Starting phenix.real_space_refine on Sun Sep 29 06:21:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/09_2024/7x6o_33024.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/09_2024/7x6o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/09_2024/7x6o_33024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/09_2024/7x6o_33024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/09_2024/7x6o_33024.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/09_2024/7x6o_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-5461/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: 12.82, per 1000 atoms: 0.59 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: 4.69 Conformation dependent library (CDL) restraints added in 2.8 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: 3.71 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: 7.16 Time building geometry restraints manager: 5.55 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: 0.00 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: 0.900 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: 0.770 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 47.990 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.470 ------------------------------------------------------------------------------- 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 22098 Z= 0.136 Angle : 0.487 13.437 29991 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 *********************** 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 fitting. rotamer outliers: 44 poor density : 527 time to evaluate : 3.085 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: 0.3184 time to fit residues: 275.8638 Evaluate side-chains 442 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 432 time to evaluate : 2.133 ------------------------------------------------------------------------------- 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: 1.9990 chunk 206 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 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: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 22098 Z= 0.321 Angle : 0.683 10.087 29991 Z= 0.364 Chirality : 0.047 0.275 3315 Planarity : 0.005 0.057 3864 Dihedral : 4.444 59.231 3020 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.28 % Allowed : 7.87 % Favored : 89.86 % 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: -1.94 (0.14), residues: 2757 helix: -1.60 (0.23), residues: 294 sheet: -0.97 (0.17), residues: 828 loop : -1.39 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 14 HIS 0.007 0.002 HIS F 61 PHE 0.029 0.002 PHE A 154 TYR 0.023 0.002 TYR H 94 ARG 0.010 0.001 ARG D 61 *********************** 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 544 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 489 time to evaluate : 2.796 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: 0.7649 (mp) cc_final: 0.7440 (mt) REVERT: A 170 LYS cc_start: 0.7889 (tttt) cc_final: 0.7437 (mmtt) REVERT: A 175 TYR cc_start: 0.6746 (t80) cc_final: 0.6434 (t80) REVERT: A 231 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7800 (ttt-90) REVERT: A 234 GLU cc_start: 0.4890 (pm20) cc_final: 0.4601 (pm20) REVERT: A 293 LYS cc_start: 0.6904 (mttt) cc_final: 0.6681 (mttt) REVERT: A 321 LYS cc_start: 0.7166 (tptt) cc_final: 0.6674 (tptt) REVERT: A 323 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7069 (mtt90) REVERT: B 102 LEU cc_start: 0.7091 (mt) cc_final: 0.6691 (mt) REVERT: B 103 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6732 (mm-30) REVERT: B 110 TYR cc_start: 0.7189 (t80) cc_final: 0.6859 (t80) REVERT: B 131 LYS cc_start: 0.7351 (tttt) cc_final: 0.7007 (tttt) REVERT: B 140 PHE cc_start: 0.5593 (m-80) cc_final: 0.5202 (m-80) REVERT: B 149 MET cc_start: 0.5727 (mmt) cc_final: 0.5306 (mmm) REVERT: B 153 LYS cc_start: 0.7421 (ttpt) cc_final: 0.6731 (ttpt) REVERT: C 27 PHE cc_start: 0.6187 (p90) cc_final: 0.5868 (p90) REVERT: C 67 ARG cc_start: 0.6851 (mtm180) cc_final: 0.6519 (mtm180) REVERT: D 4 MET cc_start: 0.4472 (mmm) cc_final: 0.3595 (ttm) REVERT: D 23 CYS cc_start: 0.3895 (p) cc_final: 0.3637 (p) REVERT: D 81 GLU cc_start: 0.6819 (pm20) cc_final: 0.6497 (pm20) REVERT: D 82 ASP cc_start: 0.6726 (m-30) cc_final: 0.5718 (m-30) REVERT: E 112 ARG cc_start: 0.6882 (mtp85) cc_final: 0.6644 (mtp85) REVERT: E 122 GLU cc_start: 0.7150 (tt0) cc_final: 0.6906 (tt0) REVERT: E 217 SER cc_start: 0.7595 (m) cc_final: 0.7061 (m) REVERT: E 318 LYS cc_start: 0.7518 (mtmt) cc_final: 0.7182 (pttt) REVERT: G 40 SER cc_start: 0.8521 (m) cc_final: 0.8313 (p) REVERT: G 41 THR cc_start: 0.8413 (m) cc_final: 0.7942 (p) REVERT: I 29 PHE cc_start: 0.6561 (t80) cc_final: 0.6192 (t80) REVERT: I 67 ARG cc_start: 0.7150 (mtm180) cc_final: 0.6719 (mtm180) REVERT: I 112 TYR cc_start: 0.6282 (m-80) cc_final: 0.5491 (m-10) REVERT: I 115 TYR cc_start: 0.6899 (m-80) cc_final: 0.6570 (m-80) REVERT: I 163 PHE cc_start: 0.5287 (t80) cc_final: 0.4925 (t80) REVERT: K 4 MET cc_start: 0.4580 (mmm) cc_final: 0.4032 (ttt) REVERT: K 37 GLN cc_start: 0.7209 (tt0) cc_final: 0.6669 (tt0) REVERT: K 53 ARG cc_start: 0.6620 (mtp85) cc_final: 0.6346 (mtp85) REVERT: K 82 ASP cc_start: 0.5919 (m-30) cc_final: 0.5451 (m-30) REVERT: F 70 TRP cc_start: 0.6745 (t60) cc_final: 0.6368 (t60) REVERT: F 106 ILE cc_start: 0.7240 (mt) cc_final: 0.7015 (mp) REVERT: F 170 LYS cc_start: 0.8053 (tttt) cc_final: 0.7691 (tttt) REVERT: F 179 LYS cc_start: 0.7333 (mmtt) cc_final: 0.6925 (mttt) REVERT: F 191 HIS cc_start: 0.5416 (m-70) cc_final: 0.4728 (m-70) REVERT: F 231 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7520 (mtp85) REVERT: F 318 LYS cc_start: 0.7323 (mtmt) cc_final: 0.7117 (mmmm) REVERT: F 321 LYS cc_start: 0.7593 (pttt) cc_final: 0.7387 (tppt) REVERT: F 322 LEU cc_start: 0.8262 (mt) cc_final: 0.7965 (mt) REVERT: H 53 ASN cc_start: 0.7650 (m-40) cc_final: 0.7420 (m-40) REVERT: H 92 TRP cc_start: 0.5006 (m-10) cc_final: 0.3885 (m-10) REVERT: H 103 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6174 (mm-30) REVERT: J 104 SER cc_start: 0.7504 (p) cc_final: 0.7195 (t) REVERT: J 163 PHE cc_start: 0.5431 (t80) cc_final: 0.5161 (t80) REVERT: L 4 MET cc_start: 0.5138 (mmm) cc_final: 0.4782 (ttm) REVERT: L 37 GLN cc_start: 0.7427 (tt0) cc_final: 0.6548 (tt0) REVERT: L 