Starting phenix.real_space_refine on Wed Jun 18 08:39:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tqu_26072/06_2025/7tqu_26072.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqu_26072/06_2025/7tqu_26072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tqu_26072/06_2025/7tqu_26072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqu_26072/06_2025/7tqu_26072.map" model { file = "/net/cci-nas-00/data/ceres_data/7tqu_26072/06_2025/7tqu_26072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqu_26072/06_2025/7tqu_26072.cif" } resolution = 3.8 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= 0.000 sd= 0.002 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 127 5.16 5 C 13211 2.51 5 N 3554 2.21 5 O 3999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20891 Number of models: 1 Model: "" Number of chains: 17 Chain: "H" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 560 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "a" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "b" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2043 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain breaks: 1 Chain: "c" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1801 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 20, 'TRANS': 212} Chain: "d" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "e" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2219 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 20, 'TRANS': 261} Chain: "f" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2057 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 16, 'TRANS': 248} Chain: "g" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1810 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 20, 'TRANS': 213} Chain: "h" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "i" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "j" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2029 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 16, 'TRANS': 244} Chain breaks: 1 Chain: "k" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1826 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 20, 'TRANS': 215} Chain: "l" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "a" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.32, per 1000 atoms: 0.64 Number of scatterers: 20891 At special positions: 0 Unit cell: (166.155, 166.155, 165.11, 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 127 16.00 O 3999 8.00 N 3554 7.00 C 13211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.54 Conformation dependent library (CDL) restraints added in 2.9 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5204 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 14.9% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'H' and resid 51 through 54 Processing helix chain 'L' and resid 26 through 28 No H-bonds generated for 'chain 'L' and resid 26 through 28' Processing helix chain 'a' and resid 51 through 55 Processing helix chain 'a' and resid 71 through 77 Processing helix chain 'a' and resid 92 through 98 removed outlier: 5.072A pdb=" N LYS a 97 " --> pdb=" O GLY a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 118 Processing helix chain 'a' and resid 167 through 172 Processing helix chain 'a' and resid 225 through 229 Processing helix chain 'a' and resid 282 through 286 removed outlier: 4.307A pdb=" N ILE a 286 " --> pdb=" O SER a 283 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 37 No H-bonds generated for 'chain 'b' and resid 35 through 37' Processing helix chain 'b' and resid 82 through 86 Processing helix chain 'b' and resid 89 through 98 Processing helix chain 'b' and resid 150 through 154 removed outlier: 4.132A pdb=" N ARG b 153 " --> pdb=" O PRO b 150 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 193 removed outlier: 4.295A pdb=" N PHE b 191 " --> pdb=" O GLY b 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 43 through 48 Processing helix chain 'c' and resid 64 through 69 Processing helix chain 'c' and resid 93 through 96 Processing helix chain 'c' and resid 97 through 104 Processing helix chain 'c' and resid 143 through 149 Processing helix chain 'c' and resid 181 through 185 removed outlier: 4.021A pdb=" N GLU c 185 " --> pdb=" O ASP c 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 39 Processing helix chain 'd' and resid 50 through 55 Processing helix chain 'e' and resid 41 through 45 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 71 through 76 Processing helix chain 'e' and resid 92 through 98 removed outlier: 4.649A pdb=" N LYS e 97 " --> pdb=" O GLY e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 118 Processing helix chain 'e' and resid 167 through 172 Processing helix chain 'e' and resid 225 through 230 Processing helix chain 'e' and resid 282 through 286 Processing helix chain 'f' and resid 35 through 37 No H-bonds generated for 'chain 'f' and resid 35 through 37' Processing helix chain 'f' and resid 43 through 47 Processing helix chain 'f' and resid 82 through 86 removed outlier: 3.733A pdb=" N LEU f 86 " --> pdb=" O LEU f 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 82 through 86' Processing helix chain 'f' and resid 89 through 98 Processing helix chain 'f' and resid 144 through 149 Processing helix chain 'f' and resid 150 through 154 removed outlier: 4.294A pdb=" N ARG f 153 " --> pdb=" O PRO f 150 " (cutoff:3.500A) Processing helix chain 'f' and resid 167 through 172 removed outlier: 3.601A pdb=" N ARG f 172 " --> pdb=" O ALA f 168 " (cutoff:3.500A) Processing helix chain 'f' and resid 186 through 193 removed outlier: 4.397A pdb=" N PHE f 191 " --> pdb=" O GLY f 188 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 48 Processing helix chain 'g' and resid 64 through 69 Processing helix chain 'g' and resid 97 through 104 Processing helix chain 'g' and resid 143 through 148 Processing helix chain 'h' and resid 35 through 39 Processing helix chain 'h' and resid 50 through 55 Processing helix chain 'i' and resid 51 through 55 Processing helix chain 'i' and resid 71 through 76 Processing helix chain 'i' and resid 92 through 98 removed outlier: 4.763A pdb=" N LYS i 97 " --> pdb=" O GLY i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 118 removed outlier: 3.887A pdb=" N LYS i 116 " --> pdb=" O GLN i 112 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 172 Processing helix chain 'i' and resid 225 through 229 Processing helix chain 'j' and resid 35 through 37 No H-bonds generated for 'chain 'j' and resid 35 through 37' Processing helix chain 'j' and resid 43 through 47 removed outlier: 3.869A pdb=" N ALA j 47 " --> pdb=" O ASP j 44 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 60 Processing helix chain 'j' and resid 82 through 86 Processing helix chain 'j' and resid 89 through 99 Processing helix chain 'j' and resid 150 through 154 removed outlier: 4.087A pdb=" N ARG j 153 " --> pdb=" O PRO j 150 " (cutoff:3.500A) Processing helix chain 'j' and resid 186 through 193 removed outlier: 4.244A pdb=" N PHE j 191 " --> pdb=" O