Starting phenix.real_space_refine on Sun Aug 24 20:19:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0k_39706/08_2025/8z0k_39706_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0k_39706/08_2025/8z0k_39706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z0k_39706/08_2025/8z0k_39706_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0k_39706/08_2025/8z0k_39706_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z0k_39706/08_2025/8z0k_39706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0k_39706/08_2025/8z0k_39706.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.038 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: 5 Type Number sf(0) Gaussians P 102 5.49 5 S 111 5.16 5 C 14306 2.51 5 N 3852 2.21 5 O 4666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23037 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2620 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 309} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2588 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 308} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2580 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "E" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1979 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 246} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2458 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'GLN:plan1': 2, 'HIS:plan': 2, 'ASP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 110 Chain: "G" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2597 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "H" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2346 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 750 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "J" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 148 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "L" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1249 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 11, 'rna3p_pur': 21, 'rna3p_pyr': 13} Link IDs: {'rna2p': 24, 'rna3p': 33} Chain breaks: 1 Chain: "M" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1109 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 3 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 4, 'HIS:plan': 4, 'GLU:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 5.82, per 1000 atoms: 0.25 Number of scatterers: 23037 At special positions: 0 Unit cell: (106.5, 150, 164.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 102 15.00 O 4666 8.00 N 3852 7.00 C 14306 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: 2.00 Conformation dependent library (CDL) restraints added in 993.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5038 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 34 sheets defined 30.6% alpha, 9.6% beta 29 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.700A pdb=" N ARG A 40 " --> pdb=" O PHE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.610A pdb=" N GLU A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.812A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.763A pdb=" N ALA A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.657A pdb=" N GLN A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.656A pdb=" N ILE A 254 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'B' and resid 63 through 70 removed outlier: 3.641A pdb=" N GLU B 68 " --> pdb=" O PRO B 64 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.626A pdb=" N ARG B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.671A pdb=" N ALA B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.726A pdb=" N GLN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 removed outlier: 3.609A pdb=" N ILE B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.642A pdb=" N ARG C 40 " --> pdb=" O PHE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.771A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.697A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.695A pdb=" N GLN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.626A pdb=" N ILE C 254 " --> pdb=" O HIS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.691A pdb=" N ARG D 40 " --> pdb=" O PHE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.656A pdb=" N GLU D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.630A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.640A pdb=" N ALA D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.719A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 removed outlier: 3.559A pdb=" N ILE D 254 " --> pdb=" O HIS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 305 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 27 through 43 removed outlier: 3.951A pdb=" N PHE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 128 Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.591A pdb=" N ASP E 152 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE E 153 " --> pdb=" O LEU E 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 149 through 153' Processing helix chain 'E' and resid 163 through 168 Processing helix chain 'E' and resid 173 through 185 removed outlier: 3.636A pdb=" N GLU E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 239 removed outlier: 3.748A pdb=" N LEU E 239 " --> pdb=" O ASN E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 17 through 29 removed outlier: 3.727A pdb=" N ILE F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 93 removed outlier: 3.895A pdb=" N GLY F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 110 removed outlier: 3.634A pdb=" N GLU F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 122 removed outlier: 3.641A pdb=" N GLU F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU F 120 " --> pdb=" O HIS F 116 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 134 Processing helix chain 'F' and resid 166 through 178 removed outlier: 3.802A pdb=" N ASN F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 199 removed outlier: 3.871A pdb=" N GLY F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 217 through 221 removed outlier: 3.926A pdb=" N GLU F 221 " --> pdb=" O LYS F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 254 No H-bonds generated for 'chain 'F' and resid 252 through 254' Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 