82 ASP cc_start: 0.6354 (m-30) cc_final: 0.4496 (m-30) REVERT: L 94 PHE cc_start: 0.6766 (p90) cc_final: 0.6445 (p90) REVERT: L 97 THR cc_start: 0.7244 (m) cc_final: 0.6898 (p) outliers start: 55 outliers final: 32 residues processed: 521 average time/residue: 0.3549 time to fit residues: 280.8233 Evaluate side-chains 482 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 450 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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 20 LEU 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 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 51 ILE Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 226 ILE 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 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 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.0030 chunk 206 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 268 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- 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 B 50 ASN B 53 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 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5678 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22098 Z= 0.250 Angle : 0.619 10.229 29991 Z= 0.326 Chirality : 0.046 0.234 3315 Planarity : 0.004 0.041 3864 Dihedral : 4.149 37.338 3010 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.65 % Allowed : 9.15 % Favored : 88.20 % 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: -1.29 (0.15), residues: 2757 helix: -0.56 (0.27), residues: 276 sheet: -0.44 (0.18), residues: 816 loop : -1.12 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 148 HIS 0.006 0.001 HIS F 190 PHE 0.043 0.002 PHE C 29 TYR 0.027 0.002 TYR A 88 ARG 0.006 0.000 ARG F 112 *********************** 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 524 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 460 time to evaluate : 2.344 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 42 LEU cc_start: 0.7733 (mp) cc_final: 0.7516 (mt) REVERT: A 170 LYS cc_start: 0.7829 (tttt) cc_final: 0.7372 (mmtt) REVERT: A 175 TYR cc_start: 0.6693 (t80) cc_final: 0.6431 (t80) REVERT: A 293 LYS cc_start: 0.7180 (mttt) cc_final: 0.6902 (mttt) REVERT: A 321 LYS cc_start: 0.7376 (tptt) cc_final: 0.7069 (tptt) REVERT: B 88 PHE cc_start: 0.5951 (m-80) cc_final: 0.4112 (m-80) REVERT: B 102 LEU cc_start: 0.7082 (mt) cc_final: 0.6695 (mt) REVERT: B 103 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6815 (mm-30) REVERT: B 110 TYR cc_start: 0.7209 (t80) cc_final: 0.6855 (t80) REVERT: B 114 ASN cc_start: 0.6962 (m-40) cc_final: 0.6327 (m110) REVERT: B 131 LYS cc_start: 0.7322 (tttt) cc_final: 0.6926 (tttt) REVERT: B 140 PHE cc_start: 0.5762 (m-80) cc_final: 0.5340 (m-80) REVERT: B 149 MET cc_start: 0.5470 (mmt) cc_final: 0.4869 (mmm) REVERT: C 67 ARG cc_start: 0.7105 (mtm180) cc_final: 0.6724 (mtm180) REVERT: D 81 GLU cc_start: 0.6822 (pm20) cc_final: 0.6463 (pm20) REVERT: D 82 ASP cc_start: 0.6794 (m-30) cc_final: 0.5713 (m-30) REVERT: E 122 GLU cc_start: 0.7256 (tt0) cc_final: 0.6937 (tt0) REVERT: E 179 LYS cc_start: 0.7379 (mttt) cc_final: 0.7151 (mttt) REVERT: E 231 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7455 (mtp-110) REVERT: G 41 THR cc_start: 0.8476 (m) cc_final: 0.8045 (p) REVERT: G 68 LYS cc_start: 0.7957 (tppt) cc_final: 0.7653 (mmtt) REVERT: G 88 PHE cc_start: 0.5751 (m-80) cc_final: 0.5098 (m-80) REVERT: G 103 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7055 (mm-30) REVERT: G 149 MET cc_start: 0.6116 (mmp) cc_final: 0.5815 (mmm) REVERT: I 29 PHE cc_start: 0.6765 (t80) cc_final: 0.6321 (t80) REVERT: I 112 TYR cc_start: 0.6240 (m-80) cc_final: 0.5776 (m-10) REVERT: I 115 TYR cc_start: 0.7050 (m-80) cc_final: 0.6576 (m-80) REVERT: I 163 PHE cc_start: 0.5466 (t80) cc_final: 0.5131 (t80) REVERT: K 6 GLN cc_start: 0.6210 (mp10) cc_final: 0.5516 (mp10) REVERT: K 82 ASP cc_start: 0.6004 (m-30) cc_final: 0.5590 (m-30) REVERT: F 106 ILE cc_start: 0.7215 (mt) cc_final: 0.6951 (mp) REVERT: F 170 LYS cc_start: 0.8046 (tttt) cc_final: 0.7661 (tttt) REVERT: F 179 LYS cc_start: 0.7382 (mmtt) cc_final: 0.7006 (mttp) REVERT: F 191 HIS cc_start: 0.5704 (m-70) cc_final: 0.5058 (m-70) REVERT: F 231 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7498 (mtp85) REVERT: F 319 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.8018 (m) REVERT: F 321 LYS cc_start: 0.7801 (pttt) cc_final: 0.7598 (tppt) REVERT: F 322 LEU cc_start: 0.8183 (mt) cc_final: 0.7825 (mt) REVERT: H 37 ASP cc_start: 0.6413 (OUTLIER) cc_final: 0.5547 (m-30) REVERT: H 51 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7678 (ttmt) REVERT: H 103 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6274 (mm-30) REVERT: H 118 LEU cc_start: 0.8194 (mm) cc_final: 0.7813 (mm) REVERT: H 131 LYS cc_start: 0.7348 (tttt) cc_final: 0.6945 (tttt) REVERT: J 72 ARG cc_start: 0.5757 (ttm170) cc_final: 0.4654 (ttm-80) REVERT: J 163 PHE cc_start: 0.5653 (t80) cc_final: 0.5234 (t80) REVERT: L 37 GLN cc_start: 0.7488 (tt0) cc_final: 0.6549 (tt0) REVERT: L 82 ASP cc_start: 0.6113 (m-30) cc_final: 0.5611 (m-30) REVERT: L 94 PHE cc_start: 0.6895 (p90) cc_final: 0.6599 (p90) REVERT: L 97 THR cc_start: 0.7158 (m) cc_final: 0.6749 (p) outliers start: 64 outliers final: 36 residues processed: 498 average time/residue: 0.3458 time to fit residues: 263.1113 Evaluate side-chains 479 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 441 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE 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 276 ILE 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 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 15 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 211 VAL 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 G residue 119 TYR Chi-restraints excluded: chain I residue 12 VAL 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 175 LEU Chi-restraints excluded: chain F residue 71 ILE 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 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 245 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 128 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 B 42 GLN B 81 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN F 290 GLN H 53 ASN H 