GLY j 188 " (cutoff:3.500A) Processing helix chain 'k' and resid 42 through 47 removed outlier: 4.196A pdb=" N LEU k 46 " --> pdb=" O ASN k 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 64 through 69 Processing helix chain 'k' and resid 97 through 104 Processing helix chain 'k' and resid 143 through 148 Processing helix chain 'l' and resid 35 through 39 Processing helix chain 'l' and resid 50 through 55 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.538A pdb=" N UNK H 10 " --> pdb=" O UNK H 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 33 through 35 removed outlier: 3.514A pdb=" N UNK H 106 " --> pdb=" O UNK H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 47 through 49 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA7, first strand: chain 'L' and resid 18 through 21 Processing sheet with id=AA8, first strand: chain 'L' and resid 43 through 45 Processing sheet with id=AA9, first strand: chain 'L' and resid 47 through 49 removed outlier: 6.777A pdb=" N UNK L 52 " --> pdb=" O UNK L 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 39 through 40 Processing sheet with id=AB2, first strand: chain 'a' and resid 39 through 40 Processing sheet with id=AB3, first strand: chain 'a' and resid 80 through 89 removed outlier: 6.687A pdb=" N VAL a 254 " --> pdb=" O VAL a 82 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE a 84 " --> pdb=" O VAL a 252 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL a 252 " --> pdb=" O ILE a 84 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER a 86 " --> pdb=" O THR a 250 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR a 250 " --> pdb=" O SER a 86 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR a 88 " --> pdb=" O ILE a 248 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE a 248 " --> pdb=" O THR a 88 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE a 261 " --> pdb=" O ARG a 124 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG a 124 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS a 263 " --> pdb=" O TYR a 122 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR a 122 " --> pdb=" O CYS a 263 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS a 265 " --> pdb=" O PHE a 120 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE a 120 " --> pdb=" O CYS a 265 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 188 through 191 removed outlier: 5.022A pdb=" N PHE a 120 " --> pdb=" O CYS a 265 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS a 265 " --> pdb=" O PHE a 120 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR a 122 " --> pdb=" O CYS a 263 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS a 263 " --> pdb=" O TYR a 122 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG a 124 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE a 261 " --> pdb=" O ARG a 124 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N CYS a 263 " --> pdb=" O VAL c 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 100 through 104 Processing sheet with id=AB6, first strand: chain 'i' and resid 31 through 33 removed outlier: 3.889A pdb=" N SER i 33 " --> pdb=" O GLN b 15 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP k 156 " --> pdb=" O THR b 24 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE k 82 " --> pdb=" O CYS k 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 32 through 33 removed outlier: 6.708A pdb=" N ILE b 32 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS b 99 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY b 262 " --> pdb=" O HIS b 99 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU b 101 " --> pdb=" O PHE b 260 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE b 260 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG b 103 " --> pdb=" O THR b 258 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR b 258 " --> pdb=" O ARG b 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 32 through 33 removed outlier: 6.708A pdb=" N ILE b 32 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS b 99 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY b 262 " --> pdb=" O HIS b 99 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU b 101 " --> pdb=" O PHE b 260 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE b 260 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG b 103 " --> pdb=" O THR b 258 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR b 258 " --> pdb=" O ARG b 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 155 through 156 removed outlier: 6.263A pdb=" N ALA b 121 " --> pdb=" O LEU b 234 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLN b 119 " --> pdb=" O PRO b 236 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 82 through 85 removed outlier: 3.579A pdb=" N PHE c 82 " --> pdb=" O CYS c 191 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS c 128 " --> pdb=" O GLN c 194 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ARG c 196 " --> pdb=" O THR c 126 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR c 126 " --> pdb=" O ARG c 196 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP c 156 " --> pdb=" O THR f 24 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 176 through 177 Processing sheet with id=AC3, first strand: chain 'd' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'e' and resid 31 through 33 removed outlier: 6.483A pdb=" N HIS g 152 " --> pdb=" O THR j 22 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR j 24 " --> pdb=" O HIS g 152 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE g 154 " --> pdb=" O THR j 24 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY g 127 " --> pdb=" O LEU g 157 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS g 191 " --> pdb=" O PHE g 82 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE g 82 " --> pdb=" O CYS g 191 " (cutoff:3.500A) 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 39 through 40 Processing sheet with id=AC7, first strand: chain 'e' and resid 80 through 89 removed outlier: 6.679A pdb=" N VAL e 254 " --> pdb=" O VAL e 82 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE e 84 " --> pdb=" O VAL e 252 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL e 252 " --> pdb=" O ILE e 84 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER e 86 " --> pdb=" O THR e 250 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR e 250 " --> pdb=" O SER e 86 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR e 88 " --> pdb=" O ILE e 248 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE e 248 " --> pdb=" O THR e 88 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE e 261 " --> pdb=" O ARG e 124 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG e 124 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N CYS e 263 " --> pdb=" O TYR e 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR e 122 " --> pdb=" O CYS e 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 80 through 89 removed outlier: 6.679A pdb=" N VAL e 254 " --> pdb=" O VAL e 82 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE e 84 " --> pdb=" O VAL e 252 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL e 252 " --> pdb=" O ILE e 84 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER e 86 " --> pdb=" O THR e 250 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR e 250 " --> pdb=" O SER e 86 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR e 88 " --> pdb=" O ILE e 248 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE e 248 " --> pdb=" O THR e 88 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE e 261 " --> pdb=" O ARG e 124 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG e 124 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N CYS e 263 " --> pdb=" O TYR e 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR e 122 " --> pdb=" O CYS e 263 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 100 through 104 Processing sheet with id=AD1, first strand: chain 'f' and resid 32 through 33 removed outlier: 6.585A pdb=" N ILE f 32 " --> pdb=" O VAL f 209 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS f 99 " --> pdb=" O GLY f 262 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY f 262 " --> pdb=" O HIS f 99 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU f 101 " --> pdb=" O PHE f 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE f 260 " --> pdb=" O LEU f 101 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG f 103 " --> pdb=" O THR f 258 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR f 258 " --> pdb=" O ARG f 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 32 through 33 removed outlier: 6.585A pdb=" N ILE f 32 " --> pdb=" O VAL f 209 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS f 99 " --> pdb=" O GLY f 262 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY f 262 " --> pdb=" O HIS f 99 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU f 101 " --> pdb=" O PHE f 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE f 260 " --> pdb=" O LEU f 101 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG f 103 " --> pdb=" O THR f 258 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR f 258 " --> pdb=" O ARG f 103 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'f' and resid 155 through 156 removed outlier: 6.163A pdb=" N ALA f 121 " --> pdb=" O LEU f 234 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN f 119 " --> pdb=" O PRO f 236 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'g' and resid 176 through 177 Processing sheet with id=AD5, first strand: chain 'h' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'i' and resid 39 through 40 Processing sheet with id=AD7, first strand: chain 'i' and resid 39 through 40 Processing sheet with id=AD8, first strand: chain 'i' and resid 80 through 89 removed outlier: 6.708A pdb=" N VAL i 254 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE i 84 " --> pdb=" O VAL i 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL i 252 " --> pdb=" O ILE i 84 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER i 86 " --> pdb=" O THR i 250 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR i 250 " --> pdb=" O SER i 86 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR i 88 " --> pdb=" O ILE i 248 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE i 248 " --> pdb=" O THR i 88 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE i 261 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG i 124 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N CYS i 263 " --> pdb=" O TYR i 122 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR i 122 " --> pdb=" O CYS i 263 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'i' and resid 80 through 89 removed outlier: 6.708A pdb=" N VAL i 254 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE i 84 " --> pdb=" O VAL i 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL i 252 " --> pdb=" O ILE i 84 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER i 86 " --> pdb=" O THR i 250 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR i 250 " --> pdb=" O SER i 86 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR i 88 " --> pdb=" O ILE i 248 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE i 248 " --> pdb=" O THR i 88 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE i 261 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG i 124 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N CYS i 263 " --> pdb=" O TYR i 122 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR i 122 " --> pdb=" O CYS i 263 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'i' and resid 100 through 104 Processing sheet with id=AE2, first strand: chain 'j' and resid 32 through 33 removed outlier: 6.402A pdb=" N ILE j 32 " --> pdb=" O VAL j 209 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU j 101 " --> pdb=" O PHE j 260 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE j 260 " --> pdb=" O LEU j 101 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG j 103 " --> pdb=" O THR j 258 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR j 258 " --> pdb=" O ARG j 103 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'j' and resid 32 through 33 removed outlier: 6.402A pdb=" N ILE j 32 " --> pdb=" O VAL j 209 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU j 101 " --> pdb=" O PHE j 260 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE j 260 " --> pdb=" O LEU j 101 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG j 103 " --> pdb=" O THR j 258 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR j 258 " --> pdb=" O ARG j 103 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'j' and resid 155 through 156 removed outlier: 6.157A pdb=" N ALA j 121 " --> pdb=" O LEU j 234 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLN j 119 " --> pdb=" O PRO j 236 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'k' and resid 108 through 109 Processing sheet with id=AE6, first strand: chain 'l' and resid 4 through 7 687 hydrogen bonds defined for protein. 1635 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: 7.25 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4147 1.31 - 1.45: 7272 1.45 - 1.59: 9767 1.59 - 1.73: 23 1.73 - 1.87: 200 Bond restraints: 21409 Sorted by residual: bond pdb=" CB ILE k 236 " pdb=" CG1 ILE k 236 " ideal model delta sigma weight residual 1.530 1.676 -0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" CA PRO i 268 " pdb=" CB PRO i 268 " ideal model delta sigma weight residual 1.539 1.483 0.057 9.30e-03 1.16e+04 3.72e+01 bond pdb=" CB HIS f 224 " pdb=" CG HIS f 224 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.58e+01 bond pdb=" CA VAL k 221 " pdb=" C VAL k 221 " ideal model delta sigma weight residual 1.520 1.580 -0.060 1.00e-02 1.00e+04 3.56e+01 bond pdb=" CB HIS b 224 " pdb=" CG HIS b 224 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.27e+01 ... (remaining 21404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 26102 2.85 - 5.70: 2815 5.70 - 8.55: 269 8.55 - 11.40: 34 11.40 - 14.25: 3 Bond angle restraints: 29223 Sorted by residual: angle pdb=" N VAL k 221 " pdb=" CA VAL k 221 " pdb=" C VAL k 221 " ideal model delta sigma weight residual 113.20 124.52 -11.32 9.60e-01 1.09e+00 1.39e+02 angle pdb=" C PRO k 135 " pdb=" N PRO k 136 " pdb=" CA PRO k 136 " ideal model delta sigma weight residual 120.21 129.27 -9.06 9.60e-01 1.09e+00 8.90e+01 angle pdb=" N TRP e 264 " pdb=" CA TRP e 264 " pdb=" C TRP e 264 " ideal model delta sigma weight residual 112.59 123.35 -10.76 1.22e+00 6.72e-01 7.77e+01 angle pdb=" C ARG k 222 " pdb=" CA ARG k 222 " pdb=" CB ARG k 222 " ideal model delta sigma weight residual 116.54 106.57 9.97 1.15e+00 7.56e-01 7.52e+01 angle pdb=" N LEU b 234 " pdb=" CA LEU b 234 " pdb=" C LEU b 234 " ideal model delta sigma weight residual 113.88 103.35 10.53 1.23e+00 6.61e-01 7.33e+01 ... (remaining 29218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12371 17.81 - 35.63: 288 35.63 - 53.44: 67 53.44 - 71.26: 26 71.26 - 89.07: 10 Dihedral angle restraints: 12762 sinusoidal: 4702 harmonic: 8060 Sorted by residual: dihedral pdb=" C LEU f 82 " pdb=" N LEU f 82 " pdb=" CA LEU f 82 " pdb=" CB LEU f 82 " ideal model delta harmonic sigma weight residual -122.60 -132.84 10.24 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C LEU b 82 " pdb=" N LEU b 82 " pdb=" CA LEU b 82 " pdb=" CB LEU b 82 " ideal model delta harmonic sigma weight residual -122.60 -132.15 9.55 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" CA ALA g 138 " pdb=" C ALA g 138 " pdb=" N LYS g 139 " pdb=" CA LYS g 139 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 12759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2446 0.102 - 0.204: 720 0.204 - 0.306: 117 0.306 - 0.408: 11 0.408 - 0.510: 6 Chirality restraints: 3300 Sorted by residual: chirality pdb=" CA TRP e 264 " pdb=" N TRP e 264 " pdb=" C TRP e 264 " pdb=" CB TRP e 264 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CB VAL i 16 " pdb=" CA VAL i 16 " pdb=" CG1 VAL i 16 " pdb=" CG2 VAL i 16 " both_signs ideal model delta sigma weight residual False -2.63 -3.12 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CA LEU f 82 " pdb=" N LEU f 82 " pdb=" C LEU f 82 " pdb=" CB LEU f 82 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 ... (remaining 3297 not shown) Planarity restraints: 3804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP b 79 " 0.079 2.00e-02 2.50e+03 3.85e-02 3.71e+01 pdb=" CG TRP b 79 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP b 79 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP b 79 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP b 79 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP b 79 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP b 79 " -0.051 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 79 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 79 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP b 79 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 142 " -0.068 2.00e-02 2.50e+03 3.59e-02 2.57e+01 pdb=" CG TYR b 142 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR b 142 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR b 142 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR b 142 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR b 142 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR b 142 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR b 142 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 137 " -0.049 2.00e-02 2.50e+03 2.64e-02 1.39e+01 pdb=" CG TYR a 137 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR a 137 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR a 137 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR a 137 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR a 137 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR a 137 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR a 137 " -0.041 2.00e-02 2.50e+03 ... (remaining 3801 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 8320 2.88 - 3.39: 19172 3.39 - 3.89: 35913 3.89 - 4.40: 42902 4.40 - 4.90: 68609 Nonbonded interactions: 174916 Sorted by model distance: nonbonded pdb=" N VAL i 42 " pdb=" N GLU i 43 " model vdw 2.375 2.560 nonbonded pdb=" N VAL a 42 " pdb=" N GLU a 43 " model vdw 2.384 2.560 nonbonded pdb=" N GLN c 194 " pdb=" O GLN c 194 " model vdw 2.401 2.496 nonbonded pdb=" NZ LYS c 139 " pdb=" OD2 ASP c 146 " model vdw 2.418 3.120 nonbonded pdb=" N LEU b 234 " pdb=" N ALA b 235 " model vdw 2.418 2.560 ... (remaining 174911 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 'H' and resid 13 through 114) selection = chain 'L' } ncs_group { reference = (chain 'a' and (resid 17 through 298 or resid 300)) selection = chain 'e' selection = (chain 'i' and (resid 17 through 298 or resid 300)) } ncs_group { reference = (chain 'b' and (resid 8 through 164 or resid 169 through 272)) selection = (chain 'f' and (resid 8 through 164 or resid 169 through 272)) selection = chain 'j' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 1 through 233) selection = (chain 'k' and resid 1 through 233) } ncs_group { reference = chain 'd' selection = chain 'h' 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: 1.410 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: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 50.870 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.110 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.021 0.147 21409 Z= 1.117 Angle : 1.812 14.251 29223 Z= 1.226 Chirality : 0.096 0.510 3300 Planarity : 0.009 0.058 3804 Dihedral : 9.740 89.070 7558 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.16), residues: 2516 helix: -2.76 (0.27), residues: 210 sheet: 1.53 (0.20), residues: 608 loop : 0.62 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.009 TRP b 79 HIS 0.012 0.002 HIS j 118 PHE 0.042 0.006 PHE j 117 TYR 0.068 0.007 TYR b 142 ARG 0.009 0.001 ARG c 93 Details of bonding type rmsd hydrogen bonds : bond 0.14883 ( 561) hydrogen bonds : angle 8.14010 ( 1635) covalent geometry : bond 0.02057 (21409) covalent geometry : angle 1.81172 (29223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 789 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 64 TYR cc_start: 0.8109 (m-80) cc_final: 0.7824 (m-10) REVERT: a 78 ARG cc_start: 0.8474 (mmt-90) cc_final: 0.6472 (mtm180) REVERT: a 97 LYS cc_start: 0.8917 (pttt) cc_final: 0.8699 (pttt) REVERT: a 109 ASP cc_start: 0.8370 (m-30) cc_final: 0.7890 (m-30) REVERT: a 122 TYR cc_start: 0.9106 (m-80) cc_final: 0.8829 (m-80) REVERT: a 127 LEU cc_start: 0.9449 (tp) cc_final: 0.9231 (tp) REVERT: a 169 THR cc_start: 0.9136 (p) cc_final: 0.8879 (t) REVERT: b 64 TYR cc_start: 0.9398 (m-80) cc_final: 0.8959 (m-80) REVERT: b 74 THR cc_start: 0.8918 (p) cc_final: 0.8718 (p) REVERT: b 193 TYR cc_start: 0.9133 (m-80) cc_final: 0.8928 (m-10) REVERT: b 214 ASN cc_start: 0.8991 (t0) cc_final: 0.8726 (m-40) REVERT: b 264 ARG cc_start: 0.7204 (ptt180) cc_final: 0.5248 (mmt90) REVERT: c 49 ILE cc_start: 0.8971 (mt) cc_final: 0.8735 (mt) REVERT: c 50 ASP cc_start: 0.7563 (m-30) cc_final: 0.7314 (m-30) REVERT: c 53 ILE cc_start: 0.9627 (mt) cc_final: 0.9335 (mt) REVERT: c 55 MET