282 through 293 removed outlier: 3.712A pdb=" N LYS F 291 " --> pdb=" O ALA F 287 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 335 removed outlier: 3.714A pdb=" N ARG F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 40 removed outlier: 4.031A pdb=" N ARG G 40 " --> pdb=" O PHE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 71 removed outlier: 3.677A pdb=" N LYS G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.525A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 145 removed outlier: 3.726A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 145 " --> pdb=" O ASN G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.703A pdb=" N GLN G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.574A pdb=" N ILE G 254 " --> pdb=" O HIS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 312 through 326 Processing helix chain 'H' and resid 39 through 43 removed outlier: 3.609A pdb=" N PHE H 43 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.531A pdb=" N ARG H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.594A pdb=" N ALA H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 removed outlier: 3.715A pdb=" N GLN H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.627A pdb=" N ILE H 254 " --> pdb=" O HIS H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 302 Processing helix chain 'H' and resid 312 through 326 Processing helix chain 'M' and resid 15 through 23 removed outlier: 3.581A pdb=" N ASP M 23 " --> pdb=" O ILE M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 36 removed outlier: 3.835A pdb=" N VAL M 27 " --> pdb=" O ASP M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 69 Processing helix chain 'M' and resid 131 through 135 Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 109 removed outlier: 3.913A pdb=" N SER A 108 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 327 " --> pdb=" O PHE A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 45 through 46 current: chain 'A' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 167 through 168 current: chain 'A' and resid 246 through 249 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 57 Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 21 removed outlier: 3.646A pdb=" N SER B 108 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 45 through 46 current: chain 'B' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 167 through 168 current: chain 'B' and resid 246 through 249 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 57 Processing sheet with id=AA7, first strand: chain 'C' and resid 106 through 109 removed outlier: 3.886A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 168 current: chain 'C' and resid 246 through 249 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 57 Processing sheet with id=AB1, first strand: chain 'C' and resid 260 through 262 Processing sheet with id=AB2, first strand: chain 'D' and resid 106 through 109 removed outlier: 6.479A pdb=" N SER D 20 " --> pdb=" O TYR D 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 167 through 168 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 57 Processing sheet with id=AB5, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AB7, first strand: chain 'E' and resid 2 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 2 through 16 current: chain 'E' and resid 100 through 112 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 100 through 112 current: chain 'E' and resid 213 through 228 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 213 through 228 current: chain 'E' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 248 through 252 current: chain 'F' and resid 157 through 163 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AB9, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AC1, first strand: chain 'F' and resid 35 through 37 removed outlier: 3.610A pdb=" N ASP F 78 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AC3, first strand: chain 'F' and resid 245 through 246 Processing sheet with id=AC4, first strand: chain 'F' and resid 301 through 304 Processing sheet with id=AC5, first strand: chain 'G' and resid 19 through 21 removed outlier: 3.710A pdb=" N SER G 108 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 46 current: chain 'G' and resid 167 through 168 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 50 through 57 Processing sheet with id=AC8, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AC9, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.950A pdb=" N ALA G 283 " --> pdb=" O ILE G 288 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE G 288 " --> pdb=" O ALA G 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 106 through 109 removed outlier: 3.766A pdb=" N SER H 108 " --> pdb=" O SER H 20 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 46 current: chain 'H' and resid 167 through 172 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AD4, first strand: chain 'H' and resid 282 through 283 removed outlier: 4.207A pdb=" N ALA H 283 " --> pdb=" O ILE H 288 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE H 288 " --> pdb=" O ALA H 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'M' and resid 40 through 42 removed outlier: 3.687A pdb=" N GLY M 40 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN M 4 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 98 through 100 Processing sheet with id=AD7, first strand: chain 'M' and resid 144 through 146 562 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5126 1.33 - 1.46: 6470 1.46 - 1.58: 11765 1.58 - 1.71: 197 1.71 - 1.84: 176 Bond restraints: 23734 Sorted by residual: bond pdb=" C THR H 199 " pdb=" N PHE H 200 " ideal model delta sigma weight residual 1.335 1.232 0.103 1.36e-02 5.41e+03 5.76e+01 bond pdb=" C VAL D 139 " pdb=" N ASN D 140 " ideal model delta sigma weight residual 1.334 1.229 0.106 1.43e-02 4.89e+03 5.47e+01 bond pdb=" C THR C 42 " pdb=" N PHE C 43 " ideal model delta sigma weight residual 1.330 1.431 -0.101 1.45e-02 4.76e+03 4.83e+01 bond pdb=" CA ASP C 293 " pdb=" C ASP C 293 " ideal model delta sigma weight residual 1.523 1.456 0.068 1.34e-02 5.57e+03 2.55e+01 bond pdb=" CA ASP G 293 " pdb=" C ASP G 293 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.34e-02 