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22098 Z= 0.223 Angle : 0.602 10.457 29991 Z= 0.313 Chirality : 0.045 0.215 3315 Planarity : 0.004 0.038 3864 Dihedral : 4.157 38.279 3007 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.48 % Allowed : 10.93 % Favored : 86.58 % 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: -1.03 (0.15), residues: 2757 helix: -0.48 (0.27), residues: 294 sheet: -0.24 (0.18), residues: 825 loop : -0.94 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 14 HIS 0.008 0.001 HIS B 72 PHE 0.040 0.002 PHE C 29 TYR 0.029 0.002 TYR A 108 ARG 0.005 0.000 ARG F 112 *********************** 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 515 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 455 time to evaluate : 2.384 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: 0.7681 (mp) cc_final: 0.7459 (mt) REVERT: A 170 LYS cc_start: 0.7796 (tttt) cc_final: 0.7372 (mmtt) REVERT: A 175 TYR cc_start: 0.6660 (t80) cc_final: 0.6393 (t80) REVERT: A 231 ARG cc_start: 0.8026 (mtp-110) cc_final: 0.7689 (ttt-90) REVERT: A 293 LYS cc_start: 0.7247 (mttt) cc_final: 0.6954 (mttt) REVERT: A 312 LYS cc_start: 0.7425 (mttt) cc_final: 0.7219 (mttt) REVERT: A 321 LYS cc_start: 0.7370 (tptt) cc_final: 0.7163 (tptt) REVERT: B 42 GLN cc_start: 0.7547 (tp40) cc_final: 0.7210 (tp-100) REVERT: B 82 LYS cc_start: 0.8575 (pttt) cc_final: 0.8274 (pttt) REVERT: B 102 LEU cc_start: 0.7063 (mt) cc_final: 0.6828 (mt) REVERT: B 103 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6990 (mm-30) REVERT: B 110 TYR cc_start: 0.7211 (t80) cc_final: 0.6917 (t80) REVERT: B 114 ASN cc_start: 0.6927 (m-40) cc_final: 0.6308 (m110) REVERT: B 131 LYS cc_start: 0.7332 (tttt) cc_final: 0.6932 (tttt) REVERT: B 140 PHE cc_start: 0.5781 (m-80) cc_final: 0.5331 (m-80) REVERT: B 149 MET cc_start: 0.5490 (mmt) cc_final: 0.4832 (mmm) REVERT: C 67 ARG cc_start: 0.7077 (mtm180) cc_final: 0.6747 (mtm180) REVERT: C 122 GLN cc_start: 0.6151 (mm-40) cc_final: 0.5921 (mm-40) REVERT: D 81 GLU cc_start: 0.6829 (pm20) cc_final: 0.6456 (pm20) REVERT: D 82 ASP cc_start: 0.7000 (m-30) cc_final: 0.5811 (m-30) REVERT: E 15 ILE cc_start: 0.5592 (tt) cc_final: 0.4954 (tt) REVERT: E 40 VAL cc_start: 0.8204 (t) cc_final: 0.7998 (t) REVERT: E 122 GLU cc_start: 0.7252 (tt0) cc_final: 0.6908 (tt0) REVERT: E 231 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7445 (mtp-110) REVERT: E 267 MET cc_start: 0.5945 (ppp) cc_final: 0.5100 (ppp) REVERT: G 41 THR cc_start: 0.8503 (m) cc_final: 0.8083 (p) REVERT: G 68 LYS cc_start: 0.7937 (tppt) cc_final: 0.7717 (mmtt) REVERT: G 88 PHE cc_start: 0.6336 (m-80) cc_final: 0.5546 (m-80) REVERT: G 95 ASN cc_start: 0.8434 (t0) cc_final: 0.8224 (t0) REVERT: G 103 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7137 (mm-30) REVERT: G 121 LYS cc_start: 0.8066 (tttt) cc_final: 0.7784 (tmtt) REVERT: G 149 MET cc_start: 0.6079 (mmp) cc_final: 0.5729 (mmm) REVERT: I 29 PHE cc_start: 0.6813 (t80) cc_final: 0.6392 (t80) REVERT: I 112 TYR cc_start: 0.6121 (m-80) cc_final: 0.5885 (m-10) REVERT: I 115 TYR cc_start: 0.7047 (m-80) cc_final: 0.6487 (m-80) REVERT: K 6 GLN cc_start: 0.6060 (mp10) cc_final: 0.5654 (mp10) REVERT: K 82 ASP cc_start: 0.6365 (m-30) cc_final: 0.6035 (m-30) REVERT: F 106 ILE cc_start: 0.7290 (mt) cc_final: 0.7050 (mp) REVERT: F 166 ASN cc_start: 0.6064 (m-40) cc_final: 0.5839 (t0) REVERT: F 170 LYS cc_start: 0.8042 (tttt) cc_final: 0.7658 (tttt) REVERT: F 179 LYS cc_start: 0.7407 (mmtt) cc_final: 0.7045 (mttt) REVERT: F 191 HIS cc_start: 0.5596 (m-70) cc_final: 0.4998 (m-70) REVERT: F 231 ARG cc_start: 0.7726 (mtp85) cc_final: 0.7452 (mtp85) REVERT: F 319 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8209 (m) REVERT: F 323 ARG cc_start: 0.7726 (mtt-85) cc_final: 0.6968 (mmm160) REVERT: H 50 ASN cc_start: 0.7942 (t0) cc_final: 0.7352 (t0) REVERT: H 81 ASN cc_start: 0.8244 (t0) cc_final: 0.8021 (t0) REVERT: H 103 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6344 (mm-30) REVERT: H 131 LYS cc_start: 0.7312 (tttt) cc_final: 0.6939 (tttt) REVERT: J 163 PHE cc_start: 0.5690 (t80) cc_final: 0.5403 (t80) REVERT: L 81 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6019 (pm20) REVERT: L 97 THR cc_start: 0.7124 (m) cc_final: 0.6908 (p) outliers start: 60 outliers final: 38 residues processed: 492 average time/residue: 0.3391 time to fit residues: 253.3447 Evaluate side-chains 482 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 442 time to evaluate : 2.314 ------------------------------------------------------------------------------- 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 B residue 22 TYR 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 60 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 42 LEU 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 119 TYR 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 15 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 211 VAL 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 22 TYR Chi-restraints excluded: chain H residue 121 LYS 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 Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 196 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22098 Z= 0.188 Angle : 0.588 10.861 29991 Z= 0.304 Chirality : 0.044 0.201 3315 Planarity : 0.004 0.046 3864 Dihedral : 4.109 37.975 3007 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.90 % Allowed : 12.84 % Favored : 85.26 % 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: -0.80 (0.16), residues: 2757 helix: -0.35 (0.28), residues: 294 sheet: 0.03 (0.18), residues: 840 loop : -0.85 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 14 HIS 0.007 0.001 HIS B 72 PHE 0.041 0.002 PHE C 29 TYR 0.028 0.001 TYR A 108 ARG 0.007 0.000 ARG K 61 *********************** 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 489 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 443 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.7780 (tttt) cc_final: 0.7349 (mmtt) REVERT: A 171 LEU cc_start: 0.7332 (mt) cc_final: 0.7056 (tp) REVERT: A 175 TYR cc_start: 0.6683 (t80) cc_final: 0.6429 (t80) REVERT: A 234 GLU cc_start: 0.5447 (pm20) cc_final: 0.5026 (pm20) REVERT: A 293 LYS cc_start: 0.7088 (mttt) cc_final: 0.6810 (mttt) REVERT: A 318 LYS cc_start: 0.7072 (ttmt) cc_final: 0.6775 (ttmt) REVERT: B 82 LYS cc_start: 0.8574 (pttt) cc_final: 0.8248 (pttt) REVERT: B 103 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7182 (mm-30) REVERT: B 110 TYR cc_start: 0.7197 (t80) cc_final: 0.6754 (t80) REVERT: B 114 ASN cc_start: 0.6857 (m-40) cc_final: 0.6132 (m-40) REVERT: B 131 LYS cc_start: 0.7303 (tttt) cc_final: 0.6874 (tttt) REVERT: B 140 PHE cc_start: 0.5834 (m-80) cc_final: 0.5367 (m-80) REVERT: B 149 MET cc_start: 0.5595 (mmt) cc_final: 0.4890 (mmm) REVERT: C 67 ARG cc_start: 0.7121 (mtm180) cc_final: 0.6739 (mtm180) REVERT: C 122 GLN cc_start: 0.6235 (mm-40) cc_final: 0.6026 (mm-40) REVERT: D 81 GLU cc_start: 0.6938 (pm20) cc_final: 0.6577 (pm20) REVERT: D 82 ASP cc_start: 0.7002 (m-30) cc_final: 0.5825 (m-30) REVERT: E 15 ILE cc_start: 0.5755 (tt) cc_final: 0.5069 (pt) REVERT: E 122 GLU cc_start: 0.7210 (tt0) cc_final: 0.6879 (tt0) REVERT: E 231 ARG cc_start: 0.8079 (mtt-85) cc_final: 0.7446 (mtp-110) REVERT: G 17 MET cc_start: 0.6537 (ttp) cc_final: 0.6264 (ttp) REVERT: G 41 THR cc_start: 0.8455 (m) cc_final: 0.8206 (p) REVERT: G 68 LYS cc_start: 0.7919 (tppt) cc_final: 0.7702 (mmtt) REVERT: G 88 PHE cc_start: 0.6366 (m-80) cc_final: 0.5317 (m-80) REVERT: G 95 ASN cc_start: 0.8337 (t0) cc_final: 0.8125 (t0) REVERT: G 103 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7164 (mm-30) REVERT: G 149 MET cc_start: 0.6004 (mmp) cc_final: 0.5714 (mmm) REVERT: I 29 PHE cc_start: 0.6796 (t80) cc_final: 0.6436 (t80) REVERT: I 115 TYR cc_start: 0.7009 (m-80) cc_final: 0.6458 (m-80) REVERT: K 36 TYR cc_start: 0.5332 (m-80) cc_final: 0.4566 (m-80) REVERT: K 82 ASP cc_start: 0.6534 (m-30) cc_final: 0.6012 (m-30) REVERT: F 166 ASN cc_start: 0.6006 (m-40) cc_final: 0.5784 (t0) REVERT: F 170 LYS cc_start: 0.8037 (tttt) cc_final: 0.7741 (mptt) REVERT: F 179 LYS cc_start: 0.7397 (mmtt) cc_final: 0.7025 (mttp) REVERT: F 191 HIS cc_start: 0.5518 (m-70) cc_final: 0.4989 (m-70) REVERT: F 230 VAL cc_start: 0.7635 (t) cc_final: 0.7179 (p) REVERT: F 231 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7465 (mtp85) REVERT: F 319 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8116 (m) REVERT: F 322 LEU cc_start: 0.8008 (mt) cc_final: 0.7743 (mt) REVERT: F 323 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.7211 (mtp85) REVERT: H 103 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6196 (mm-30) REVERT: H 131 LYS cc_start: 0.7302 (tttt) cc_final: 0.6906 (tttt) REVERT: H 149 MET cc_start: 0.6607 (mmp) cc_final: 0.6369 (mmp) REVERT: J 163 PHE cc_start: 0.5681 (t80) cc_final: 0.5393 (t80) REVERT: L 97 THR cc_start: 0.7162 (m) cc_final: 0.6937 (p) outliers start: 46 outliers final: 32 residues processed: 475 average time/residue: 0.3509 time to fit residues: 252.4677 Evaluate side-chains 459 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 426 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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 124 PHE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 22 TYR 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 D residue 163 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 324 LEU 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 31 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 259 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 118 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 20.0000 chunk 237 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 154 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 264 optimal weight: 0.1980 chunk 219 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 290 GLN ** B 104 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** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 22098 Z= 0.359 Angle : 0.695 10.493 29991 Z= 0.366 Chirality : 0.047 0.223 3315 Planarity : 0.004 0.067 3864 Dihedral : 4.647 40.021 3007 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.90 % Allowed : 12.71 % Favored : 84.39 % 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: -0.89 (0.16), residues: 2757 helix: -0.55 (0.27), residues: 279 sheet: -0.10 (0.18), residues: 861 loop : -0.85 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 14 HIS 0.009 0.002 HIS A 61 PHE 0.032 0.002 PHE C 29 TYR 0.032 0.002 TYR E 88 ARG 0.005 0.001 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 6 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 533 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 463 time to evaluate : 2.273 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: A 170 LYS cc_start: 0.7920 (tttt) cc_final: 0.7443 (mmtt) REVERT: A 171 LEU cc_start: 0.7512 (mt) cc_final: 0.7276 (tp) REVERT: A 175 TYR cc_start: 0.6727 (t80) cc_final: 0.6468 (t80) REVERT: A 217 SER cc_start: 0.7553 (m) cc_final: 0.7157 (p) REVERT: A 293 LYS cc_start: 0.7498 (mttt) cc_final: 0.7190 (mttt) REVERT: A 312 LYS cc_start: 0.7382 (mttt) cc_final: 0.6828 (mptt) REVERT: A 318 LYS cc_start: 0.7401 (ttmt) cc_final: 0.6888 (ttmt) REVERT: B 82 LYS cc_start: 0.8625 (pttt) cc_final: 0.8160 (pttm) REVERT: B 110 TYR cc_start: 0.7305 (t80) cc_final: 0.6915 (t80) REVERT: B 114 ASN cc_start: 0.7038 (m-40) cc_final: 0.6256 (m-40) REVERT: B 131 LYS cc_start: 0.7460 (tttt) cc_final: 0.6995 (tttt) REVERT: B 140 PHE cc_start: 0.5892 (m-80) cc_final: 0.5577 (m-80) REVERT: B 149 MET cc_start: 0.5921 (mmt) cc_final: 0.5321 (mmm) REVERT: B 158 ASP cc_start: 0.7084 (t0) cc_final: 0.6573 (t0) REVERT: C 36 TRP cc_start: 0.6513 (m100) cc_final: 0.5749 (m100) REVERT: C 70 ILE cc_start: 0.5007 (OUTLIER) cc_final: 0.4681 (tp) REVERT: C 122 GLN cc_start: 0.6077 (mm-40) cc_final: 0.5872 (mm-40) REVERT: D 81 GLU cc_start: 0.7029 (pm20) cc_final: 0.6704 (pm20) REVERT: E 38 HIS cc_start: 0.6557 (m170) cc_final: 0.6325 (m170) REVERT: E 231 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7575 (mtp-110) REVERT: G 17 MET cc_start: 0.6765 (ttp) cc_final: 0.6462 (ttp) REVERT: G 60 ASN cc_start: 0.7976 (p0) cc_final: 0.7377 (p0) REVERT: G 95 ASN cc_start: 0.8419 (t0) cc_final: 0.8207 (t0) REVERT: G 103 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7293 (mm-30) REVERT: G 121 LYS cc_start: 0.8248 (tttt) cc_final: 0.7845 (tmtt) REVERT: G 149 MET cc_start: 0.6253 (mmp) cc_final: 0.5980 (mmm) REVERT: G 158 ASP cc_start: 0.7080 (t0) cc_final: 0.6714 (t0) REVERT: I 