cc_start: 0.9132 (tpp) cc_final: 0.8896 (tpp) REVERT: c 74 ASP cc_start: 0.8256 (p0) cc_final: 0.7989 (p0) REVERT: c 156 ASP cc_start: 0.8992 (t0) cc_final: 0.8771 (t0) REVERT: d 24 THR cc_start: 0.8742 (p) cc_final: 0.8517 (t) REVERT: d 36 SER cc_start: 0.8096 (p) cc_final: 0.7717 (t) REVERT: d 61 MET cc_start: 0.7445 (ttm) cc_final: 0.7214 (ttp) REVERT: e 31 VAL cc_start: 0.9368 (t) cc_final: 0.8992 (p) REVERT: e 47 SER cc_start: 0.9290 (m) cc_final: 0.9033 (t) REVERT: e 51 ILE cc_start: 0.9324 (pt) cc_final: 0.9063 (pt) REVERT: e 98 LYS cc_start: 0.8817 (mttt) cc_final: 0.8268 (tptt) REVERT: e 105 ILE cc_start: 0.9445 (mt) cc_final: 0.8924 (tt) REVERT: e 146 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.7155 (mpt180) REVERT: e 205 ASP cc_start: 0.8645 (t0) cc_final: 0.8134 (t0) REVERT: e 209 ARG cc_start: 0.8010 (ptm-80) cc_final: 0.7568 (mtt-85) REVERT: e 226 LEU cc_start: 0.9286 (tp) cc_final: 0.8986 (tp) REVERT: e 242 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.6995 (ppt170) REVERT: e 262 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7684 (mtt-85) REVERT: f 13 VAL cc_start: 0.9402 (t) cc_final: 0.9063 (p) REVERT: f 15 GLN cc_start: 0.9182 (tt0) cc_final: 0.8961 (tt0) REVERT: f 91 MET cc_start: 0.8683 (mmm) cc_final: 0.8471 (mmt) REVERT: f 129 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8480 (mm-30) REVERT: f 191 PHE cc_start: 0.9275 (m-80) cc_final: 0.9026 (m-10) REVERT: f 214 ASN cc_start: 0.9025 (t0) cc_final: 0.8819 (t0) REVERT: f 264 ARG cc_start: 0.6357 (ptt180) cc_final: 0.4696 (mtt-85) REVERT: g 10 SER cc_start: 0.9123 (t) cc_final: 0.8835 (p) REVERT: g 77 SER cc_start: 0.9076 (t) cc_final: 0.8642 (m) REVERT: g 91 ASP cc_start: 0.8258 (t0) cc_final: 0.8025 (t0) REVERT: g 178 CYS cc_start: 0.8697 (m) cc_final: 0.8454 (m) REVERT: g 232 GLN cc_start: 0.8894 (tt0) cc_final: 0.6491 (pm20) REVERT: g 234 LYS cc_start: 0.7486 (mmtt) cc_final: 0.6806 (tttm) REVERT: h 24 THR cc_start: 0.9092 (p) cc_final: 0.8864 (t) REVERT: i 47 SER cc_start: 0.9006 (m) cc_final: 0.8593 (p) REVERT: i 55 VAL cc_start: 0.9155 (m) cc_final: 0.8944 (m) REVERT: i 58 THR cc_start: 0.9427 (p) cc_final: 0.9071 (p) REVERT: i 78 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.7367 (mtm180) REVERT: i 90 SER cc_start: 0.8890 (p) cc_final: 0.8566 (m) REVERT: i 146 ARG cc_start: 0.7707 (tpp-160) cc_final: 0.7160 (ptp-170) REVERT: i 172 SER cc_start: 0.8538 (m) cc_final: 0.8158 (p) REVERT: i 182 TYR cc_start: 0.8902 (t80) cc_final: 0.8700 (t80) REVERT: i 264 TRP cc_start: 0.8248 (m100) cc_final: 0.7699 (m100) REVERT: j 26 GLN cc_start: 0.9080 (mt0) cc_final: 0.8816 (mt0) REVERT: j 132 MET cc_start: 0.8697 (mtp) cc_final: 0.8375 (mtm) REVERT: j 145 TYR cc_start: 0.9031 (t80) cc_final: 0.8753 (t80) REVERT: j 214 ASN cc_start: 0.9070 (t0) cc_final: 0.8719 (t0) REVERT: j 256 MET cc_start: 0.8969 (mtp) cc_final: 0.8610 (mtm) REVERT: k 42 ASN cc_start: 0.8153 (t0) cc_final: 0.7837 (t0) REVERT: k 43 MET cc_start: 0.9001 (mmm) cc_final: 0.8396 (mmm) REVERT: k 157 LEU cc_start: 0.9172 (mt) cc_final: 0.8870 (mt) REVERT: k 197 ILE cc_start: 0.9030 (mt) cc_final: 0.8821 (mt) REVERT: k 205 THR cc_start: 0.8721 (p) cc_final: 0.7954 (p) outliers start: 0 outliers final: 0 residues processed: 789 average time/residue: 0.3305 time to fit residues: 393.9774 Evaluate side-chains 513 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 34 GLN a 112 GLN a 148 GLN b 61 ASN b 111 GLN b 162 ASN b 196 GLN b 203 ASN c 75 ASN c 104 ASN d 4 GLN d 21 ASN e 99 HIS ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 162 ASN g 69 GLN g 73 ASN g 104 ASN i 34 GLN ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 148 GLN i 198 ASN i 230 ASN j 113 ASN j 147 ASN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 96 HIS k 108 HIS ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 229 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.110897 restraints weight = 37792.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.113355 restraints weight = 18196.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114933 restraints weight = 10886.351| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21409 Z= 0.160 Angle : 0.662 8.511 29223 Z= 0.350 Chirality : 0.046 0.186 3300 Planarity : 0.005 0.049 3804 Dihedral : 5.835 44.684 3000 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.04 % Allowed : 10.24 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2516 helix: -2.47 (0.28), residues: 216 sheet: 1.14 (0.19), residues: 660 loop : 0.24 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 80 HIS 0.007 0.002 HIS i 99 PHE 0.026 0.002 PHE c 115 TYR 0.029 0.002 TYR c 68 ARG 0.006 0.001 ARG j 76 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 561) hydrogen bonds : angle 6.29641 ( 1635) covalent geometry : bond 0.00354 (21409) covalent geometry : angle 0.66181 (29223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 606 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 78 ARG cc_start: 0.8524 (mmt-90) cc_final: 0.6234 (mtm180) REVERT: a 97 LYS cc_start: 0.8792 (pttt) cc_final: 0.8430 (pptt) REVERT: b 64 TYR cc_start: 0.9278 (m-80) cc_final: 0.8985 (m-80) REVERT: b 145 TYR cc_start: 0.9213 (t80) cc_final: 0.8828 (t80) REVERT: b 193 TYR cc_start: 0.9106 (m-80) cc_final: 0.8857 (m-10) REVERT: b 214 ASN cc_start: 0.8844 (t0) cc_final: 0.8620 (m-40) REVERT: c 48 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8694 (mt-10) REVERT: c 53 ILE cc_start: 0.9662 (mt) cc_final: 0.9455 (mt) REVERT: c 148 MET cc_start: 0.8888 (tmm) cc_final: 0.8282 (ppp) REVERT: c 176 ARG cc_start: 0.8971 (mtt-85) cc_final: 0.8730 (mtt-85) REVERT: d 14 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6651 (tm-30) REVERT: d 36 SER cc_start: 0.7901 (p) cc_final: 0.7419 (t) REVERT: d 44 GLN cc_start: 0.7638 (tt0) cc_final: 0.7373 (tt0) REVERT: e 31 VAL cc_start: 0.9188 (t) cc_final: 0.8754 (p) REVERT: e 47 SER cc_start: 0.9097 (m) cc_final: 0.8711 (t) REVERT: e 97 LYS cc_start: 0.8061 (pttm) cc_final: 0.7793 (tptt) REVERT: e 98 LYS cc_start: 0.8674 (mttt) cc_final: 0.8170 (tptt) REVERT: e 146 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7111 (mpt180) REVERT: e 154 TYR cc_start: 0.8827 (t80) cc_final: 0.8434 (t80) REVERT: e 209 ARG cc_start: 0.7812 (ptm-80) cc_final: 0.7082 (mtt90) REVERT: e 229 ILE cc_start: 0.8904 (pt) cc_final: 0.8692 (tp) REVERT: e 242 ARG cc_start: 0.7372 (mmm-85) cc_final: 0.6595 (ptt180) REVERT: f 13 VAL cc_start: 0.9190 (t) cc_final: 0.8810 (p) REVERT: f 89 MET cc_start: 0.8819 (mmp) cc_final: 0.8277 (mmt) REVERT: f 91 MET cc_start: 0.8119 (mmm) cc_final: 0.7781 (mmt) REVERT: f 223 LYS cc_start: 0.9041 (mttm) cc_final: 0.8795 (mttm) REVERT: g 10 SER cc_start: 0.9112 (t) cc_final: 0.8772 (p) REVERT: g 61 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8464 (mmtm) REVERT: g 77 SER cc_start: 0.9136 (t) cc_final: 0.8623 (m) REVERT: g 91 ASP cc_start: 0.8377 (t0) cc_final: 0.8119 (t0) REVERT: g 178 CYS cc_start: 0.8550 (m) cc_final: 0.8255 (m) REVERT: g 226 ASP cc_start: 0.6432 (m-30) cc_final: 0.6218 (m-30) REVERT: g 232 GLN cc_start: 