5.57e+03 2.48e+01 ... (remaining 23729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 31587 2.78 - 5.55: 864 5.55 - 8.33: 122 8.33 - 11.10: 26 11.10 - 13.88: 6 Bond angle restraints: 32605 Sorted by residual: angle pdb=" N GLU M 66 " pdb=" CA GLU M 66 " pdb=" C GLU M 66 " ideal model delta sigma weight residual 112.87 99.66 13.21 1.20e+00 6.94e-01 1.21e+02 angle pdb=" N THR M 162 " pdb=" CA THR M 162 " pdb=" C THR M 162 " ideal model delta sigma weight residual 108.96 122.84 -13.88 1.49e+00 4.50e-01 8.67e+01 angle pdb=" N LEU F 2 " pdb=" CA LEU F 2 " pdb=" C LEU F 2 " ideal model delta sigma weight residual 112.59 102.62 9.97 1.22e+00 6.72e-01 6.67e+01 angle pdb=" N SER M 3 " pdb=" CA SER M 3 " pdb=" C SER M 3 " ideal model delta sigma weight residual 108.14 119.45 -11.31 1.52e+00 4.33e-01 5.53e+01 angle pdb=" N ALA M 69 " pdb=" CA ALA M 69 " pdb=" C ALA M 69 " ideal model delta sigma weight residual 112.87 104.06 8.81 1.20e+00 6.94e-01 5.39e+01 ... (remaining 32600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 13655 35.90 - 71.79: 582 71.79 - 107.69: 34 107.69 - 143.58: 1 143.58 - 179.48: 8 Dihedral angle restraints: 14280 sinusoidal: 6493 harmonic: 7787 Sorted by residual: dihedral pdb=" O4' C L 34 " pdb=" C1' C L 34 " pdb=" N1 C L 34 " pdb=" C2 C L 34 " ideal model delta sinusoidal sigma weight residual 232.00 52.52 179.48 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C L 52 " pdb=" C1' C L 52 " pdb=" N1 C L 52 " pdb=" C2 C L 52 " ideal model delta sinusoidal sigma weight residual -128.00 50.36 -178.36 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ILE H 286 " pdb=" C ILE H 286 " pdb=" N GLY H 287 " pdb=" CA GLY H 287 " ideal model delta harmonic sigma weight residual 180.00 146.90 33.10 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 14277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2931 0.069 - 0.137: 614 0.137 - 0.206: 115 0.206 - 0.275: 12 0.275 - 0.343: 2 Chirality restraints: 3674 Sorted by residual: chirality pdb=" CB ILE E 231 " pdb=" CA ILE E 231 " pdb=" CG1 ILE E 231 " pdb=" CG2 ILE E 231 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA SER M 47 " pdb=" N SER M 47 " pdb=" C SER M 47 " pdb=" CB SER M 47 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE E 21 " pdb=" CA ILE E 21 " pdb=" CG1 ILE E 21 " pdb=" CG2 ILE E 21 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3671 not shown) Planarity restraints: 3838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE M 25 " 0.078 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO M 26 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO M 26 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO M 26 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 291 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO H 292 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO H 292 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 292 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 132 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C ILE F 132 " -0.069 2.00e-02 2.50e+03 pdb=" O ILE F 132 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU F 133 " 0.023 2.00e-02 2.50e+03 ... (remaining 3835 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 38 2.44 - 3.05: 13140 3.05 - 3.67: 31994 3.67 - 4.28: 50268 4.28 - 4.90: 83957 Nonbonded interactions: 179397 Sorted by model distance: nonbonded pdb=" O ASP M 64 " pdb=" CB ALA M 67 " model vdw 1.824 3.460 nonbonded pdb=" OH TYR G 265 " pdb=" O PHE G 273 " model vdw 2.264 3.040 nonbonded pdb=" N ASP M 64 " pdb=" CB ALA M 67 " model vdw 2.265 3.540 nonbonded pdb=" N GLU M 66 " pdb=" N ALA M 67 " model vdw 2.294 2.560 nonbonded pdb=" O SER E 123 " pdb=" OG1 THR E 127 " model vdw 2.300 3.040 ... (remaining 179392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 37 or (resid 38 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 51 or resid 79 through \ 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) or re \ sid 168 through 174 or (resid 175 and (name N or name CA or name C or name O or \ name CB )) or resid 176 through 231 or (resid 236 through 239 and (name N or nam \ e CA or name C or name O or name CB )) or resid 240 through 283 or (resid 284 an \ d (name N or name CA or name C or name O or name CB )) or resid 285 through 287 \ or (resid 288 and (name N or name CA or name C or name O or name CB )) or resid \ 289 through 330 or (resid 331 and (name N or name CA or name C or name O or name \ CB )) or resid 332 through 333)) selection = (chain 'B' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 37 or (resid 38 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 51 or resid 79 through 166 or (re \ sid 167 and (name N or name CA or name C or name O or name CB )) or resid 168 th \ rough 174 or (resid 175 and (name N or name CA or name C or name O or name CB )) \ or resid 176 through 231 or (resid 236 and (name N or name CA or name C or name \ O or name CB )) or resid 237 or (resid 238 through 239 and (name N or name CA o \ r name C or name O or name CB )) or resid 240 through 283 or (resid 284 and (nam \ e N or name CA or name C or name O or name CB )) or resid 285 through 287 or (re \ sid 288 and (name N or name CA or name C or name O or name CB )) or resid 289 th \ rough 330 or (resid 331 and (name N or name CA or name C or name O or name CB )) \ or resid 332 through 333)) selection = (chain 'C' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 37 or (resid 38 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 51 or resid 79 through 166 or (re \ sid 167 and (name N or name CA or name C or name O or name CB )) or resid 168 th \ rough 174 or (resid 175 and (name N or name CA or name C or name O or name CB )) \ or resid 176 through 231 or (resid 236 through 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 283 or (resid 284 and (name N \ or name CA or name C or name O or name CB )) or resid 285 through 287 or (resid \ 288 and (name N or name CA or name C or name O or name CB )) or resid 289 throug \ h 330 or (resid 331 and (name N or name CA or name C or name O or name CB )) or \ resid 332 through 333)) selection = (chain 'D' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 37 or (resid 38 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 