29 PHE cc_start: 0.6880 (t80) cc_final: 0.6412 (t80) REVERT: K 4 MET cc_start: 0.3927 (ttt) cc_final: 0.3659 (tmm) REVERT: K 36 TYR cc_start: 0.5393 (m-80) cc_final: 0.4653 (m-80) REVERT: K 82 ASP cc_start: 0.6950 (m-30) cc_final: 0.6322 (m-30) REVERT: F 33 ASN cc_start: 0.7075 (m-40) cc_final: 0.6874 (m-40) REVERT: F 121 PHE cc_start: 0.6517 (t80) cc_final: 0.5953 (t80) REVERT: F 160 TRP cc_start: 0.6691 (OUTLIER) cc_final: 0.6382 (m100) REVERT: F 170 LYS cc_start: 0.8124 (tttt) cc_final: 0.7771 (mptt) REVERT: F 179 LYS cc_start: 0.7501 (mmtt) cc_final: 0.7131 (mttp) REVERT: F 191 HIS cc_start: 0.5602 (m-70) cc_final: 0.4978 (m-70) REVERT: F 231 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7532 (mtp85) REVERT: F 318 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7360 (mmmm) REVERT: F 319 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8367 (p) REVERT: F 321 LYS cc_start: 0.7507 (mmmt) cc_final: 0.7185 (tppt) REVERT: F 322 LEU cc_start: 0.8132 (mt) cc_final: 0.7824 (mt) REVERT: F 323 ARG cc_start: 0.7783 (mtt-85) cc_final: 0.7188 (mtt-85) REVERT: F 324 LEU cc_start: 0.8172 (tp) cc_final: 0.7963 (tt) REVERT: H 68 LYS cc_start: 0.8515 (mmtt) cc_final: 0.7769 (mmmt) REVERT: H 103 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6140 (mm-30) REVERT: H 131 LYS cc_start: 0.7406 (tttt) cc_final: 0.7017 (tttt) REVERT: H 149 MET cc_start: 0.6712 (mmp) cc_final: 0.6473 (mmp) REVERT: H 158 ASP cc_start: 0.7439 (t0) cc_final: 0.7179 (t0) REVERT: J 163 PHE cc_start: 0.5833 (t80) cc_final: 0.5549 (t80) REVERT: L 97 THR cc_start: 0.7398 (m) cc_final: 0.6965 (p) outliers start: 70 outliers final: 47 residues processed: 503 average time/residue: 0.3340 time to fit residues: 255.5512 Evaluate side-chains 498 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 448 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 90 VAL 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 296 ILE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain C residue 2 VAL 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 163 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 42 LEU 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 G residue 14 TRP 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 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 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 80 LEU 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 31 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 149 optimal weight: 0.3980 chunk 222 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 22098 Z= 0.215 Angle : 0.622 10.540 29991 Z= 0.323 Chirality : 0.045 0.200 3315 Planarity : 0.004 0.048 3864 Dihedral : 4.375 40.835 3005 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.40 % Allowed : 14.00 % Favored : 83.60 % 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: -0.73 (0.16), residues: 2757 helix: -0.37 (0.28), residues: 288 sheet: 0.13 (0.18), residues: 834 loop : -0.81 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP F 70 HIS 0.007 0.001 HIS B 72 PHE 0.032 0.002 PHE C 29 TYR 0.030 0.002 TYR A 108 ARG 0.006 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 7 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 512 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 454 time to evaluate : 2.171 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: A 121 PHE cc_start: 0.6423 (t80) cc_final: 0.6083 (t80) REVERT: A 123 ARG cc_start: 0.7290 (ttm110) cc_final: 0.7063 (ttm110) REVERT: A 170 LYS cc_start: 0.7743 (tttt) cc_final: 0.7352 (mmtt) REVERT: A 171 LEU cc_start: 0.7437 (mt) cc_final: 0.7121 (tp) REVERT: A 175 TYR cc_start: 0.6682 (t80) cc_final: 0.6417 (t80) REVERT: A 293 LYS cc_start: 0.7330 (mttt) cc_final: 0.7020 (mttt) REVERT: A 312 LYS cc_start: 0.7297 (mttt) cc_final: 0.6969 (mptt) REVERT: A 318 LYS cc_start: 0.7357 (ttmt) cc_final: 0.6846 (ttmt) REVERT: B 82 LYS cc_start: 0.8481 (pttt) cc_final: 0.8065 (pttm) REVERT: B 114 ASN cc_start: 0.7036 (m-40) cc_final: 0.6833 (m110) REVERT: B 131 LYS cc_start: 0.7425 (tttt) cc_final: 0.6955 (tttt) REVERT: B 140 PHE cc_start: 0.5876 (m-80) cc_final: 0.5544 (m-80) REVERT: B 149 MET cc_start: 0.5665 (mmt) cc_final: 0.4970 (mmm) REVERT: C 70 ILE cc_start: 0.4785 (OUTLIER) cc_final: 0.4260 (tp) REVERT: C 122 GLN cc_start: 0.6012 (mm-40) cc_final: 0.5780 (mm-40) REVERT: D 81 GLU cc_start: 0.7000 (pm20) cc_final: 0.6674 (pm20) REVERT: E 170 LYS cc_start: 0.7959 (ttpp) cc_final: 0.7747 (ttpp) REVERT: E 231 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7593 (mtp-110) REVERT: E 323 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7334 (mmm160) REVERT: G 17 MET cc_start: 0.6596 (ttp) cc_final: 0.6325 (ttp) REVERT: G 48 ILE cc_start: 0.8292 (mm) cc_final: 0.7990 (mm) REVERT: G 60 ASN cc_start: 0.7939 (p0) cc_final: 0.7286 (p0) REVERT: G 68 LYS cc_start: 0.7987 (tppt) cc_final: 0.7718 (mmtt) REVERT: G 86 ASP cc_start: 0.7474 (m-30) cc_final: 0.7236 (m-30) REVERT: G 88 PHE cc_start: 0.6571 (m-80) cc_final: 0.5382 (m-80) REVERT: G 103 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7332 (mm-30) REVERT: G 121 LYS cc_start: 0.8099 (tttt) cc_final: 0.7796 (tmtt) REVERT: G 149 MET cc_start: 0.6090 (mmp) cc_final: 0.5794 (mmm) REVERT: G 158 ASP cc_start: 0.7113 (t0) cc_final: 0.6778 (t0) REVERT: I 29 PHE cc_start: 0.6868 (t80) cc_final: 0.6500 (t80) REVERT: K 6 GLN cc_start: 0.5763 (mm-40) cc_final: 0.5329 (mp10) REVERT: K 36 TYR cc_start: 0.5280 (m-80) cc_final: 0.4494 (m-80) REVERT: K 82 ASP cc_start: 0.6890 (m-30) cc_final: 0.6245 (m-30) REVERT: F 160 TRP cc_start: 0.6528 (OUTLIER) cc_final: 0.6309 (m100) REVERT: F 170 LYS cc_start: 0.8111 (tttt) cc_final: 0.7725 (mptt) REVERT: F 179 LYS cc_start: 0.7425 (mmtt) cc_final: 0.7076 (mttp) REVERT: F 191 HIS cc_start: 0.5544 (m-70) cc_final: 0.5051 (m-70) REVERT: F 231 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7514 (mtp85) REVERT: F 319 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8228 (p) REVERT: F 321 LYS cc_start: 0.7513 (mmmt) cc_final: 0.7175 (tppt) REVERT: F 322 LEU cc_start: 0.8053 (mt) cc_final: 0.7713 (mt) REVERT: F 323 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7112 (mtt-85) REVERT: H 68 LYS cc_start: 0.8526 (mmtt) cc_final: 0.7674 (mmmt) REVERT: H 103 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6227 (mm-30) REVERT: H 105 GLU cc_start: 0.6990 (tp30) cc_final: 0.6633 (tp30) REVERT: H 131 LYS cc_start: 0.7349 (tttt) cc_final: 0.6976 (tttt) REVERT: H 158 ASP cc_start: 0.7367 (t0) cc_final: 0.7140 (t0) REVERT: J 104 SER cc_start: 0.8099 (m) cc_final: 0.7609 (t) REVERT: J 108 TYR cc_start: 0.6433 (m-80) cc_final: 0.6149 (m-80) REVERT: J 163 PHE cc_start: 0.5752 (t80) cc_final: 0.5498 (t80) REVERT: L 97 THR cc_start: 0.7335 (m) cc_final: 0.6985 (p) outliers start: 58 outliers final: 43 residues processed: 488 average time/residue: 0.3427 time to fit residues: 253.4465 Evaluate side-chains 488 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 442 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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 90 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 18 ARG 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 276 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain G residue 14 TRP Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 CYS 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 15 ILE 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 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 19 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 206 optimal weight: 0.0170 overall best weight: 1.7024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 22098 Z= 0.312 Angle : 0.687 10.372 29991 Z= 0.358 Chirality : 0.047 0.305 3315 Planarity : 0.004 0.050 3864 Dihedral : 4.680 43.013 3005 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.69 % Allowed : 14.24 % Favored : 83.06 % 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: -0.76 (0.16), residues: 2757 helix: -0.38 (0.29), residues: 279 sheet: 0.12 (0.18), residues: 852 loop : -0.85 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP F 70 HIS 0.009 0.002 HIS B 72 PHE 0.039 0.002 PHE F 154 TYR 0.031 0.002 TYR E 88 ARG 0.005 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 8 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 fitting. rotamer outliers: 65 poor density : 456 time to evaluate : 2.232 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: 0.7816 (tttt) cc_final: 0.7443 (mmtt) REVERT: A 171 LEU cc_start: 0.7572 (mt) cc_final: 0.7221 (tp) REVERT: A 175 TYR cc_start: 0.6733 (t80) cc_final: 0.6443 (t80) REVERT: A 231 ARG cc_start: 0.7859 (ttt-90) cc_final: 0.7647 (ttt-90) REVERT: A 234 GLU cc_start: 0.5487 (pm20) cc_final: 0.5222 (pm20) REVERT: A 293 LYS cc_start: 0.7607 (mttt) cc_final: 0.7293 (mttt) REVERT: A 312 LYS cc_start: 0.7515 (mttt) cc_final: 0.6906 (mptt) REVERT: A 318 LYS cc_start: 0.7617 (ttmt) cc_final: 0.7101 (ttmt) REVERT: B 110 TYR cc_start: 0.7309 (t80) cc_final: 0.7046 (t80) REVERT: B 131 LYS cc_start: 0.7499 (tttt) cc_final: 0.7030 (tttt) REVERT: B 140 PHE cc_start: 0.6071 (m-80) cc_final: 0.5734 (m-80) REVERT: B 149 MET cc_start: 0.5926 (mmt) cc_final: 0.5319 (mmm) REVERT: C 36 TRP cc_start: 0.6401 (m100) cc_final: 0.5390 (m100) REVERT: C 70 ILE cc_start: 0.4749 (OUTLIER) cc_final: 0.4444 (tp) REVERT: C 122 GLN cc_start: 0.5971 (mm-40) cc_final: 0.5752 (mm-40) REVERT: D 81 GLU cc_start: 0.7042 (pm20) cc_final: 0.6699 (pm20) REVERT: E 38 HIS cc_start: 0.6542 (m170) cc_final: 0.6247 (m170) REVERT: E 121 PHE cc_start: 0.6480 (t80) cc_final: 0.5855 (t80) REVERT: E 170 LYS cc_start: 0.7986 (ttpp) cc_final: 0.7764 (ttpp) REVERT: E 231 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7627 (mtp-110) REVERT: E 267 MET cc_start: 0.6539 (ppp) cc_final: 0.5628 (ppp) REVERT: E 312 LYS cc_start: 0.7403 (mttt) cc_final: 0.7172 (mttt) REVERT: E 323 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7210 (mtp85) REVERT: G 17 MET cc_start: 0.6745 (ttp) cc_final: 0.6440 (ttp) REVERT: G 48 ILE cc_start: 0.8407 (mm) cc_final: 0.8114 (mm) REVERT: G 60 ASN cc_start: 0.7986 (p0) cc_final: 0.7358 (p0) REVERT: G 86 ASP cc_start: 0.7556 (m-30) cc_final: 0.7340 (m-30) REVERT: G 103 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7342 (mm-30) REVERT: G 121 LYS cc_start: 0.8187 (tttt) cc_final: 0.7814 (tmtt) REVERT: G 149 MET cc_start: 0.6183 (mmp) cc_final: 0.5922 (mmm) REVERT: G 158 ASP cc_start: 0.7188 (t0) cc_final: 0.6849 (t0) REVERT: I 19 ARG cc_start: 0.2609 (tmt170) cc_final: 0.2384 (tmt170) REVERT: I 29 PHE cc_start: 0.6965 (t80) cc_final: 0.6552 (t80) REVERT: K 36 TYR cc_start: 0.5250 (m-80) cc_final: 0.4476 (m-80) REVERT: K 78 LEU cc_start: 0.6784 (tp) cc_final: 0.6380 (mp) REVERT: K 82 ASP cc_start: 0.7060 (m-30) cc_final: 0.6411 (m-30) REVERT: F 70 TRP cc_start: 0.6365 (t60) cc_final: 0.5705 (t60) REVERT: F 160 TRP cc_start: 0.6718 (OUTLIER) cc_final: 0.6419 (m100) REVERT: F 170 LYS cc_start: 0.8157 (tttt) cc_final: 0.7782 (mptt) REVERT: F 179 LYS cc_start: 0.7499 (mmtt) cc_final: 0.7128 (mttp) REVERT: F 191 HIS cc_start: 0.5539 (m-70) cc_final: 0.4979 (m-70) REVERT: F 231 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7518 (mtp85) REVERT: F 238 ASN cc_start: 0.4959 (m-40) cc_final: 0.4559 (m-40) REVERT: F 319 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8300 (p) REVERT: F 321 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7195 (tppt) REVERT: F 322 LEU cc_start: 0.8114 (mt) cc_final: 0.7806 (mt) REVERT: F 323 ARG cc_start: 0.7785 (mtt-85) cc_final: 0.7163 (mtt-85) REVERT: H 68 LYS cc_start: 0.8518 (mmtt) cc_final: 0.7768 (mmmt) REVERT: H 103 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6361 (mm-30) REVERT: H 105 GLU cc_start: 0.7047 (tp30) cc_final: 0.6676 (tp30) REVERT: H 131 LYS cc_start: 0.7395 (tttt) cc_final: 0.6984 (tttt) REVERT: H 156 THR cc_start: 0.8255 (m) cc_final: 0.7998 (p) REVERT: H 158 ASP cc_start: 0.7420 (t0) cc_final: 0.6690 (t70) REVERT: J 104 SER cc_start: 0.7966 (m) cc_final: 0.7556 (t) REVERT: L 37 GLN cc_start: 0.7761 (tt0) cc_final: 0.7484 (tt0) REVERT: L 72 THR cc_start: 0.7655 (m) cc_final: 0.7397 (t) outliers start: 65 outliers final: 45 residues processed: 493 average time/residue: 0.3426 time to fit residues: 257.7434 Evaluate side-chains 498 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 450 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 90 VAL 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 296 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU 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 