0.8759 (tt0) cc_final: 0.6221 (pm20) REVERT: g 234 LYS cc_start: 0.7513 (mmtt) cc_final: 0.6971 (tmtt) REVERT: h 39 ASN cc_start: 0.8648 (m-40) cc_final: 0.8394 (m-40) REVERT: h 59 ASP cc_start: 0.8345 (m-30) cc_final: 0.8046 (m-30) REVERT: i 34 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: i 78 ARG cc_start: 0.8278 (mmt-90) cc_final: 0.7332 (mtm180) REVERT: i 90 SER cc_start: 0.8789 (p) cc_final: 0.8516 (t) REVERT: i 146 ARG cc_start: 0.7905 (tpp-160) cc_final: 0.6650 (ptm160) REVERT: i 172 SER cc_start: 0.9006 (m) cc_final: 0.8771 (p) REVERT: i 205 ASP cc_start: 0.8065 (t0) cc_final: 0.7780 (t0) REVERT: i 264 TRP cc_start: 0.7917 (m100) cc_final: 0.7282 (m100) REVERT: j 33 VAL cc_start: 0.9317 (t) cc_final: 0.8826 (m) REVERT: j 141 SER cc_start: 0.8387 (p) cc_final: 0.8165 (p) REVERT: j 232 LEU cc_start: 0.9424 (mt) cc_final: 0.9184 (mt) REVERT: j 252 THR cc_start: 0.9515 (m) cc_final: 0.9029 (p) REVERT: j 256 MET cc_start: 0.8978 (mtp) cc_final: 0.8706 (mtm) REVERT: k 55 MET cc_start: 0.9189 (tpp) cc_final: 0.8945 (tpp) REVERT: k 59 ASP cc_start: 0.7453 (t0) cc_final: 0.6876 (p0) REVERT: k 61 LYS cc_start: 0.9260 (mmtp) cc_final: 0.8782 (mptt) REVERT: k 75 ASN cc_start: 0.8404 (t0) cc_final: 0.7839 (p0) REVERT: k 112 SER cc_start: 0.9002 (m) cc_final: 0.8708 (p) REVERT: k 157 LEU cc_start: 0.9196 (mt) cc_final: 0.8974 (mt) REVERT: k 206 SER cc_start: 0.8922 (t) cc_final: 0.8572 (p) REVERT: k 207 MET cc_start: 0.7929 (mpp) cc_final: 0.7680 (mpp) outliers start: 45 outliers final: 27 residues processed: 632 average time/residue: 0.3254 time to fit residues: 315.1676 Evaluate side-chains 541 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 513 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain i residue 34 GLN Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 153 ARG Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain l residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 59 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 11 ASN c 96 HIS c 232 GLN d 4 GLN e 34 GLN e 49 GLN e 99 HIS f 15 GLN ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN g 69 GLN ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN j 261 ASN k 152 HIS ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.111298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.099737 restraints weight = 39431.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.102046 restraints weight = 19577.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.103570 restraints weight = 11992.551| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 21409 Z= 0.383 Angle : 0.783 9.924 29223 Z= 0.411 Chirality : 0.052 0.203 3300 Planarity : 0.006 0.052 3804 Dihedral : 6.254 57.945 3000 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.03 % Allowed : 11.24 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2516 helix: -2.24 (0.29), residues: 232 sheet: 0.42 (0.19), residues: 659 loop : -0.23 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP j 80 HIS 0.008 0.002 HIS h 13 PHE 0.035 0.003 PHE j 239 TYR 0.024 0.002 TYR a 180 ARG 0.008 0.001 ARG i 238 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 561) hydrogen bonds : angle 6.10467 ( 1635) covalent geometry : bond 0.00884 (21409) covalent geometry : angle 0.78288 (29223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 507 time to evaluate : 2.175 Fit side-chains REVERT: a 34 GLN cc_start: 0.8446 (mt0) cc_final: 0.8180 (mt0) REVERT: a 43 GLU cc_start: 0.8333 (mp0) cc_final: 0.7683 (mp0) REVERT: a 78 ARG cc_start: 0.8838 (mmt-90) cc_final: 0.6295 (mtm180) REVERT: a 96 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8146 (tm-30) REVERT: a 97 LYS cc_start: 0.8899 (pttt) cc_final: 0.8435 (pptt) REVERT: a 196 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8588 (pt) REVERT: a 209 ARG cc_start: 0.5346 (mmt-90) cc_final: 0.4809 (ttp-170) REVERT: a 238 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8563 (ttp-170) REVERT: b 88 ASP cc_start: 0.7208 (p0) cc_final: 0.6995 (p0) REVERT: b 172 ARG cc_start: 0.6210 (mpt180) cc_final: 0.5758 (mmt-90) REVERT: c 48 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8997 (mt-10) REVERT: c 148 MET cc_start: 0.8896 (tmm) cc_final: 0.8349 (ppp) REVERT: c 176 ARG cc_start: 0.8886 (mtt-85) cc_final: 0.8530 (mtt-85) REVERT: c 218 ASP cc_start: 0.9133 (p0) cc_final: 0.8860 (p0) REVERT: d 14 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6934 (tm-30) REVERT: d 32 TYR cc_start: 0.9157 (m-80) cc_final: 0.8758 (m-80) REVERT: d 36 SER cc_start: 0.7983 (p) cc_final: 0.7501 (t) REVERT: d 44 GLN cc_start: 0.7912 (tt0) cc_final: 0.7388 (tt0) REVERT: e 97 LYS cc_start: 0.8231 (pttm) cc_final: 0.7940 (tptp) REVERT: e 98 LYS cc_start: 0.8785 (mttt) cc_final: 0.8286 (tptt) REVERT: e 105 ILE cc_start: 0.9361 (mt) cc_final: 0.8992 (tt) REVERT: e 146 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7248 (mpt180) REVERT: e 209 ARG cc_start: 0.8210 (ptm-80) cc_final: 0.7300 (mtt-85) REVERT: e 229 ILE cc_start: 0.9139 (pt) cc_final: 0.8903 (tp) REVERT: e 242 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.6524 (ptt180) REVERT: e 289 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8704 (tt) REVERT: f 13 VAL cc_start: 0.9280 (t) cc_final: 0.8807 (p) REVERT: f 192 VAL cc_start: 0.9445 (OUTLIER) cc_final: 0.9194 (t) REVERT: f 221 MET cc_start: 0.8926 (mtp) cc_final: 0.8689 (mtp) REVERT: g 10 SER cc_start: 0.9155 (t) cc_final: 0.8798 (p) REVERT: g 61 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8613 (mmtm) REVERT: g 77 SER cc_start: 0.9235 (t) cc_final: 0.8752 (m) REVERT: g 232 GLN cc_start: 0.9093 (tt0) cc_final: 0.6686 (pm20) REVERT: g 234 LYS cc_start: 0.7675 (mmtt) cc_final: 0.6968 (tttm) REVERT: i 32 ASN cc_start: 0.8685 (m-40) cc_final: 0.8401 (t0) REVERT: i 78 ARG cc_start: 0.8486 (mmt-90) cc_final: 0.7367 (mtm180) REVERT: i 90 SER cc_start: 0.8892 (p) cc_final: 0.8544 (t) REVERT: i 146 ARG cc_start: 0.8561 (tpp-160) cc_final: 0.6855 (ptp-170) REVERT: i 172 SER cc_start: 0.9128 (m) cc_final: 0.8813 (p) REVERT: i 264 TRP cc_start: 0.8289 (m100) cc_final: 0.7296 (m100) REVERT: j 33 VAL cc_start: 0.9558 (t) cc_final: 0.9160 (m) REVERT: j 44 ASP cc_start: 0.8537 (m-30) cc_final: 0.8314 (m-30) REVERT: j 153 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7590 (mtm-85) REVERT: j 232 LEU cc_start: 0.9430 (mt) cc_final: 0.9210 (mt) REVERT: k 43 MET cc_start: 0.8559 (mmm) cc_final: 0.8358 (tpp) REVERT: k 61 LYS cc_start: 0.9388 (mmtp) cc_final: 0.8976 (mmtp) REVERT: k 75 ASN cc_start: 0.8429 (t0) cc_final: 0.7873 (p0) REVERT: k 145 LYS cc_start: 0.8831 (mttt) cc_final: 0.8346 (tptt) REVERT: k 148 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7939 (ptt) REVERT: k 216 CYS cc_start: 0.8901 (m) cc_final: 0.8638 (m) REVERT: l 23 SER cc_start: 0.8894 (p) cc_final: 0.8690 (m) outliers start: 111 outliers final: 74 residues processed: 565 average time/residue: 0.3321 time to fit residues: 285.9685 Evaluate side-chains 544 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 464 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 