51 or resid 79 through 166 or (re \ sid 167 and (name N or name CA or name C or name O or name CB )) or resid 168 th \ rough 174 or (resid 175 and (name N or name CA or name C or name O or name CB )) \ or resid 176 through 237 or (resid 238 through 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 283 or (resid 284 and (name N \ or name CA or name C or name O or name CB )) or resid 285 through 287 or (resid \ 288 and (name N or name CA or name C or name O or name CB )) or resid 289 throug \ h 330 or (resid 331 and (name N or name CA or name C or name O or name CB )) or \ resid 332 through 333)) selection = (chain 'G' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 37 or (resid 38 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 51 or resid 79 through 166 or (re \ sid 167 and (name N or name CA or name C or name O or name CB )) or resid 168 th \ rough 174 or (resid 175 and (name N or name CA or name C or name O or name CB )) \ or resid 176 through 231 or (resid 236 through 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 283 or (resid 284 and (name N \ or name CA or name C or name O or name CB )) or resid 285 through 287 or (resid \ 288 and (name N or name CA or name C or name O or name CB )) or resid 289 throug \ h 330 or (resid 331 and (name N or name CA or name C or name O or name CB )) or \ resid 332 through 333)) selection = (chain 'H' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 238 or (resid 239 and (name N or name CA or name C or nam \ e O or name CB )) or resid 240 through 333)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.060 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.007 0.106 23734 Z= 0.431 Angle : 1.100 13.877 32605 Z= 0.656 Chirality : 0.059 0.343 3674 Planarity : 0.009 0.115 3838 Dihedral : 18.237 179.478 9242 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.53 % Favored : 93.78 % Rotamer: Outliers : 1.52 % Allowed : 15.46 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.14), residues: 2606 helix: -1.67 (0.15), residues: 702 sheet: 0.67 (0.24), residues: 447 loop : -2.62 (0.12), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 115 TYR 0.037 0.003 TYR B 138 PHE 0.034 0.002 PHE D 273 TRP 0.025 0.002 TRP F 74 HIS 0.019 0.002 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00700 (23734) covalent geometry : angle 1.09972 (32605) hydrogen bonds : bond 0.21842 ( 634) hydrogen bonds : angle 7.92055 ( 1737) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 709 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 PHE cc_start: 0.8881 (t80) cc_final: 0.8671 (t80) REVERT: A 243 PHE cc_start: 0.8236 (t80) cc_final: 0.7926 (t80) REVERT: A 262 ASP cc_start: 0.8781 (t0) cc_final: 0.8519 (t0) REVERT: B 228 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7761 (mm-30) REVERT: B 262 ASP cc_start: 0.8597 (t0) cc_final: 0.8320 (t0) REVERT: C 167 LYS cc_start: 0.8590 (tttt) cc_final: 0.8376 (tttm) REVERT: D 78 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8281 (mtmm) REVERT: D 166 ASP cc_start: 0.7426 (t0) cc_final: 0.6955 (t0) REVERT: E 234 ASP cc_start: 0.7629 (t0) cc_final: 0.7423 (t0) REVERT: F 56 ASP cc_start: 0.7717 (t0) cc_final: 0.7395 (t0) REVERT: F 95 MET cc_start: 0.6834 (mtm) cc_final: 0.6630 (mtm) REVERT: G 166 ASP cc_start: 0.7512 (t0) cc_final: 0.7277 (t0) REVERT: G 249 MET cc_start: 0.8908 (mtm) cc_final: 0.8645 (mtt) REVERT: G 267 ASP cc_start: 0.7657 (t0) cc_final: 0.7336 (t0) REVERT: G 302 ASP cc_start: 0.8222 (m-30) cc_final: 0.8010 (m-30) REVERT: H 163 THR cc_start: 0.8402 (m) cc_final: 0.8148 (m) REVERT: H 244 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7795 (mt-10) REVERT: M 29 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.6532 (t-90) outliers start: 34 outliers final: 11 residues processed: 724 average time/residue: 0.6990 time to fit residues: 573.9749 Evaluate side-chains 654 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 642 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 204 ARG Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain M residue 29 HIS Chi-restraints excluded: chain M residue 36 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 250 HIS A 256 ASN A 279 ASN A 317 HIS A 333 GLN D 18 ASN D 140 ASN E 52 ASN E 104 ASN E 165 ASN E 203 HIS E 236 ASN F 34 ASN F 35 HIS F 63 ASN F 144 ASN F 149 GLN F 170 ASN F 193 ASN G 26 ASN G 140 ASN G 151 ASN G 317 HIS H 18 ASN H 26 ASN H 151 ASN H 178 ASN H 208 ASN H 279 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.118799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.101744 restraints weight = 32725.844| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.53 r_work: 0.3356 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23734 Z= 0.229 Angle : 0.659 7.268 32605 Z= 0.357 Chirality : 0.045 0.258 3674 Planarity : 0.006 0.079 3838 Dihedral : 19.072 179.029 4273 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.60 % Favored : 95.28 % Rotamer: Outliers : 3.99 % Allowed : 16.09 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.15), residues: 2606 helix: -0.19 (0.18), residues: 744 sheet: 0.68 (0.24), residues: 478 loop : -2.43 (0.13), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 115 TYR 0.017 0.002 TYR A 265 PHE 0.014 0.002 PHE A 172 TRP 0.014 0.002 TRP C 33 HIS 0.005 0.002 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00546 (23734) covalent geometry : angle 0.65943 (32605) hydrogen bonds : bond 0.06594 ( 634) hydrogen bonds : angle 5.27867 ( 1737) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 616 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8372 (t80) cc_final: 0.8049 (t80) REVERT: B 204 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8075 (ttm170) REVERT: B 229 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7381 (tpp) REVERT: D 303 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8438 (ttp80) REVERT: E 160 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8435 (p) REVERT: F 62 MET cc_start: 0.8350 (mmm) cc_final: 0.8092 (mpp) REVERT: F 85 LYS cc_start: 0.8620 (mttp) cc_final: 0.8350 (mtmp) REVERT: F 127 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7198 (mt-10) REVERT: F 230 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8442 (mtpp) REVERT: G 70 