: 0.4130 (m-80) REVERT: D 82 ASP cc_start: 0.6356 (m-30) cc_final: 0.5142 (m-30) REVERT: E 217 SER cc_start: 0.6550 (m) cc_final: 0.5919 (p) REVERT: E 231 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7390 (mtp-110) REVERT: E 249 LYS cc_start: 0.6322 (ttpt) cc_final: 0.5878 (ttmm) REVERT: E 267 MET cc_start: 0.5526 (ppp) cc_final: 0.5188 (ppp) REVERT: G 40 SER cc_start: 0.8776 (m) cc_final: 0.8373 (p) REVERT: G 53 ASN cc_start: 0.7116 (m-40) cc_final: 0.6803 (m-40) REVERT: G 81 ASN cc_start: 0.7269 (t0) cc_final: 0.7035 (t0) REVERT: G 131 LYS cc_start: 0.7249 (tttt) cc_final: 0.7049 (tttt) REVERT: I 67 ARG cc_start: 0.6780 (mtm180) cc_final: 0.6365 (mtm180) REVERT: I 115 TYR cc_start: 0.6761 (m-80) cc_final: 0.6165 (m-80) REVERT: I 163 PHE cc_start: 0.5121 (t80) cc_final: 0.4845 (t80) REVERT: K 4 MET cc_start: 0.5849 (mmm) cc_final: 0.4715 (ttt) REVERT: K 5 THR cc_start: 0.6528 (m) cc_final: 0.6320 (t) REVERT: K 37 GLN cc_start: 0.7607 (tt0) cc_final: 0.7041 (tt0) REVERT: K 63 SER cc_start: 0.7054 (t) cc_final: 0.6827 (t) REVERT: K 82 ASP cc_start: 0.6077 (m-30) cc_final: 0.4199 (m-30) REVERT: F 108 TYR cc_start: 0.6935 (t80) cc_final: 0.6696 (t80) REVERT: F 170 LYS cc_start: 0.7852 (tttt) cc_final: 0.7424 (mptt) REVERT: F 179 LYS cc_start: 0.7009 (mmtt) cc_final: 0.6677 (mttp) REVERT: F 191 HIS cc_start: 0.5112 (m-70) cc_final: 0.4739 (m-70) REVERT: F 312 LYS cc_start: 0.7113 (mttt) cc_final: 0.6665 (mmtt) REVERT: F 321 LYS cc_start: 0.7114 (pttt) cc_final: 0.6903 (tppt) REVERT: F 322 LEU cc_start: 0.8057 (mt) cc_final: 0.7789 (mt) REVERT: F 323 ARG cc_start: 0.7212 (ttm-80) cc_final: 0.6997 (ttt90) REVERT: H 131 LYS cc_start: 0.7329 (tttt) cc_final: 0.7017 (tttt) REVERT: H 149 MET cc_start: 0.5754 (mmt) cc_final: 0.5504 (mmp) REVERT: L 4 MET cc_start: 0.5946 (mmm) cc_final: 0.5184 (tpp) REVERT: L 37 GLN cc_start: 0.7502 (tt0) cc_final: 0.6756 (tt0) REVERT: L 82 ASP cc_start: 0.6256 (m-30) cc_final: 0.6044 (m-30) REVERT: L 97 THR cc_start: 0.7518 (m) cc_final: 0.7203 (p) outliers start: 44 outliers final: 10 residues processed: 560 average time/residue: 0.3518 time to fit residues: 307.5296 Evaluate side-chains 442 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 432 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 50.0000 chunk 247 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 166 ASN B 25 HIS B 50 ASN B 95 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 HIS G 42 GLN G 62 GLN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN H 25 HIS H 81 ASN H 95 ASN ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.245704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.208587 restraints weight = 33976.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.214228 restraints weight = 18074.