Starting phenix.real_space_refine on Thu Jun 19 16:29:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0k_39706/06_2025/8z0k_39706_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0k_39706/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0k_39706/06_2025/8z0k_39706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0k_39706/06_2025/8z0k_39706.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0k_39706/06_2025/8z0k_39706_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0k_39706/06_2025/8z0k_39706_neut.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 6} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 15.05, per 1000 atoms: 0.65 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: 5.21 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 7.29 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: 6.76 Time building geometry restraints manager: 6.34 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: 3.440 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: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 54.880 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.250 ------------------------------------------------------------------------------- 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 : 5.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.002 TRP F 74 HIS 0.019 0.002 HIS A 60 PHE 0.034 0.002 PHE D 273 TYR 0.037 0.003 TYR B 138 ARG 0.016 0.001 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.21842 ( 634) hydrogen bonds : angle 7.92055 ( 1737) covalent geometry : bond 0.00700 (23734) covalent geometry : angle 1.09972 (32605) *********************** 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 : 2.240 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: 1.3319 time to fit residues: 1098.0131 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 : 2.273 ------------------------------------------------------------------------------- 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 227 optimal weight: 0.5980 chunk 203 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 156 optimal weight: 0.0010 chunk 244 optimal weight: 4.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN G 317 HIS H 18 ASN H 151 ASN H 178 ASN H 208 ASN H 279 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.122105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105127 restraints weight = 32656.633| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.53 r_work: 0.3404 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23734 Z= 0.134 Angle : 0.601 7.792 32605 Z= 0.324 Chirality : 0.042 0.220 3674 Planarity : 0.006 0.074 3838 Dihedral : 19.096 179.351 4273 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.78 % Rotamer: Outliers : 3.54 % Allowed : 16.32 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 2606 helix: -0.16 (0.18), residues: 750 sheet: 0.83 (0.23), residues: 487 loop : -2.35 (0.13), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 264 HIS 0.004 0.001 HIS E 203 PHE 0.012 0.001 PHE H 43 TYR 0.013 0.001 TYR A 265 ARG 0.007 0.000 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 634) hydrogen bonds : angle 5.09363 ( 1737) covalent geometry : bond 0.00302 (23734) covalent geometry : angle 0.60121 (32605) *********************** 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 721 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 642 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8307 (t80) cc_final: 0.8025 (t80) REVERT: E 160 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8401 (p) REVERT: F 62 MET cc_start: 0.8342 (mmm) cc_final: 0.8080 (mpp) REVERT: F 85 LYS cc_start: 0.8564 (mttp) cc_final: 0.8343 (mtmp) REVERT: F 127 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7182 (mt-10) REVERT: G 70 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7416 (tt0) REVERT: G 166 ASP cc_start: 0.7655 (t0) cc_final: 0.7415 (t0) REVERT: G 252 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8103 (pt0) REVERT: G 302 ASP cc_start: 0.8210 (m-30) cc_final: 0.8003 (m-30) REVERT: H 244 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7762 (mt-10) REVERT: M 103 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7506 (mmm160) outliers start: 79 outliers final: 30 residues processed: 669 average time/residue: 1.3954 time to fit residues: 1061.6011 Evaluate side-chains 648 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 616 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 301 ILE 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 252 GLN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 10 VAL 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 233 GLU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 120 GLU 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 H residue 42 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain H residue 275 ILE 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 209 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 267 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 C 18 ASN C 26 ASN C 80 GLN C 178 ASN D 18 ASN D 308 ASN E 52 ASN E 165 ASN E 183 GLN E 236 ASN F 71 ASN G 26 ASN G 140 ASN H 18 ASN H 178 ASN H 208 ASN H 279 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.099238 restraints weight = 32777.304| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.52 r_work: 0.3317 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 23734 Z= 0.305 Angle : 0.678 8.001 32605 Z= 0.365 Chirality : 0.048 0.273 3674 Planarity : 0.006 0.068 3838 Dihedral : 18.797 178.919 4253 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 4.30 % Allowed : 16.72 