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7494 (tt0) REVERT: G 166 ASP cc_start: 0.7700 (t0) cc_final: 0.7477 (t0) REVERT: G 206 TYR cc_start: 0.8466 (p90) cc_final: 0.8208 (p90) REVERT: G 252 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: H 119 TYR cc_start: 0.8514 (m-10) cc_final: 0.8271 (m-10) REVERT: H 244 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8112 (mt-10) REVERT: H 315 ASP cc_start: 0.7283 (m-30) cc_final: 0.7073 (t0) REVERT: M 103 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7784 (mmm160) outliers start: 89 outliers final: 40 residues processed: 655 average time/residue: 0.7279 time to fit residues: 538.4133 Evaluate side-chains 655 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 610 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 230 LYS Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain H residue 26 ASN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain M residue 36 ASP Chi-restraints excluded: chain M residue 151 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 259 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 252 GLN A 279 ASN A 308 ASN C 80 GLN C 178 ASN D 18 ASN D 308 ASN E 52 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN E 183 GLN E 236 ASN G 26 ASN G 186 ASN H 18 ASN H 26 ASN H 34 GLN H 178 ASN H 279 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100181 restraints weight = 32826.326| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.53 r_work: 0.3331 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 23734 Z= 0.245 Angle : 0.631 7.223 32605 Z= 0.340 Chirality : 0.045 0.257 3674 Planarity : 0.006 0.069 3838 Dihedral : 18.803 179.052 4257 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.49 % Favored : 95.40 % Rotamer: Outliers : 3.99 % Allowed : 16.90 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.15), residues: 2606 helix: 0.53 (0.19), residues: 739 sheet: 0.75 (0.24), residues: 480 loop : -2.33 (0.13), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 115 TYR 0.026 0.002 TYR M 46 PHE 0.016 0.002 PHE G 43 TRP 0.015 0.002 TRP C 33 HIS 0.005 0.001 HIS E 59 Details of bonding type rmsd covalent geometry : bond 0.00590 (23734) covalent geometry : angle 0.63084 (32605) hydrogen bonds : bond 0.06389 ( 634) hydrogen bonds : angle 4.93051 ( 1737) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 607 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8461 (t80) cc_final: 0.8081 (t80) REVERT: B 204 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8068 (ttm170) REVERT: C 229 MET cc_start: 0.8653 (tpp) cc_final: 0.7828 (ttp) REVERT: D 303 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8547 (ttp80) REVERT: E 2 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8113 (mtpp) REVERT: E 160 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8465 (p) REVERT: F 20 ILE cc_start: 0.8656 (mt) cc_final: 0.8437 (mp) REVERT: F 62 MET cc_start: 0.8396 (mmm) cc_final: 0.8145 (mpp) REVERT: F 83 ASP cc_start: 0.7838 (t0) cc_final: 0.7536 (t0) REVERT: F 85 LYS cc_start: 0.8652 (mttp) cc_final: 0.8339 (mtmp) REVERT: F 320 MET cc_start: 0.6343 (mtm) cc_final: 0.6034 (mtm) REVERT: G 70 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7496 (tt0) REVERT: G 166 ASP cc_start: 0.7784 (t0) cc_final: 0.7577 (t0) REVERT: H 157 ILE cc_start: 0.8444 (mt) cc_final: 0.8173 (tt) REVERT: H 244 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7965 (mm-30) outliers start: 89 outliers final: 46 residues processed: 648 average time/residue: 0.7531 time to fit residues: 549.4054 Evaluate side-chains 639 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 591 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 151 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 252 GLN A 308 ASN B 80 GLN B 178 ASN C 18 ASN C 80 GLN D 18 ASN D 140 ASN D 308 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN G 252 GLN H 34 GLN H 178 ASN H 279 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.117180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099997 restraints weight = 32963.997| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.53 r_work: 0.3330 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23734 Z= 0.224 Angle : 0.603 7.530 32605 Z= 0.324 Chirality : 0.044 0.249 3674 Planarity : 0.005 0.065 3838 Dihedral : 18.613 178.706 4255 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 3.90 % Allowed : 17.53 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.15), residues: 2606 helix: 0.89 (0.19), residues: 745 sheet: 0.80 (0.24), residues: 486 loop : -2.24 (0.13), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 115 TYR 0.020 0.002 TYR M 46 PHE 0.025 0.002 PHE C 273 TRP 0.015 0.002 TRP C 33 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00540 (23734) covalent geometry : angle 0.60324 (32605) hydrogen bonds : bond 0.05789 ( 634) hydrogen bonds : angle 4.73946 ( 1737) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 587 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8504 (t80) cc_final: 0.8181 (t80) REVERT: B 204 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8112 (ttm170) REVERT: B 229 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7273 (tpp) REVERT: C 229 MET cc_start: 0.8642 (tpp) cc_final: 0.7811 (ttp) REVERT: D 303 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8466 (ttp80) REVERT: E 160 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8472 (p) REVERT: F 20 ILE cc_start: 0.8550 (mt) cc_final: 0.8330 (mp) REVERT: F 62 MET cc_start: 0.8422 (mmm) cc_final: 0.8185 (mpp) REVERT: F 83 ASP cc_start: 0.7850 (t0) cc_final: 0.7554 (t0) REVERT: F 85 LYS cc_start: 0.8687 (mttp) cc_final: 0.8339 (mtmp) REVERT: F 320 MET cc_start: 0.6327 (mtm) cc_final: 0.5981 (mtm) REVERT: G 70 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7505 (tt0) REVERT: G 166 ASP cc_start: 0.7783 (t0) cc_final: 0.7567 (t0) REVERT: H 157 ILE cc_start: 0.8431 (mt) cc_final: 0.8167 (tt) REVERT: H 244 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7811 (mt-10) REVERT: H 315 ASP cc_start: 0.7339 (m-30) cc_final: 0.7115 (t0) outliers start: 87 outliers final: 58 residues processed: 623 average time/residue: 0.7640 time to fit residues: 535.6159 Evaluate side-chains 643 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 582 