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.217688 restraints weight = 11203.864| |-----------------------------------------------------------------------------| r_work (final): 0.4610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5586 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22128 Z= 0.216 Angle : 0.669 10.054 30051 Z= 0.356 Chirality : 0.047 0.251 3315 Planarity : 0.005 0.066 3864 Dihedral : 4.310 59.805 3020 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.19 % Allowed : 8.07 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.88 (0.14), residues: 2757 helix: -1.49 (0.24), residues: 294 sheet: -0.86 (0.17), residues: 816 loop : -1.41 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 14 HIS 0.006 0.001 HIS F 61 PHE 0.029 0.002 PHE A 154 TYR 0.023 0.002 TYR H 94 ARG 0.008 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.05364 ( 676) hydrogen bonds : angle 6.71907 ( 1950) SS BOND : bond 0.00421 ( 30) SS BOND : angle 1.59921 ( 60) covalent geometry : bond 0.00451 (22098) covalent geometry : angle 0.66548 (29991) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 481 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7589 (mp) cc_final: 0.7343 (mt) REVERT: A 170 LYS cc_start: 0.7822 (tttt) cc_final: 0.7391 (mmtt) REVERT: A 175 TYR cc_start: 0.6730 (t80) cc_final: 0.6393 (t80) REVERT: A 234 GLU cc_start: 0.4885 (pm20) cc_final: 0.4583 (pm20) REVERT: A 249 LYS cc_start: 0.7061 (ttpt) cc_final: 0.6842 (ttmm) REVERT: A 321 LYS cc_start: 0.7175 (tptt) cc_final: 0.6945 (tptt) REVERT: B 103 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6802 (mm-30) REVERT: B 110 TYR cc_start: 0.7150 (t80) cc_final: 0.6828 (t80) REVERT: B 131 LYS cc_start: 0.7374 (tttt) cc_final: 0.7022 (tttt) REVERT: B 140 PHE cc_start: 0.5804 (m-80) cc_final: 0.5212 (m-80) REVERT: B 149 MET cc_start: 0.5529 (mmt) cc_final: 0.5090 (mmm) REVERT: B 153 LYS cc_start: 0.7421 (ttpt) cc_final: 0.6684 (ttpt) REVERT: C 27 PHE cc_start: 0.6403 (p90) cc_final: 0.6103 (p90) REVERT: C 67 ARG cc_start: 0.6833 (mtm180) cc_final: 0.6482 (mtm180) REVERT: D 4 MET cc_start: 0.4527 (mmm) cc_final: 0.3654 (ttm) REVERT: D 65 SER cc_start: 0.7708 (p) cc_final: 0.7415 (t) REVERT: D 81 GLU cc_start: 0.6724 (pm20) cc_final: 0.6416 (pm20) REVERT: D 82 ASP cc_start: 0.6607 (m-30) cc_final: 0.5584 (m-30) REVERT: E 112 ARG cc_start: 0.6825 (mtp85) cc_final: 0.6621 (mtp85) REVERT: E 122 GLU cc_start: 0.7015 (tt0) cc_final: 0.6789 (tt0) REVERT: E 231 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7435 (mtp-110) REVERT: E 318 LYS cc_start: 0.7383 (mtmt) cc_final: 0.7071 (pttt) REVERT: G 40 SER cc_start: 0.8651 (m) cc_final: 0.8441 (p) REVERT: G 41 THR cc_start: 0.8395 (m) cc_final: 0.7946 (p) REVERT: I 29 PHE cc_start: 0.6497 (t80) cc_final: 0.6233 (t80) REVERT: I 67 ARG cc_start: 0.7353 (mtm180) cc_final: 0.6843 (mtm180) REVERT: I 112 TYR cc_start: 0.6186 (m-80) cc_final: 0.5471 (m-10) REVERT: I 115 TYR cc_start: 0.6926 (m-80) cc_final: 0.6594 (m-80) REVERT: I 163 PHE cc_start: 0.5242 (t80) cc_final: 0.4849 (t80) REVERT: K 4 MET cc_start: 0.4618 (mmm) cc_final: 0.4064 (ttt) REVERT: K 37 GLN cc_start: 0.7270 (tt0) cc_final: 0.6729 (tt0) REVERT: K 82 ASP cc_start: 0.5878 (m-30) cc_final: 0.5425 (m-30) REVERT: F 70 TRP cc_start: 0.6700 (t60) cc_final: 0.6390 (t60) REVERT: F 106 ILE cc_start: 0.7152 (mt) cc_final: 0.6933 (mp) REVERT: F 170 LYS cc_start: 0.8024 (tttt) cc_final: 0.7713 (tttt) REVERT: F 179 LYS cc_start: 0.7287 (mmtt) cc_final: 0.6925 (mttt) REVERT: F 321 LYS cc_start: 0.7502 (pttt) cc_final: 0.7259 (tppt) REVERT: F 322 LEU cc_start: 0.8223 (mt) cc_final: 0.7844 (mt) REVERT: F 323 ARG cc_start: 0.7228 (ttm-80) cc_final: 0.6927 (ttm-80) REVERT: H 40 SER cc_start: 0.8518 (m) cc_final: 0.8277 (p) REVERT: H 81 ASN cc_start: 0.8022 (t0) cc_final: 0.7780 (t160) REVERT: H 92 TRP cc_start: 0.4819 (m-10) cc_final: 0.3693 (m-10) REVERT: H 103 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6349 (mm-30) REVERT: H 131 LYS cc_start: 0.7256 (tttt) cc_final: 0.7037 (tttt) REVERT: J 104 SER cc_start: 0.7516 (p) cc_final: 0.7141 (t) REVERT: J 106 ASN cc_start: 0.7092 (m-40) cc_final: 0.6829 (m-40) REVERT: J 163 PHE cc_start: 0.5415 (t80) cc_final: 0.5198 (t80) REVERT: L 4 MET cc_start: 0.5341 (mmm) cc_final: 0.4964 (ttm) REVERT: L 37 GLN cc_start: 0.7455 (tt0) cc_final: 0.6588 (tt0) REVERT: L 82 ASP cc_start: 0.6369 (m-30) cc_final: 0.5679 (m-30) REVERT: L 94 PHE cc_start: 0.6664 (p90) cc_final: 0.6352 (p90) REVERT: L 97 THR cc_start: 0.7193 (m) cc_final: 0.6946 (p) outliers start: 53 outliers final: 31 residues processed: 512 average time/residue: 0.3861 time to fit residues: 302.9215 Evaluate side-chains 481 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 450 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 234 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 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 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN A 306 HIS B 50 ASN B 62 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 100 GLN H 53 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.222818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.186340 restraints weight = 34880.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.192308 restraints weight = 17985.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.196022 restraints weight = 10830.153| |-----------------------------------------------------------------------------| r_work (final): 0.4558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 22128 Z= 0.248 Angle : 0.693 10.983 30051 Z= 0.366 Chirality : 0.047 0.236 3315 Planarity : 0.004 0.042 3864 Dihedral : 4.385 35.875 3011 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.98 % Allowed : 9.15 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.39 (0.15), residues: 2757 helix: -0.74 (0.27), residues: 279 sheet: -0.50 (0.18), residues: 822 loop : -1.17 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 14 HIS 0.008 0.002 HIS A 61 PHE 0.042 0.002 PHE C 29 TYR 0.029 0.002 TYR A 88 ARG 0.005 0.001 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.05496 ( 676) hydrogen bonds : angle 6.34783 ( 1950) SS BOND : bond 0.00668 ( 30) SS BOND : angle 1.63839 ( 60) covalent geometry : bond 0.00523 (22098) covalent geometry : angle 0.69019 (29991) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 477 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7833 (mp) cc_final: 0.7615 (mt) REVERT: A 170 LYS cc_start: 0.7884 (tttt) cc_final: 0.7449 (mmtt) REVERT: A 177 ASN cc_start: 0.7215 (t0) cc_final: 0.6472 (t0) REVERT: A 179 LYS cc_start: 0.6613 (ttpp) cc_final: 0.6130 (tttm) REVERT: A 293 LYS cc_start: 0.7281 (mttt) cc_final: 0.6930 (mttt) REVERT: A 321 LYS cc_start: 0.7422 (tptt) cc_final: 0.7220 (tptt) REVERT: A 329 ARG cc_start: 0.5737 (ttt90) cc_final: 0.5290 (ptt90) REVERT: B 84 VAL cc_start: 0.5702 (t) cc_final: 0.5495 (t) REVERT: B 88 PHE cc_start: 0.6134 (m-80) cc_final: 0.4158 (m-80) REVERT: B 103 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 110 TYR cc_start: 0.7124 (t80) cc_final: 0.6778 (t80) REVERT: B 114 ASN cc_start: 0.6915 (m-40) cc_final: 0.6215 (m-40) REVERT: B 131 LYS cc_start: 0.7349 (tttt) cc_final: 0.6950 (tttt) REVERT: B 140 PHE cc_start: 0.5770 (m-80) cc_final: 0.5351 (m-80) REVERT: B 149 MET cc_start: 0.5593 (mmt) cc_final: 0.4932 (mmm) REVERT: C 67 ARG cc_start: 0.7103 (mtm180) cc_final: 0.6745 (mtm180) REVERT: D 4 MET cc_start: 0.4396 (mmm) cc_final: 0.4060 (ttm) REVERT: D 81 GLU cc_start: 0.6773 (pm20) cc_final: 0.6429 (pm20) REVERT: D 82 ASP cc_start: 0.6911 (m-30) cc_final: 0.5775 (m-30) REVERT: E 15 ILE cc_start: 0.5591 (tt) cc_final: 0.5086 (tt) REVERT: E 122 GLU cc_start: 0.7256 (tt0) cc_final: 0.6952 (tt0) REVERT: E 172 SER cc_start: 0.7047 (t) cc_final: 0.6807 (p) REVERT: E 231 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7591 (mtp-110) REVERT: E 315 LYS cc_start: 0.3867 (mttt) cc_final: 0.3627 (mttt) REVERT: G 40 SER cc_start: 0.8552 (m) cc_final: 0.8347 (p) REVERT: G 103 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7259 (mm-30) REVERT: G 121 LYS cc_start: 0.8048 (tttt) cc_final: 0.7818 (tttt) REVERT: I 29 PHE cc_start: 0.6808 (t80) cc_final: 0.6414 (t80) REVERT: I 112 TYR cc_start: 0.6396 (m-80) cc_final: 0.6059 (m-10) REVERT: I 115 TYR cc_start: 0.7081 (m-80) cc_final: 0.6681 (m-80) REVERT: K 82 ASP cc_start: 0.6130 (m-30) cc_final: 0.5803 (m-30) REVERT: F 106 ILE cc_start: 0.7338 (mt) cc_final: 0.7088 (mp) REVERT: F 170 LYS cc_start: 0.8063 (tttt) cc_final: 0.7686 (tttt) REVERT: F 176 ILE cc_start: 0.7679 (mt) cc_final: 0.7352 (mp) REVERT: F 179 LYS cc_start: 0.7457 (mmtt) cc_final: 0.7042 (mttp) REVERT: F 191 HIS cc_start: 0.5614 (m-70) cc_final: 0.4920 (m-70) REVERT: F 318 LYS cc_start: 0.7497 (mtmt) cc_final: 0.7088 (mmmm) REVERT: F 319 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8171 (m) REVERT: F 321 LYS cc_start: 0.7891 (pttt) cc_final: 0.7591 (tppt) REVERT: F 322 LEU cc_start: 0.8231 (mt) cc_final: 0.7878 (mt) REVERT: H 50 ASN cc_start: 0.8029 (t0) cc_final: 0.7755 (t0) REVERT: H 103 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6596 (mm-30) REVERT: H 118 LEU cc_start: 0.8222 (mm) cc_final: 0.7893 (mm) REVERT: J 163 PHE cc_start: 0.5703 (t80) cc_final: 0.5240 (t80) REVERT: L 81 GLU cc_start: 0.7504 (pt0) cc_final: 0.6703 (pm20) REVERT: L 94 PHE cc_start: 0.6940 (p90) cc_final: 0.6637 (p90) REVERT: L 97 THR cc_start: 0.7273 (m) cc_final: 0.6938 (p) outliers start: 72 outliers final: 46 residues processed: 521 average time/residue: 0.3569 time to fit residues: 285.5738 Evaluate side-chains 497 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 450 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 104 optimal weight: 0.1980 chunk 257 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 269 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 290 GLN B 42 GLN B 81 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN G 42 GLN G 53 ASN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 GLN H 79 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.224833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.189112 restraints weight = 34883.