93 SER Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain G residue 14 TRP Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 CYS 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 15 ILE Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain J residue 2 VAL 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 Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 0.9980 chunk 252 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 245 optimal weight: 30.0000 chunk 147 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 22098 Z= 0.294 Angle : 0.688 12.211 29991 Z= 0.357 Chirality : 0.047 0.250 3315 Planarity : 0.004 0.055 3864 Dihedral : 4.817 45.404 3005 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.48 % Allowed : 15.07 % Favored : 82.44 % 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: -0.84 (0.16), residues: 2757 helix: -0.58 (0.28), residues: 288 sheet: 0.03 (0.18), residues: 855 loop : -0.86 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP F 70 HIS 0.009 0.001 HIS H 72 PHE 0.037 0.002 PHE F 154 TYR 0.030 0.002 TYR A 17 ARG 0.005 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 9 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 506 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 446 time to evaluate : 2.506 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 170 LYS cc_start: 0.7806 (tttt) cc_final: 0.7429 (mmtt) REVERT: A 171 LEU cc_start: 0.7529 (mt) cc_final: 0.7186 (tp) REVERT: A 175 TYR cc_start: 0.6744 (t80) cc_final: 0.6447 (t80) REVERT: A 231 ARG cc_start: 0.7912 (ttt-90) cc_final: 0.7680 (ttt-90) REVERT: A 293 LYS cc_start: 0.7569 (mttt) cc_final: 0.7260 (mttt) REVERT: A 312 LYS cc_start: 0.7331 (mttt) cc_final: 0.6997 (mptt) REVERT: A 318 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7223 (ttmt) REVERT: B 97 GLU cc_start: 0.8174 (tp30) cc_final: 0.7799 (tp30) REVERT: B 100 VAL cc_start: 0.8041 (t) cc_final: 0.7802 (p) REVERT: B 110 TYR cc_start: 0.7339 (t80) cc_final: 0.7080 (t80) REVERT: B 131 LYS cc_start: 0.7550 (tttt) cc_final: 0.7078 (tttt) REVERT: B 140 PHE cc_start: 0.6008 (m-80) cc_final: 0.5726 (m-80) REVERT: B 149 MET cc_start: 0.6006 (mmt) cc_final: 0.5382 (mmm) REVERT: B 158 ASP cc_start: 0.7286 (t0) cc_final: 0.6716 (t0) REVERT: C 36 TRP cc_start: 0.6434 (m100) cc_final: 0.5408 (m100) REVERT: C 70 ILE cc_start: 0.4730 (OUTLIER) cc_final: 0.4435 (tp) REVERT: C 114 PHE cc_start: 0.8090 (m-10) cc_final: 0.7776 (m-80) REVERT: C 122 GLN cc_start: 0.5937 (mm-40) cc_final: 0.5703 (mm-40) REVERT: D 81 GLU cc_start: 0.7033 (pm20) cc_final: 0.6692 (pm20) REVERT: E 38 HIS cc_start: 0.6561 (m170) cc_final: 0.6248 (m170) REVERT: E 121 PHE cc_start: 0.6463 (t80) cc_final: 0.5803 (t80) REVERT: E 170 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7765 (ttpp) REVERT: E 231 ARG cc_start: 0.8187 (mtt-85) cc_final: 0.7653 (mtp-110) REVERT: E 237 MET cc_start: 0.5166 (tpp) cc_final: 0.4883 (tpp) REVERT: E 267 MET cc_start: 0.6535 (ppp) cc_final: 0.5599 (ppp) REVERT: E 312 LYS cc_start: 0.7310 (mttt) cc_final: 0.6939 (mttt) REVERT: G 17 MET cc_start: 0.6760 (ttp) cc_final: 0.6454 (ttp) REVERT: G 48 ILE cc_start: 0.8376 (mm) cc_final: 0.8085 (mm) REVERT: G 60 ASN cc_start: 0.7970 (p0) cc_final: 0.7336 (p0) REVERT: G 86 ASP cc_start: 0.7610 (m-30) cc_final: 0.7347 (m-30) REVERT: G 88 PHE cc_start: 0.6425 (m-80) cc_final: 0.4618 (m-80) REVERT: G 95 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8062 (t0) REVERT: G 121 LYS cc_start: 0.8094 (tttt) cc_final: 0.7730 (tmtt) REVERT: G 158 ASP cc_start: 0.7194 (t0) cc_final: 0.6876 (t0) REVERT: I 29 PHE cc_start: 0.7046 (t80) cc_final: 0.6677 (t80) REVERT: K 82 ASP cc_start: 0.7110 (m-30) cc_final: 0.6395 (m-30) REVERT: F 70 TRP cc_start: 0.6546 (t60) cc_final: 0.5762 (t60) REVERT: F 160 TRP cc_start: 0.6687 (OUTLIER) cc_final: 0.6425 (m100) REVERT: F 170 LYS cc_start: 0.8178 (tttt) cc_final: 0.7797 (mptt) REVERT: F 179 LYS cc_start: 0.7489 (mmtt) cc_final: 0.7129 (mttp) REVERT: F 191 HIS cc_start: 0.5507 (m-70) cc_final: 0.5013 (m-70) REVERT: F 231 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7607 (ttt-90) REVERT: F 238 ASN cc_start: 0.4864 (m-40) cc_final: 0.4629 (m-40) REVERT: F 296 ILE cc_start: 0.8014 (mt) cc_final: 0.7649 (tp) REVERT: F 319 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8334 (p) REVERT: F 321 LYS cc_start: 0.7626 (mmmt) cc_final: 0.7240 (tppt) REVERT: F 322 LEU cc_start: 0.8126 (mt) cc_final: 0.7797 (mt) REVERT: F 323 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.7140 (mtt-85) REVERT: H 68 LYS cc_start: 0.8512 (mmtt) cc_final: 0.7742 (mmmt) REVERT: H 92 TRP cc_start: 0.5673 (m-10) cc_final: 0.5404 (m-90) REVERT: H 103 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6469 (mm-30) REVERT: H 105 GLU cc_start: 0.7018 (tp30) cc_final: 0.6665 (tp30) REVERT: H 119 TYR cc_start: 0.7460 (m-80) cc_final: 0.6293 (t80) REVERT: H 131 LYS cc_start: 0.7382 (tttt) cc_final: 0.7019 (tttt) REVERT: H 156 THR cc_start: 0.8254 (m) cc_final: 0.7994 (p) REVERT: H 158 ASP cc_start: 0.7306 (t0) cc_final: 0.6582 (t0) REVERT: J 104 SER cc_start: 0.7761 (m) cc_final: 0.7488 (t) REVERT: L 37 GLN cc_start: 0.7710 (tt0) cc_final: 0.7461 (tt0) REVERT: L 72 THR cc_start: 0.7817 (m) cc_final: 0.7545 (t) outliers start: 60 outliers final: 48 residues processed: 479 average time/residue: 0.3457 time to fit residues: 251.9546 Evaluate side-chains 492 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 440 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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 90 VAL 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 296 ILE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU 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 93 SER Chi-restraints excluded: chain E residue 276 ILE 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 74 GLU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 72 THR 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 160 TRP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 271 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 167 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN ** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN I 33 ASN F 74 ASN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 160 