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 174 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 221 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 260 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 239 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 308 ASN B 178 ASN C 80 GLN C 178 ASN D 18 ASN D 308 ASN E 94 HIS E 165 ASN G 140 ASN H 34 GLN H 178 ASN H 279 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.118278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.101105 restraints weight = 32739.797| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.52 r_work: 0.3347 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23734 Z= 0.160 Angle : 0.558 7.247 32605 Z= 0.299 Chirality : 0.042 0.229 3674 Planarity : 0.005 0.067 3838 Dihedral : 18.512 178.870 4255 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 3.59 % Allowed : 18.65 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.16), residues: 2606 helix: 1.18 (0.19), residues: 744 sheet: 0.73 (0.23), residues: 510 loop : -2.13 (0.14), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 115 TYR 0.016 0.001 TYR M 46 PHE 0.024 0.001 PHE C 273 TRP 0.012 0.001 TRP C 33 HIS 0.006 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00377 (23734) covalent geometry : angle 0.55752 (32605) hydrogen bonds : bond 0.04922 ( 634) hydrogen bonds : angle 4.53629 ( 1737) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 590 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8497 (t80) cc_final: 0.8160 (t80) REVERT: B 229 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7255 (tpp) REVERT: C 229 MET cc_start: 0.8599 (tpp) cc_final: 0.7723 (ttp) REVERT: D 303 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8421 (ttp80) REVERT: E 160 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8441 (p) REVERT: F 20 ILE cc_start: 0.8503 (mt) cc_final: 0.8283 (mp) REVERT: F 62 MET cc_start: 0.8400 (mmm) cc_final: 0.8153 (mpp) REVERT: F 83 ASP cc_start: 0.7850 (t0) cc_final: 0.7582 (t0) REVERT: F 85 LYS cc_start: 0.8688 (mttp) cc_final: 0.8361 (mtmp) REVERT: F 205 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8548 (ttmm) REVERT: F 320 MET cc_start: 0.6300 (mtm) cc_final: 0.5676 (mtm) REVERT: G 70 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7486 (tt0) REVERT: G 166 ASP cc_start: 0.7770 (t0) cc_final: 0.7555 (t0) REVERT: H 157 ILE cc_start: 0.8412 (mt) cc_final: 0.8161 (tt) REVERT: H 229 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8529 (tpt) REVERT: H 244 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7745 (mt-10) REVERT: H 315 ASP cc_start: 0.7255 (m-30) cc_final: 0.7034 (t0) outliers start: 80 outliers final: 62 residues processed: 624 average time/residue: 0.7521 time to fit residues: 528.8441 Evaluate side-chains 658 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 593 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain H residue 26 ASN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 174 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 308 ASN B 80 GLN B 178 ASN C 18 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN C 178 ASN D 18 ASN D 140 ASN D 308 ASN E 165 ASN H 178 ASN H 279 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.118202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101064 restraints weight = 33055.830| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.52 r_work: 0.3348 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23734 Z= 0.159 Angle : 0.551 7.525 32605 Z= 0.295 Chirality : 0.042 0.226 3674 Planarity : 0.005 0.068 3838 Dihedral : 18.453 178.994 4255 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 3.94 % Allowed : 18.65 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.16), residues: 2606 helix: 1.33 (0.20), residues: 744 sheet: 0.79 (0.23), residues: 514 loop : -2.08 (0.14), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 115 TYR 0.014 0.001 TYR G 206 PHE 0.023 0.001 PHE C 273 TRP 0.011 0.001 TRP C 33 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00379 (23734) covalent geometry : angle 0.55084 (32605) hydrogen bonds : bond 0.04823 ( 634) hydrogen bonds : angle 4.43909 ( 1737) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 601 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8459 (p0) cc_final: 0.8252 (p0) REVERT: A 243 PHE cc_start: 0.8510 (t80) cc_final: 0.8163 (t80) REVERT: B 229 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7255 (tpp) REVERT: C 229 MET cc_start: 0.8612 (tpp) cc_final: 0.7737 (ttp) REVERT: D 303 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8291 (ttp80) REVERT: D 309 GLU cc_start: 0.7756 (tt0) cc_final: 0.7286 (tt0) REVERT: E 128 MET cc_start: 0.8500 (ttp) cc_final: 0.8274 (ttp) REVERT: E 160 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8445 (p) REVERT: F 2 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7662 (tp) REVERT: F 20 ILE cc_start: 0.8484 (mt) cc_final: 0.8260 (mp) REVERT: F 62 MET cc_start: 0.8395 (mmm) cc_final: 0.8157 (mpp) REVERT: F 83 ASP cc_start: 0.7867 (t0) cc_final: 0.7482 (t0) REVERT: F 85 LYS cc_start: 0.8704 (mttp) cc_final: 0.8253 (mtmp) REVERT: F 205 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8540 (ttmm) REVERT: F 320 MET cc_start: 0.6278 (mtm) cc_final: 0.5738 (mtm) REVERT: G 70 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7478 (tt0) REVERT: G 166 ASP cc_start: 0.7758 (t0) cc_final: 0.7538 (t0) REVERT: G 206 TYR cc_start: 0.8084 (p90) cc_final: 0.7751 (p90) REVERT: H 157 ILE cc_start: 0.8425 (mt) cc_final: 0.8182 (tt) REVERT: H 229 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8521 (tpt) REVERT: H 244 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7678 (tt0) REVERT: H 315 ASP cc_start: 0.7273 (m-30) cc_final: 0.7064 (t0) REVERT: M 103 ARG cc_start: 0.8149 (mmm160) cc_final: 0.7820 (mmm160) outliers start: 88 outliers final: 70 residues processed: 638 average time/residue: 0.7380 time to fit residues: 530.4303 Evaluate side-chains 663 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 589 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 174 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 0.0050 chunk 205 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 265 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 140 ASN A 