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 2606 helix: 0.45 (0.19), residues: 744 sheet: 0.84 (0.24), residues: 457 loop : -2.33 (0.13), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 33 HIS 0.007 0.002 HIS E 59 PHE 0.018 0.002 PHE A 172 TYR 0.025 0.002 TYR M 46 ARG 0.007 0.001 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.07457 ( 634) hydrogen bonds : angle 5.09383 ( 1737) covalent geometry : bond 0.00737 (23734) covalent geometry : angle 0.67762 (32605) *********************** 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 717 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 621 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8443 (t80) cc_final: 0.8128 (t80) REVERT: B 204 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8139 (ttm170) REVERT: C 229 MET cc_start: 0.8628 (tpp) cc_final: 0.7693 (ttp) REVERT: E 160 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8486 (p) REVERT: E 178 MET cc_start: 0.8781 (ttt) cc_final: 0.8580 (ttt) REVERT: F 20 ILE cc_start: 0.8676 (mt) cc_final: 0.8461 (mp) REVERT: F 62 MET cc_start: 0.8377 (mmm) cc_final: 0.8134 (mpp) REVERT: F 83 ASP cc_start: 0.7823 (t0) cc_final: 0.7524 (t0) REVERT: F 85 LYS cc_start: 0.8673 (mttp) cc_final: 0.8353 (mtmp) REVERT: G 70 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7528 (tt0) REVERT: G 166 ASP cc_start: 0.7809 (t0) cc_final: 0.7598 (t0) REVERT: H 244 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8093 (mt-10) outliers start: 96 outliers final: 53 residues processed: 670 average time/residue: 1.4744 time to fit residues: 1114.0905 Evaluate side-chains 657 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 602 time to evaluate : 2.322 ------------------------------------------------------------------------------- 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 156 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 14 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 205 GLU 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 184 GLU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 259 ARG 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 26 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 267 ASP 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 104 GLU 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 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 252 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 174 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 60 optimal weight: 0.9980 chunk 152 optimal weight: 0.0040 chunk 156 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 112 optimal weight: 0.0770 chunk 36 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 308 ASN B 80 GLN B 178 ASN C 80 GLN D 18 ASN D 140 ASN D 144 ASN D 308 ASN E 165 ASN G 252 GLN 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 = 0.3709 r_free = 0.3709 target = 0.120685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.103484 restraints weight = 33072.236| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.55 r_work: 0.3372 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23734 Z= 0.117 Angle : 0.539 7.395 32605 Z= 0.290 Chirality : 0.041 0.203 3674 Planarity : 0.005 0.064 3838 Dihedral : 18.683 179.092 4253 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.16 % Rotamer: Outliers : 3.32 % Allowed : 18.06 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 2606 helix: 1.03 (0.19), residues: 742 sheet: 0.75 (0.23), residues: 515 loop : -2.17 (0.14), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 33 HIS 0.005 0.001 HIS A 317 PHE 0.010 0.001 PHE F 219 TYR 0.021 0.001 TYR M 46 ARG 0.006 0.000 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 634) hydrogen bonds : angle 4.47632 ( 1737) covalent geometry : bond 0.00256 (23734) covalent geometry : angle 0.53916 (32605) *********************** 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 699 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 625 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8443 (t80) cc_final: 0.8101 (t80) REVERT: B 204 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8090 (ttm170) REVERT: C 229 MET cc_start: 0.8609 (tpp) cc_final: 0.7841 (ttp) REVERT: E 160 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8398 (p) REVERT: F 20 ILE cc_start: 0.8505 (mt) cc_final: 0.8291 (mp) REVERT: F 62 MET cc_start: 0.8369 (mmm) cc_final: 0.8111 (mpp) REVERT: F 83 ASP cc_start: 0.7821 (t0) cc_final: 0.7557 (t0) REVERT: F 85 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8293 (mtmp) REVERT: G 123 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: G 166 ASP cc_start: 0.7786 (t0) cc_final: 0.7563 (t0) REVERT: H 157 ILE cc_start: 0.8355 (mt) cc_final: 0.8085 (tt) REVERT: H 244 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7981 (mm-30) REVERT: M 103 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7502 (mmm160) outliers start: 74 outliers final: 47 residues processed: 648 average time/residue: 1.4200 time to fit residues: 1040.3645 Evaluate side-chains 659 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 608 time to evaluate : 2.290 ------------------------------------------------------------------------------- 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 156 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 93 ILE 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 C residue 86 THR 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 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 208 ARG Chi-restraints excluded: chain E residue 213 ASP 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 85 LYS 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 