178 ILE Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 196 ILE Chi-restraints excluded: chain a residue 238 ARG Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 189 MET Chi-restraints excluded: chain e residue 251 SER Chi-restraints excluded: chain e residue 277 GLU Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 295 ILE Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 38 TRP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 192 VAL Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 66 GLU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 126 THR Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 153 ILE Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 71 CYS Chi-restraints excluded: chain i residue 248 ILE Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 153 ARG Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 132 SER Chi-restraints excluded: chain k residue 148 MET Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 205 THR Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 245 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 231 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 11 ASN c 232 GLN d 21 ASN d 44 GLN e 34 GLN e 99 HIS ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 226 ASN ** f 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN g 69 GLN i 89 ASN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN ** j 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.115539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.104097 restraints weight = 38822.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.106489 restraints weight = 18721.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.108075 restraints weight = 11299.337| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21409 Z= 0.120 Angle : 0.568 7.710 29223 Z= 0.295 Chirality : 0.044 0.167 3300 Planarity : 0.004 0.062 3804 Dihedral : 5.589 57.501 3000 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.17 % Allowed : 14.86 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2516 helix: -2.12 (0.30), residues: 232 sheet: 0.56 (0.20), residues: 642 loop : -0.10 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 80 HIS 0.007 0.001 HIS b 195 PHE 0.024 0.001 PHE j 239 TYR 0.015 0.001 TYR f 100 ARG 0.009 0.001 ARG f 172 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 561) hydrogen bonds : angle 5.53475 ( 1635) covalent geometry : bond 0.00279 (21409) covalent geometry : angle 0.56809 (29223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 528 time to evaluate : 2.317 Fit side-chains revert: symmetry clash REVERT: a 78 ARG cc_start: 0.8716 (mmt-90) cc_final: 0.6219 (mtm180) REVERT: a 96 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8116 (tm-30) REVERT: a 97 LYS cc_start: 0.8944 (pttt) cc_final: 0.8456 (pptt) REVERT: a 113 LEU cc_start: 0.9224 (tp) cc_final: 0.8960 (tp) REVERT: a 209 ARG cc_start: 0.5201 (mmt-90) cc_final: 0.4831 (ttp-170) REVERT: a 229 ILE cc_start: 0.8897 (pt) cc_final: 0.8177 (tp) REVERT: b 64 TYR cc_start: 0.9080 (m-80) cc_final: 0.8736 (m-80) REVERT: b 221 MET cc_start: 0.8109 (mmt) cc_final: 0.7892 (mmt) REVERT: c 48 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8781 (mt-10) REVERT: c 55 MET cc_start: 0.9040 (tpp) cc_final: 0.8482 (tpp) REVERT: c 154 ILE cc_start: 0.9221 (mp) cc_final: 0.9001 (mp) REVERT: c 176 ARG cc_start: 0.8831 (mtt-85) cc_final: 0.8626 (mtt-85) REVERT: c 218 ASP cc_start: 0.9053 (p0) cc_final: 0.8693 (p0) REVERT: d 14 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6863 (tm-30) REVERT: d 32 TYR cc_start: 0.9115 (m-80) cc_final: 0.8692 (m-80) REVERT: d 44 GLN cc_start: 0.7843 (tt0) cc_final: 0.7579 (tt0) REVERT: e 97 LYS cc_start: 0.8063 (pttm) cc_final: 0.7762 (tptt) REVERT: e 98 LYS cc_start: 0.8710 (mttt) cc_final: 0.8126 (tptt) REVERT: e 105 ILE cc_start: 0.9266 (mt) cc_final: 0.8921 (tt) REVERT: e 146 ARG cc_start: 0.7839 (mmm-85) cc_final: 0.7155 (mpt180) REVERT: e 188 ARG cc_start: 0.6265 (ptt180) cc_final: 0.5930 (ptt180) REVERT: e 209 ARG cc_start: 0.8119 (ptm-80) cc_final: 0.7313 (mtt-85) REVERT: e 242 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.6514 (ptt180) REVERT: f 89 MET cc_start: 0.9114 (mmp) cc_final: 0.8884 (mmm) REVERT: f 172 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7046 (mtt90) REVERT: f 223 LYS cc_start: 0.9264 (mttm) cc_final: 0.9045 (mttm) REVERT: g 10 SER cc_start: 0.9176 (t) cc_final: 0.8775 (p) REVERT: g 77 SER cc_start: 0.9058 (t) cc_final: 0.8588 (m) REVERT: g 123 MET cc_start: 0.8049 (tmm) cc_final: 0.7745 (tpp) REVERT: g 226 ASP cc_start: 0.6632 (m-30) cc_final: 0.6353 (m-30) REVERT: g 232 GLN cc_start: 0.8946 (tt0) cc_final: 0.6549 (pm20) REVERT: g 234 LYS cc_start: 0.7613 (mmtt) cc_final: 0.6848 (tttm) REVERT: i 78 ARG cc_start: 0.8442 (mmt-90) cc_final: 0.7253 (mtm180) REVERT: i 90 SER cc_start: 0.8853 (p) cc_final: 0.8493 (t) REVERT: i 146 ARG cc_start: 0.8481 (tpp-160) cc_final: 0.6876 (ptp-170) REVERT: i 205 ASP cc_start: 0.8097 (t0) cc_final: 0.7789 (t0) REVERT: i 264 TRP cc_start: 0.8130 (m100) cc_final: 0.7261 (m100) REVERT: j 33 VAL cc_start: 0.9410 (t) cc_final: 0.8986 (m) REVERT: j 89 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8271 (mtp) REVERT: k 59 ASP cc_start: 0.7488 (t0) cc_final: 0.6705 (p0) REVERT: k 61 LYS cc_start: 0.9338 (mmtp) cc_final: 0.8897 (mptt) REVERT: k 75 ASN cc_start: 0.8278 (t0) cc_final: 0.7683 (m110) REVERT: k 112 SER cc_start: 0.9212 (m) cc_final: 0.8855 (p) REVERT: k 206 SER cc_start: 0.8940 (t) cc_final: 0.8604 (p) REVERT: k 207 MET cc_start: 0.8027 (mpp) cc_final: 0.7743 (mpp) REVERT: k 218 ASP cc_start: 0.8546 (p0) cc_final: 0.8307 (p0) REVERT: l 23 SER cc_start: 0.8841 (p) cc_final: 0.8563 (m) outliers start: 70 outliers final: 41 residues processed: 563 average time/residue: 0.3380 time to fit residues: 289.4729 Evaluate side-chains 508 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 466 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 120 CYS Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 292 VAL Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 66 GLU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 206 SER Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 89 MET Chi-restraints excluded: chain j residue 153 ARG Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 219 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 142 optimal weight: 0.8980 chunk 19 optimal weight: 30.0000 chunk 57 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 198 ASN b 30 ASN c 232 GLN e 99 HIS ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN h 26 ASN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.101332 restraints weight = 39270.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.103618 restraints weight = 19326.