308 ASN B 178 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN D 18 ASN D 140 ASN D 308 ASN E 165 ASN E 207 GLN E 236 ASN G 140 ASN H 18 ASN H 178 ASN H 279 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.116619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099496 restraints weight = 32992.625| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.52 r_work: 0.3321 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 23734 Z= 0.249 Angle : 0.602 7.798 32605 Z= 0.321 Chirality : 0.045 0.253 3674 Planarity : 0.005 0.069 3838 Dihedral : 18.440 178.696 4255 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 3.90 % Allowed : 18.92 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.16), residues: 2606 helix: 1.26 (0.19), residues: 744 sheet: 0.80 (0.23), residues: 499 loop : -2.10 (0.14), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 115 TYR 0.021 0.002 TYR G 271 PHE 0.027 0.002 PHE G 273 TRP 0.016 0.002 TRP C 33 HIS 0.005 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00606 (23734) covalent geometry : angle 0.60204 (32605) hydrogen bonds : bond 0.06001 ( 634) hydrogen bonds : angle 4.62533 ( 1737) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 592 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 229 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.7341 (tpp) REVERT: C 229 MET cc_start: 0.8633 (tpp) cc_final: 0.7773 (ttp) REVERT: D 303 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8561 (ttp80) REVERT: E 128 MET cc_start: 0.8514 (ttp) cc_final: 0.8256 (ttp) REVERT: E 160 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8484 (p) REVERT: F 20 ILE cc_start: 0.8513 (mt) cc_final: 0.8291 (mp) REVERT: F 62 MET cc_start: 0.8395 (mmm) cc_final: 0.8156 (mpp) REVERT: F 85 LYS cc_start: 0.8737 (mttp) cc_final: 0.8315 (mtmp) REVERT: F 205 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8569 (ttmm) REVERT: F 320 MET cc_start: 0.6294 (mtm) cc_final: 0.5832 (mtm) REVERT: G 70 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7535 (tt0) REVERT: H 157 ILE cc_start: 0.8462 (mt) cc_final: 0.8229 (tt) REVERT: H 229 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8536 (tpt) REVERT: H 244 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7777 (mt-10) outliers start: 87 outliers final: 67 residues processed: 632 average time/residue: 0.7432 time to fit residues: 528.8721 Evaluate side-chains 656 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 586 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 174 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 92 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 204 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 176 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 308 ASN B 80 GLN B 178 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN D 18 ASN D 308 ASN E 165 ASN G 140 ASN H 18 ASN H 34 GLN H 178 ASN H 279 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.118547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.101368 restraints weight = 32697.131| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.52 r_work: 0.3353 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23734 Z= 0.135 Angle : 0.549 8.080 32605 Z= 0.294 Chirality : 0.042 0.219 3674 Planarity : 0.005 0.072 3838 Dihedral : 18.419 178.733 4255 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 3.14 % Allowed : 19.99 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.16), residues: 2606 helix: 1.44 (0.20), residues: 745 sheet: 0.81 (0.23), residues: 510 loop : -2.00 (0.14), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 115 TYR 0.016 0.001 TYR H 265 PHE 0.023 0.001 PHE G 273 TRP 0.011 0.001 TRP C 33 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00313 (23734) covalent geometry : angle 0.54938 (32605) hydrogen bonds : bond 0.04579 ( 634) hydrogen bonds : angle 4.37751 ( 1737) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 588 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8462 (p0) cc_final: 0.8250 (p0) REVERT: B 204 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8158 (ttm170) REVERT: B 229 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7230 (tpp) REVERT: C 229 MET cc_start: 0.8604 (tpp) cc_final: 0.7745 (ttp) REVERT: D 303 ARG cc_start: 0.8773 (ttp80) cc_final: 0.8526 (ttp80) REVERT: E 128 MET cc_start: 0.8499 (ttp) cc_final: 0.8245 (ttp) REVERT: E 160 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8425 (p) REVERT: F 20 ILE cc_start: 0.8469 (mt) cc_final: 0.8249 (mp) REVERT: F 62 MET cc_start: 0.8376 (mmm) cc_final: 0.8130 (mpp) REVERT: F 85 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8320 (mtmp) REVERT: F 205 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8554 (ttmm) REVERT: F 320 MET cc_start: 0.6248 (mtm) cc_final: 0.5731 (mtm) REVERT: G 70 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7511 (tt0) REVERT: H 157 ILE cc_start: 0.8421 (mt) cc_final: 0.8201 (tt) REVERT: H 229 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8523 (tpt) REVERT: H 244 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7681 (tt0) REVERT: M 103 ARG cc_start: 0.8129 (mmm160) cc_final: 0.7785 (mmm160) outliers start: 70 outliers final: 52 residues processed: 618 average time/residue: 0.7056 time to fit residues: 492.2520 Evaluate side-chains 637 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 580 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain H residue 310 ASP Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 174 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 175 optimal weight: 10.0000 chunk 264 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 140 ASN B 178 ASN C 80 GLN D 18 ASN D 308 ASN E 165 ASN F 51 ASN H 279 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.118411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101218 restraints weight = 33011.928| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.53 r_work: 0.3350 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23734 Z= 0.154 Angle : 0.549 8.186 32605 Z= 0.293 Chirality : 0.042 0.222 3674 Planarity : 0.005 0.066 3838 Dihedral : 18.370 178.952 4255 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.30 % Favored : 95.66 % Rotamer: Outliers : 2.69 % Allowed : 20.75 