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.195018 restraints weight = 17698.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.198726 restraints weight = 10506.229| |-----------------------------------------------------------------------------| r_work (final): 0.4575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22128 Z= 0.150 Angle : 0.606 10.655 30051 Z= 0.316 Chirality : 0.045 0.216 3315 Planarity : 0.004 0.043 3864 Dihedral : 4.180 39.259 3007 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.57 % Allowed : 11.22 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.06 (0.15), residues: 2757 helix: -0.62 (0.27), residues: 297 sheet: -0.20 (0.18), residues: 819 loop : -0.97 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 70 HIS 0.007 0.001 HIS B 72 PHE 0.040 0.002 PHE C 29 TYR 0.030 0.002 TYR A 108 ARG 0.007 0.000 ARG K 61 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 676) hydrogen bonds : angle 5.98829 ( 1950) SS BOND : bond 0.00327 ( 30) SS BOND : angle 1.37428 ( 60) covalent geometry : bond 0.00322 (22098) covalent geometry : angle 0.60368 (29991) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 452 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7737 (mp) cc_final: 0.7492 (mt) REVERT: A 170 LYS cc_start: 0.7773 (tttt) cc_final: 0.7349 (mmtt) REVERT: A 175 TYR cc_start: 0.6715 (t80) cc_final: 0.6413 (t80) REVERT: A 293 LYS cc_start: 0.7090 (mttt) cc_final: 0.6731 (mttt) REVERT: A 312 LYS cc_start: 0.7381 (mttt) cc_final: 0.7005 (mttt) REVERT: A 321 LYS cc_start: 0.7351 (tptt) cc_final: 0.7043 (tptt) REVERT: B 42 GLN cc_start: 0.7474 (tp40) cc_final: 0.7126 (tp-100) REVERT: B 68 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7517 (mmtt) REVERT: B 81 ASN cc_start: 0.7846 (t0) cc_final: 0.7561 (t0) REVERT: B 103 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6895 (mm-30) REVERT: B 110 TYR cc_start: 0.7034 (t80) cc_final: 0.6618 (t80) REVERT: B 114 ASN cc_start: 0.6726 (m-40) cc_final: 0.5912 (m-40) REVERT: B 131 LYS cc_start: 0.7319 (tttt) cc_final: 0.6891 (tttt) REVERT: B 140 PHE cc_start: 0.5782 (m-80) cc_final: 0.5289 (m-80) REVERT: B 149 MET cc_start: 0.5417 (mmt) cc_final: 0.4784 (mmm) REVERT: C 122 GLN cc_start: 0.6164 (mm-40) cc_final: 0.5941 (mm-40) REVERT: D 81 GLU cc_start: 0.6782 (pm20) cc_final: 0.6428 (pm20) REVERT: D 82 ASP cc_start: 0.6964 (m-30) cc_final: 0.5770 (m-30) REVERT: E 15 ILE cc_start: 0.5548 (tt) cc_final: 0.4895 (tt) REVERT: E 122 GLU cc_start: 0.7154 (tt0) cc_final: 0.6843 (tt0) REVERT: E 231 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7558 (mtp-110) REVERT: E 267 MET cc_start: 0.5961 (ppp) cc_final: 0.5064 (ppp) REVERT: E 315 LYS cc_start: 0.3935 (mttt) cc_final: 0.3455 (mtpt) REVERT: G 88 PHE cc_start: 0.6405 (m-80) cc_final: 0.5570 (m-80) REVERT: G 95 ASN cc_start: 0.8449 (t0) cc_final: 0.8190 (t0) REVERT: G 103 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6953 (mm-30) REVERT: G 121 LYS cc_start: 0.7963 (tttt) cc_final: 0.7740 (tttt) REVERT: I 29 PHE cc_start: 0.6774 (t80) cc_final: 0.6396 (t80) REVERT: I 115 TYR cc_start: 0.7010 (m-80) cc_final: 0.6523 (m-80) REVERT: K 6 GLN cc_start: 0.6200 (mp10) cc_final: 0.5399 (mp10) REVERT: K 82 ASP cc_start: 0.6552 (m-30) cc_final: 0.6056 (m-30) REVERT: F 88 TYR cc_start: 0.6709 (p90) cc_final: 0.6493 (p90) REVERT: F 106 ILE cc_start: 0.7347 (mt) cc_final: 0.7098 (mp) REVERT: F 160 TRP cc_start: 0.6549 (OUTLIER) cc_final: 0.6326 (m100) REVERT: F 170 LYS cc_start: 0.8014 (tttt) cc_final: 0.7635 (tttt) REVERT: F 179 LYS cc_start: 0.7408 (mmtt) cc_final: 0.7013 (mttp) REVERT: F 191 HIS cc_start: 0.5578 (m-70) cc_final: 0.4958 (m-70) REVERT: F 210 PHE cc_start: 0.6386 (t80) cc_final: 0.6145 (t80) REVERT: F 230 VAL cc_start: 0.7510 (t) cc_final: 0.7158 (p) REVERT: F 319 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8168 (m) REVERT: F 321 LYS cc_start: 0.7959 (pttt) cc_final: 0.7711 (mmmt) REVERT: F 323 ARG cc_start: 0.7401 (ttm-80) cc_final: 0.7061 (mmm160) REVERT: H 50 ASN cc_start: 0.7892 (t0) cc_final: 0.7684 (t0) REVERT: H 103 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6542 (mm-30) REVERT: H 131 LYS cc_start: 0.7295 (tttt) cc_final: 0.6902 (tttt) REVERT: H 149 MET cc_start: 0.5899 (mmt) cc_final: 0.5592 (mmp) REVERT: J 163 PHE cc_start: 0.5727 (t80) cc_final: 0.5405 (t80) REVERT: L 81 GLU cc_start: 0.7540 (pt0) cc_final: 0.6730 (pm20) REVERT: L 94 PHE cc_start: 0.6953 (p90) cc_final: 0.6601 (p90) REVERT: L 97 THR cc_start: 0.7135 (m) cc_final: 0.6779 (p) outliers start: 62 outliers final: 40 residues processed: 489 average time/residue: 0.3637 time to fit residues: 269.6305 Evaluate side-chains 477 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 435 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 121 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 213 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 253 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 167 optimal weight: 0.0570 chunk 204 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.226866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.192069 restraints weight = 34346.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.197717 restraints weight = 18212.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.201313 restraints weight = 11057.243| |-----------------------------------------------------------------------------| r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22128 Z= 0.219 Angle : 0.653 10.733 30051 Z= 0.344 Chirality : 0.046 0.218 3315 Planarity : 0.004 0.054 3864 Dihedral : 4.425 38.844 3007 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.06 % Allowed : 12.05 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2757 helix: -0.31 (0.28), residues: 279 sheet: -0.15 (0.18), residues: 849 loop : -0.89 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 14 HIS 0.007 0.001 HIS B 72 PHE 0.040 0.002 PHE C 29 TYR 0.029 0.002 TYR E 88 ARG 0.008 0.000 ARG F 112 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 