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.105201 restraints weight = 11752.904| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21409 Z= 0.225 Angle : 0.609 8.607 29223 Z= 0.315 Chirality : 0.046 0.239 3300 Planarity : 0.004 0.049 3804 Dihedral : 5.579 57.668 3000 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.76 % Allowed : 15.27 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2516 helix: -1.97 (0.31), residues: 233 sheet: 0.32 (0.20), residues: 659 loop : -0.18 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP j 80 HIS 0.005 0.001 HIS b 195 PHE 0.033 0.002 PHE j 239 TYR 0.036 0.002 TYR g 175 ARG 0.005 0.001 ARG j 12 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 561) hydrogen bonds : angle 5.49700 ( 1635) covalent geometry : bond 0.00528 (21409) covalent geometry : angle 0.60885 (29223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 474 time to evaluate : 2.299 Fit side-chains revert: symmetry clash REVERT: a 78 ARG cc_start: 0.8843 (mmt-90) cc_final: 0.6288 (mtm180) REVERT: a 97 LYS cc_start: 0.8969 (pttt) cc_final: 0.8475 (pptt) REVERT: a 154 TYR cc_start: 0.8664 (t80) cc_final: 0.8318 (t80) REVERT: a 209 ARG cc_start: 0.5431 (mmt-90) cc_final: 0.3539 (mtt90) REVERT: a 229 ILE cc_start: 0.8892 (pt) cc_final: 0.8192 (tp) REVERT: c 48 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8858 (mt-10) REVERT: c 55 MET cc_start: 0.9059 (tpp) cc_final: 0.8526 (tpp) REVERT: c 176 ARG cc_start: 0.8781 (mtt-85) cc_final: 0.8521 (mtt-85) REVERT: c 218 ASP cc_start: 0.9090 (p0) cc_final: 0.8645 (p0) REVERT: d 14 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6886 (tm-30) REVERT: d 32 TYR cc_start: 0.9151 (m-80) cc_final: 0.8691 (m-80) REVERT: d 36 SER cc_start: 0.7601 (p) cc_final: 0.7043 (t) REVERT: d 44 GLN cc_start: 0.7823 (tt0) cc_final: 0.7536 (tt0) REVERT: e 97 LYS cc_start: 0.8118 (pttm) cc_final: 0.7840 (tptt) REVERT: e 98 LYS cc_start: 0.8785 (mttt) cc_final: 0.8229 (tptt) REVERT: e 114 ARG cc_start: 0.8973 (ttp-170) cc_final: 0.8679 (ttp80) REVERT: e 135 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.5169 (tt0) REVERT: e 146 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7159 (mpt180) REVERT: e 154 TYR cc_start: 0.9073 (t80) cc_final: 0.8684 (t80) REVERT: e 188 ARG cc_start: 0.6445 (ptt180) cc_final: 0.5995 (ptt180) REVERT: f 13 VAL cc_start: 0.9240 (t) cc_final: 0.8793 (p) REVERT: f 33 VAL cc_start: 0.9266 (t) cc_final: 0.9056 (m) REVERT: f 223 LYS cc_start: 0.9292 (mttm) cc_final: 0.8988 (mttp) REVERT: g 10 SER cc_start: 0.9164 (t) cc_final: 0.8770 (p) REVERT: g 77 SER cc_start: 0.9053 (t) cc_final: 0.8616 (m) REVERT: g 123 MET cc_start: 0.8155 (tmm) cc_final: 0.7857 (tpp) REVERT: g 232 GLN cc_start: 0.8999 (tt0) cc_final: 0.6712 (pm20) REVERT: g 234 LYS cc_start: 0.7613 (mmtt) cc_final: 0.6852 (tttm) REVERT: i 32 ASN cc_start: 0.8527 (t0) cc_final: 0.8123 (t0) REVERT: i 78 ARG cc_start: 0.8481 (mmt-90) cc_final: 0.7304 (mtm180) REVERT: i 90 SER cc_start: 0.8952 (p) cc_final: 0.8588 (t) REVERT: i 146 ARG cc_start: 0.8484 (tpp-160) cc_final: 0.6790 (ptp-170) REVERT: i 205 ASP cc_start: 0.8097 (t0) cc_final: 0.7844 (t0) REVERT: i 264 TRP cc_start: 0.8190 (m100) cc_final: 0.7232 (m100) REVERT: j 44 ASP cc_start: 0.8467 (m-30) cc_final: 0.8209 (m-30) REVERT: j 89 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8249 (mtp) REVERT: k 75 ASN cc_start: 0.8285 (t0) cc_final: 0.7651 (m110) REVERT: k 206 SER cc_start: 0.8986 (t) cc_final: 0.8616 (p) REVERT: k 216 CYS cc_start: 0.9006 (m) cc_final: 0.8649 (m) REVERT: l 23 SER cc_start: 0.8903 (p) cc_final: 0.8656 (m) outliers start: 83 outliers final: 68 residues processed: 514 average time/residue: 0.3372 time to fit residues: 264.1194 Evaluate side-chains 538 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 468 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 178 ILE Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 112 CYS Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 68 SER Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 38 TRP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 111 GLN Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 183 SER Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 66 GLU Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 197 ILE Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 71 CYS Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 89 MET Chi-restraints excluded: chain j residue 217 VAL Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9406 > 50: distance: 87 - 109: 22.770 distance: 93 - 118: 30.732 distance: 99 - 105: 32.115 distance: 100 - 126: 32.388 distance: 105 - 106: 43.168 distance: 106 - 107: 24.570 distance: 107 - 108: 45.658 distance: 107 - 109: 27.329 distance: 108 - 134: 33.263 distance: 109 - 110: 17.219 distance: 110 - 111: 44.393 distance: 110 - 113: 13.800 distance: 111 - 112: 43.668 distance: 111 - 118: 45.316 distance: 113 - 114: 44.937 distance: 114 - 115: 47.270 distance: 115 - 116: 45.201 distance: 115 - 117: 34.917 distance: 118 - 119: 37.218 distance: 119 - 120: 40.575 distance: 119 - 122: 49.667 distance: 120 - 121: 33.418 distance: 120 - 126: 46.077 distance: 122 - 123: 7.410 distance: 122 - 124: 7.171 distance: 123 - 125: 34.950 distance: 126 - 127: 40.323 distance: 127 - 128: 49.615 distance: 127 - 130: 41.290 distance: 128 - 129: 66.876 distance: 128 - 134: 24.331 distance: 130 - 131: 46.483 distance: 131 - 132: 58.142 distance: 131 - 133: 59.092 distance: 134 - 135: 9.030 distance: 135 - 136: 21.589 distance: 135 - 138: 47.758 distance: 136 - 137: 44.503 distance: 136 - 142: 38.855 distance: 138 - 139: 37.156 distance: 139 - 140: 38.418 distance: 139 - 141: 53.468 distance: 142 - 143: 40.350 distance: 143 - 144: 50.485 distance: 143 - 146: 15.790 distance: 144 - 145: 39.687 distance: 144 - 154: 51.243 distance: 146 - 147: 13.517 distance: 147 - 148: 24.058 distance: 147 - 149: 15.877 distance: 148 - 150: 52.341 distance: 149 - 151: 22.919 distance: 150 - 152: 15.959 distance: 151 - 152: 10.597 distance: 152 - 153: 39.265 distance: 154 - 155: 27.327 distance: 155 - 156: 30.433 distance: 155 - 158: 40.504 distance: 156 - 157: 38.705 distance: 156 - 166: 44.847 distance: 158 - 159: 29.129 distance: 159 - 160: 26.411 distance: 159 - 161: 17.974 distance: 160 - 162: 22.336 distance: 161 - 163: 36.444 distance: 162 - 164: 16.092 distance: 163 - 164: 35.275 distance: 164 - 165: 11.402 distance: 166 - 167: 23.910 distance: 167 - 168: 40.463 distance: 167 - 170: 68.335 distance: 168 - 169: 56.013 distance: 168 - 173: 57.305 distance: 170 - 171: 5.853 distance: 170 - 172: 38.771 distance: 173 - 174: 23.547 distance: 174 - 175: 53.684 distance: 174 - 177: 54.772 distance: 175 - 176: 47.965 distance: 175 - 183: 57.698 distance: 177 - 178: 49.930 distance: 178 - 179: 56.227 distance: 178 - 180: 40.860 distance: 179 - 181: 40.530 distance: 180 - 182: 39.723 distance: 181 - 182: 38.917 distance: 183 - 184: 38.094 distance: 183 - 227: 32.728 distance: 184 - 185: 58.824 distance: 184 - 187: 55.721 distance: 185 - 186: 43.614 distance: 185 - 197: 27.762 distance: 186 - 224: 31.733 distance: 187 - 188: 40.816 distance: 188 - 189: 17.551 distance: 188 - 190: 32.557 distance: 189 - 191: 34.158 distance: 190 - 192: 45.533 distance: 190 - 193: 25.928 distance: 191 - 192: 52.523 distance: 192 - 194: 42.905 distance: 194 - 196: 22.244