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 22098 Z= 0.505 Angle : 0.868 17.044 29991 Z= 0.456 Chirality : 0.053 0.385 3315 Planarity : 0.006 0.074 3864 Dihedral : 5.812 53.697 3005 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.57 % Allowed : 15.57 % Favored : 81.86 % 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: -1.29 (0.16), residues: 2757 helix: -1.35 (0.26), residues: 291 sheet: -0.09 (0.19), residues: 822 loop : -1.17 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.004 TRP G 92 HIS 0.013 0.003 HIS H 72 PHE 0.043 0.003 PHE F 154 TYR 0.044 0.003 TYR A 17 ARG 0.008 0.001 ARG B 123 ********************** REFINEMENT MACRO_CYCLE 10 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 527 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 465 time to evaluate : 2.294 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 170 LYS cc_start: 0.7962 (tttt) cc_final: 0.7576 (mmtt) REVERT: A 171 LEU cc_start: 0.7778 (mt) cc_final: 0.7514 (tp) REVERT: A 175 TYR cc_start: 0.6830 (t80) cc_final: 0.6575 (t80) REVERT: A 231 ARG cc_start: 0.7979 (ttt-90) cc_final: 0.7696 (ttt-90) REVERT: A 293 LYS cc_start: 0.7955 (mttt) cc_final: 0.7535 (mttt) REVERT: A 312 LYS cc_start: 0.7343 (mttt) cc_final: 0.6815 (mptt) REVERT: B 42 GLN cc_start: 0.7630 (tp40) cc_final: 0.7400 (tp-100) REVERT: B 97 GLU cc_start: 0.8344 (tp30) cc_final: 0.8082 (tp30) REVERT: B 131 LYS cc_start: 0.7610 (tttt) cc_final: 0.7129 (tttt) REVERT: B 149 MET cc_start: 0.6127 (mmt) cc_final: 0.5275 (mmm) REVERT: B 158 ASP cc_start: 0.7441 (t0) cc_final: 0.6899 (t0) REVERT: C 12 VAL cc_start: 0.8011 (t) cc_final: 0.7461 (p) REVERT: C 36 TRP cc_start: 0.6486 (m100) cc_final: 0.5769 (m100) REVERT: C 70 ILE cc_start: 0.5195 (OUTLIER) cc_final: 0.4905 (tp) REVERT: C 114 PHE cc_start: 0.7979 (m-10) cc_final: 0.7676 (m-80) REVERT: C 122 GLN cc_start: 0.5811 (mm-40) cc_final: 0.5573 (mm-40) REVERT: D 53 ARG cc_start: 0.7062 (mtp85) cc_final: 0.6729 (mtp85) REVERT: D 81 GLU cc_start: 0.7129 (pm20) cc_final: 0.6758 (pm20) REVERT: E 38 HIS cc_start: 0.6965 (m170) cc_final: 0.6761 (m-70) REVERT: E 121 PHE cc_start: 0.6671 (t80) cc_final: 0.5959 (t80) REVERT: E 170 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7834 (ttpp) REVERT: E 231 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7464 (mtp-110) REVERT: E 237 MET cc_start: 0.5300 (tpp) cc_final: 0.4971 (tpp) REVERT: E 267 MET cc_start: 0.6478 (ppp) cc_final: 0.5510 (ppp) REVERT: G 17 MET cc_start: 0.6800 (ttp) cc_final: 0.6434 (ttp) REVERT: G 46 ASP cc_start: 0.7009 (m-30) cc_final: 0.6678 (m-30) REVERT: G 86 ASP cc_start: 0.7779 (m-30) cc_final: 0.7528 (m-30) REVERT: G 149 MET cc_start: 0.6080 (mmm) cc_final: 0.5652 (mmm) REVERT: G 153 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7228 (tmtt) REVERT: G 158 ASP cc_start: 0.7386 (t0) cc_final: 0.6801 (t0) REVERT: I 36 TRP cc_start: 0.5125 (m100) cc_final: 0.4702 (m100) REVERT: I 114 PHE cc_start: 0.7886 (m-80) cc_final: 0.7292 (m-80) REVERT: K 37 GLN cc_start: 0.7321 (tt0) cc_final: 0.7038 (tt0) REVERT: K 82 ASP cc_start: 0.7306 (m-30) cc_final: 0.6632 (m-30) REVERT: F 70 TRP cc_start: 0.6816 (t60) cc_final: 0.5846 (t60) REVERT: F 179 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7237 (mttp) REVERT: F 191 HIS cc_start: 0.5509 (m-70) cc_final: 0.4957 (m-70) REVERT: F 296 ILE cc_start: 0.8111 (mt) cc_final: 0.7692 (pt) REVERT: F 312 LYS cc_start: 0.7124 (mttt) cc_final: 0.6729 (mmtm) REVERT: F 319 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8359 (p) REVERT: F 321 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7304 (tppt) REVERT: F 322 LEU cc_start: 0.8182 (mt) cc_final: 0.7825 (mt) REVERT: F 323 ARG cc_start: 0.7901 (mtt-85) cc_final: 0.7092 (mtt-85) REVERT: H 51 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7714 (ttpt) REVERT: H 76 ARG cc_start: 0.5896 (ttp80) cc_final: 0.5613 (ttp80) REVERT: H 92 TRP cc_start: 0.5753 (m-10) cc_final: 0.5381 (m-90) REVERT: H 103 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6518 (mm-30) REVERT: H 119 TYR cc_start: 0.7525 (m-80) cc_final: 0.6431 (t80) REVERT: H 131 LYS cc_start: 0.7476 (tttt) cc_final: 0.7096 (tttt) REVERT: H 156 THR cc_start: 0.8521 (m) cc_final: 0.8195 (p) REVERT: H 158 ASP cc_start: 0.7395 (t0) cc_final: 0.6661 (t0) REVERT: L 36 TYR cc_start: 0.6186 (m-80) cc_final: 0.5957 (m-80) REVERT: L 37 GLN cc_start: 0.7762 (tt0) cc_final: 0.7546 (tt0) REVERT: L 72 THR cc_start: 0.7958 (m) cc_final: 0.7591 (t) outliers start: 62 outliers final: 51 residues processed: 502 average time/residue: 0.3494 time to fit residues: 265.9675 Evaluate side-chains 506 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 452 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 90 VAL 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 296 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 153 LYS 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 29 VAL Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 226 ILE 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 14 TRP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 216 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 222 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 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 = 0.4779 r_free = 0.4779 target = 0.216004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.181113 restraints weight = 33895.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.186732 restraints weight = 17635.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.190192 restraints weight = 10536.457| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 22098 Z= 0.291 Angle : 0.740 15.515 29991 Z= 0.382 Chirality : 0.049 0.288 3315 Planarity : 0.005 0.052 3864 Dihedral : 5.380 52.397 3005 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.24 % Allowed : 16.56 % Favored : 81.20 % 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: -1.15 (0.16), residues: 2757 helix: -1.34 (0.26), residues: 294 sheet: 0.00 (0.19), residues: 819 loop : -1.06 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP G 92 HIS 0.010 0.002 HIS H 72 PHE 0.057 0.003 PHE B 140 TYR 0.037 0.002 TYR F 17 ARG 0.008 0.001 ARG F 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5274.24 seconds wall clock time: 96 minutes 24.29 seconds (5784.29 seconds total)