676) hydrogen bonds : angle 6.07453 ( 1950) SS BOND : bond 0.00470 ( 30) SS BOND : angle 1.64209 ( 60) covalent geometry : bond 0.00464 (22098) covalent geometry : angle 0.64996 (29991) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 447 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.7848 (tttt) cc_final: 0.7420 (mmtt) REVERT: A 175 TYR cc_start: 0.6710 (t80) cc_final: 0.6437 (t80) REVERT: A 234 GLU cc_start: 0.5031 (pm20) cc_final: 0.4795 (pm20) REVERT: A 293 LYS cc_start: 0.7352 (mttt) cc_final: 0.6932 (mttt) REVERT: A 312 LYS cc_start: 0.7344 (mttt) cc_final: 0.6988 (mttt) REVERT: A 318 LYS cc_start: 0.7241 (ttmt) cc_final: 0.6929 (ttmt) REVERT: B 68 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7706 (mmtt) REVERT: B 82 LYS cc_start: 0.8689 (pttt) cc_final: 0.8344 (pttt) REVERT: B 103 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6924 (mm-30) REVERT: B 110 TYR cc_start: 0.7048 (t80) cc_final: 0.6663 (t80) REVERT: B 114 ASN cc_start: 0.6765 (m-40) cc_final: 0.6090 (m-40) REVERT: B 131 LYS cc_start: 0.7410 (tttt) cc_final: 0.6926 (tttt) REVERT: B 140 PHE cc_start: 0.5975 (m-80) cc_final: 0.5560 (m-80) REVERT: B 149 MET cc_start: 0.5594 (mmt) cc_final: 0.4892 (mmm) REVERT: B 158 ASP cc_start: 0.7150 (t0) cc_final: 0.6583 (t0) REVERT: C 20 LEU cc_start: 0.4873 (OUTLIER) cc_final: 0.4661 (mm) REVERT: C 70 ILE cc_start: 0.4796 (OUTLIER) cc_final: 0.4295 (tp) REVERT: C 104 SER cc_start: 0.7759 (p) cc_final: 0.7553 (p) REVERT: C 122 GLN cc_start: 0.6186 (mm-40) cc_final: 0.5960 (mm-40) REVERT: D 81 GLU cc_start: 0.6948 (pm20) cc_final: 0.6660 (pm20) REVERT: E 15 ILE cc_start: 0.5758 (tt) cc_final: 0.5298 (tt) REVERT: E 122 GLU cc_start: 0.7273 (tt0) cc_final: 0.6976 (tt0) REVERT: E 176 ILE cc_start: 0.7576 (mt) cc_final: 0.7299 (mp) REVERT: E 231 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7485 (mtp-110) REVERT: E 267 MET cc_start: 0.6373 (ppp) cc_final: 0.6097 (ppp) REVERT: E 315 LYS cc_start: 0.4136 (mttt) cc_final: 0.3857 (mttt) REVERT: G 17 MET cc_start: 0.6628 (ttp) cc_final: 0.6315 (ttp) REVERT: G 68 LYS cc_start: 0.8302 (mmmt) cc_final: 0.8038 (mmmt) REVERT: G 103 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6840 (mm-30) REVERT: G 121 LYS cc_start: 0.8108 (tttt) cc_final: 0.7803 (tttt) REVERT: I 29 PHE cc_start: 0.6817 (t80) cc_final: 0.6519 (t80) REVERT: I 112 TYR cc_start: 0.6137 (m-10) cc_final: 0.5887 (m-10) REVERT: I 115 TYR cc_start: 0.7047 (m-80) cc_final: 0.6537 (m-80) REVERT: K 6 GLN cc_start: 0.6069 (mp10) cc_final: 0.5620 (mp10) REVERT: K 36 TYR cc_start: 0.5578 (m-80) cc_final: 0.4844 (m-80) REVERT: K 82 ASP cc_start: 0.6801 (m-30) cc_final: 0.6197 (m-30) REVERT: F 88 TYR cc_start: 0.6752 (p90) cc_final: 0.6521 (p90) REVERT: F 106 ILE cc_start: 0.7562 (mt) cc_final: 0.7223 (mp) REVERT: F 121 PHE cc_start: 0.6437 (t80) cc_final: 0.5935 (t80) REVERT: F 160 TRP cc_start: 0.6670 (OUTLIER) cc_final: 0.6455 (m100) REVERT: F 170 LYS cc_start: 0.8078 (tttt) cc_final: 0.7702 (tttt) REVERT: F 179 LYS cc_start: 0.7459 (mmtt) cc_final: 0.7122 (mttp) REVERT: F 191 HIS cc_start: 0.5689 (m-70) cc_final: 0.5010 (m-70) REVERT: F 210 PHE cc_start: 0.6482 (t80) cc_final: 0.6155 (t80) REVERT: F 231 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7501 (mtp85) REVERT: F 321 LYS cc_start: 0.8009 (pttt) cc_final: 0.7805 (mtpt) REVERT: F 323 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.7284 (mmt-90) REVERT: H 103 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6236 (mm-30) REVERT: H 131 LYS cc_start: 0.7356 (tttt) cc_final: 0.6961 (tttt) REVERT: J 163 PHE cc_start: 0.5834 (t80) cc_final: 0.5542 (t80) REVERT: L 81 GLU cc_start: 0.7153 (pt0) cc_final: 0.6360 (pm20) REVERT: L 97 THR cc_start: 0.7174 (m) cc_final: 0.6893 (p) outliers start: 74 outliers final: 54 residues processed: 488 average time/residue: 0.3425 time to fit residues: 254.2317 Evaluate side-chains 486 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 429 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 160 TRP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 121 LYS Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.3305 > 50: distance: 28 - 30: 17.272 distance: 30 - 31: 21.447 distance: 31 - 32: 20.322 distance: 31 - 34: 14.788 distance: 32 - 33: 18.533 distance: 32 - 37: 9.759 distance: 34 - 35: 24.954 distance: 34 - 36: 26.769 distance: 37 - 38: 9.668 distance: 37 - 158: 7.435 distance: 38 - 39: 23.044 distance: 38 - 41: 7.633 distance: 39 - 40: 29.234 distance: 39 - 47: 25.011 distance: 41 - 42: 12.323 distance: 42 - 43: 17.940 distance: 42 - 44: 5.829 distance: 43 - 45: 12.566 distance: 44 - 46: 13.613 distance: 45 - 46: 10.520 distance: 47 - 48: 11.275 distance: 48 - 49: 16.334 distance: 48 - 51: 24.988 distance: 49 - 50: 42.778 distance: 49 - 54: 35.936 distance: 51 - 52: 10.841 distance: 51 - 53: 32.633 distance: 54 - 55: 41.265 distance: 55 - 56: 16.536 distance: 55 - 58: 50.095 distance: 56 - 57: 14.308 distance: 56 - 65: 14.603 distance: 58 - 59: 14.637 distance: 59 - 60: 25.649 distance: 59 - 61: 8.906 distance: 60 - 62: 20.074 distance: 61 - 63: 14.417 distance: 62 - 64: 19.530 distance: 63 - 64: 21.530 distance: 65 - 66: 16.847 distance: 65 - 71: 14.137 distance: 66 - 67: 27.105 distance: 66 - 69: 34.459 distance: 67 - 68: 21.293 distance: 67 - 72: 24.266 distance: 69 - 70: 10.401 distance: 70 - 71: 40.444 distance: 72 - 73: 6.641 distance: 73 - 74: 20.773 distance: 73 - 76: 23.523 distance: 74 - 75: 39.205 distance: 74 - 77: 8.637 distance: 77 - 78: 22.344 distance: 77 - 136: 21.721 distance: 78 - 79: 19.343 distance: 78 - 81: 10.273 distance: 79 - 80: 35.674 distance: 79 - 84: 27.651 distance: 80 - 133: 29.245 distance: 81 - 82: 33.084 distance: 81 - 83: 21.726 distance: 84 - 85: 17.087 distance: 85 - 86: 10.716 distance: 85 - 88: 5.692 distance: 86 - 87: 7.662 distance: 86 - 92: 20.836 distance: 88 - 89: 11.984 distance: 89 - 90: 6.945 distance: 89 - 91: 9.325 distance: 92 - 93: 4.037 distance: 93 - 94: 9.678 distance: 93 - 96: 7.005 distance: 94 - 95: 17.192 distance: 94 - 101: 11.246 distance: 96 - 97: 5.334 distance: 97 - 98: 4.370 distance: 98 - 99: 4.244 distance: 98 - 100: 4.988 distance: 101 - 102: 9.790 distance: 102 - 103: 14.217 distance: 102 - 105: 11.514 distance: 103 - 104: 14.266 distance: 103 - 107: 24.836 distance: 105 - 106: 18.595