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.16), residues: 2606 helix: 1.51 (0.19), residues: 745 sheet: 0.72 (0.23), residues: 522 loop : -1.93 (0.15), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 115 TYR 0.014 0.001 TYR H 265 PHE 0.023 0.001 PHE G 273 TRP 0.011 0.001 TRP C 33 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00365 (23734) covalent geometry : angle 0.54914 (32605) hydrogen bonds : bond 0.04664 ( 634) hydrogen bonds : angle 4.31789 ( 1737) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 584 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8458 (p0) cc_final: 0.8239 (p0) REVERT: A 243 PHE cc_start: 0.8415 (t80) cc_final: 0.8209 (t80) REVERT: B 204 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8181 (ttm170) REVERT: B 229 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7228 (tpp) REVERT: C 91 LEU cc_start: 0.8693 (tp) cc_final: 0.8489 (tp) REVERT: C 229 MET cc_start: 0.8619 (tpp) cc_final: 0.7758 (ttp) REVERT: D 303 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8533 (ttp80) REVERT: E 128 MET cc_start: 0.8496 (ttp) cc_final: 0.8230 (ttp) REVERT: E 160 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8434 (p) REVERT: F 20 ILE cc_start: 0.8454 (mt) cc_final: 0.8232 (mp) REVERT: F 62 MET cc_start: 0.8373 (mmm) cc_final: 0.8144 (mpp) REVERT: F 85 LYS cc_start: 0.8540 (mttp) cc_final: 0.8240 (mtmp) REVERT: F 205 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8562 (ttmm) REVERT: F 320 MET cc_start: 0.6250 (mtm) cc_final: 0.5754 (mtm) REVERT: G 70 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7531 (tt0) REVERT: H 157 ILE cc_start: 0.8413 (mt) cc_final: 0.8195 (tt) REVERT: H 229 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8506 (tpt) REVERT: H 244 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7725 (mt-10) REVERT: M 103 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7736 (mmm160) outliers start: 60 outliers final: 50 residues processed: 611 average time/residue: 0.6212 time to fit residues: 429.0810 Evaluate side-chains 630 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 576 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 174 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 176 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 260 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 140 ASN A 308 ASN B 80 GLN B 178 ASN D 18 ASN D 308 ASN E 165 ASN E 236 ASN F 51 ASN H 18 ASN H 34 GLN H 178 ASN H 279 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.115668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.098567 restraints weight = 32918.446| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.53 r_work: 0.3310 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 23734 Z= 0.295 Angle : 0.640 8.650 32605 Z= 0.340 Chirality : 0.047 0.270 3674 Planarity : 0.006 0.064 3838 Dihedral : 18.381 178.748 4255 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 2.87 % Allowed : 20.89 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.16), residues: 2606 helix: 1.27 (0.19), residues: 747 sheet: 0.63 (0.23), residues: 505 loop : -2.02 (0.14), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 115 TYR 0.026 0.002 TYR G 271 PHE 0.029 0.002 PHE C 273 TRP 0.016 0.002 TRP C 33 HIS 0.006 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00720 (23734) covalent geometry : angle 0.63968 (32605) hydrogen bonds : bond 0.06472 ( 634) hydrogen bonds : angle 4.66106 ( 1737) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 580 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8491 (t80) cc_final: 0.8187 (t80) REVERT: B 204 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8166 (ttm170) REVERT: B 229 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7411 (tpp) REVERT: C 91 LEU cc_start: 0.8755 (tp) cc_final: 0.8549 (tp) REVERT: C 229 MET cc_start: 0.8666 (tpp) cc_final: 0.7789 (ttp) REVERT: D 303 ARG cc_start: 0.8823 (ttp80) cc_final: 0.8513 (ttp80) REVERT: E 128 MET cc_start: 0.8490 (ttp) cc_final: 0.8214 (ttp) REVERT: E 160 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8498 (p) REVERT: F 85 LYS cc_start: 0.8515 (mttp) cc_final: 0.8232 (mtmp) REVERT: F 205 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8585 (ttmm) REVERT: F 320 MET cc_start: 0.6312 (mtm) cc_final: 0.5915 (mtm) REVERT: G 70 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7592 (tt0) REVERT: H 157 ILE cc_start: 0.8475 (mt) cc_final: 0.8260 (tt) REVERT: H 229 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8541 (tpt) REVERT: H 244 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7756 (mt-10) REVERT: M 103 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7822 (mmm160) outliers start: 64 outliers final: 48 residues processed: 608 average time/residue: 0.6479 time to fit residues: 443.0336 Evaluate side-chains 631 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 579 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 174 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 248 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 232 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 140 ASN A 308 ASN B 178 ASN D 18 ASN D 308 ASN E 165 ASN F 51 ASN H 18 ASN H 34 GLN H 279 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.118941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101770 restraints weight = 32920.603| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.53 r_work: 0.3357 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23734 Z= 0.125 Angle : 0.544 7.328 32605 Z= 0.291 Chirality : 0.041 0.210 3674 Planarity : 0.005 0.076 3838 Dihedral : 18.340 178.595 4255 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 2.20 % Allowed : 21.69 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.16), residues: 2606 helix: 1.55 (0.20), residues: 746 sheet: 0.70 (0.23), residues: 523 loop : -1.89 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 115 TYR 0.014 0.001 TYR H 265 PHE 0.022 0.001 PHE C 273 TRP 0.011 0.001 TRP C 33 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00288 (23734) covalent geometry : angle 0.54381 (32605) hydrogen bonds : bond 0.04237 ( 634) hydrogen bonds : angle 4.28145 ( 1737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11349.20 seconds wall clock time: 193 minutes 26.68 seconds (11606.68 seconds total)