F residue 306 ILE 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 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 159 GLU 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 200 PHE Chi-restraints excluded: chain H residue 252 GLN 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 10 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 279 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 34 GLN H 178 ASN H 279 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.118395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101189 restraints weight = 32953.780| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.54 r_work: 0.3338 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23734 Z= 0.196 Angle : 0.575 7.156 32605 Z= 0.308 Chirality : 0.043 0.232 3674 Planarity : 0.005 0.065 3838 Dihedral : 18.545 179.389 4253 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.55 % Rotamer: Outliers : 3.45 % Allowed : 18.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2606 helix: 1.18 (0.19), residues: 746 sheet: 0.82 (0.23), residues: 510 loop : -2.11 (0.14), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 33 HIS 0.004 0.001 HIS A 317 PHE 0.023 0.001 PHE C 273 TYR 0.017 0.001 TYR G 206 ARG 0.008 0.000 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.05420 ( 634) hydrogen bonds : angle 4.53851 ( 1737) covalent geometry : bond 0.00472 (23734) covalent geometry : angle 0.57531 (32605) *********************** 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: 77 poor density : 593 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8483 (t80) cc_final: 0.8043 (t80) REVERT: C 229 MET cc_start: 0.8639 (tpp) cc_final: 0.7754 (ttp) REVERT: E 2 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8428 (mtpt) REVERT: E 160 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8447 (p) REVERT: F 20 ILE cc_start: 0.8505 (mt) cc_final: 0.8286 (mp) REVERT: F 62 MET cc_start: 0.8382 (mmm) cc_final: 0.8126 (mpp) REVERT: F 83 ASP cc_start: 0.7839 (t0) cc_final: 0.7571 (t0) REVERT: F 85 LYS cc_start: 0.8682 (mttp) cc_final: 0.8288 (mtmp) REVERT: G 70 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7471 (tt0) REVERT: G 123 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: G 166 ASP cc_start: 0.7814 (t0) cc_final: 0.7601 (t0) REVERT: G 206 TYR cc_start: 0.8069 (p90) cc_final: 0.7182 (p90) REVERT: H 157 ILE cc_start: 0.8397 (mt) cc_final: 0.8150 (tt) REVERT: H 244 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8093 (mt-10) REVERT: M 103 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7777 (mmm160) outliers start: 77 outliers final: 53 residues processed: 622 average time/residue: 1.5304 time to fit residues: 1074.1381 Evaluate side-chains 639 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 584 time to evaluate : 2.417 ------------------------------------------------------------------------------- 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 156 GLU 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 87 GLU Chi-restraints excluded: chain B residue 118 ILE 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 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 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 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 169 LEU Chi-restraints excluded: chain F residue 234 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 123 ASP 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 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 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 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 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 108 optimal weight: 0.9990 chunk 258 optimal weight: 0.0970 chunk 249 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 189 optimal weight: 0.0270 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN D 18 ASN D 140 ASN D 308 ASN E 165 ASN E 236 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 = 0.3699 r_free = 0.3699 target = 0.119905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102729 restraints weight = 32720.403| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.53 r_work: 0.3362 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2503 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= 0.129 Angle : 0.532 7.231 32605 Z= 0.284 Chirality : 0.041 0.207 3674 Planarity : 0.005 0.069 3838 Dihedral : 18.477 179.444 4253 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 3.23 % Allowed : 19.50 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2606 helix: 1.38 (0.20), residues: 747 sheet: 0.85 (0.23), residues: 511 loop : -2.03 (0.14), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 33 HIS 0.004 0.001 HIS A 317 PHE 0.023 0.001 PHE C 273 TYR 0.022 0.001 TYR G 206 ARG 0.008 0.000 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 634) hydrogen bonds : angle 4.32850 ( 1737) covalent geometry : bond 0.00299 (23734) covalent geometry : angle 0.53150 (32605) *********************** 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 655 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 583 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8468 (t80) cc_final: 0.8025 (t80) REVERT: C 229 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7804 (ttp) REVERT: E 2 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8410 (mtpt) REVERT: E 160 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8424 (p) REVERT: F 2 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7637 (tp) REVERT: F 20 ILE cc_start: 0.8456 (mt) cc_final: 0.8239 (mp) REVERT: F 83 ASP cc_start: 0.7836 (t0) cc_final: 0.7482 (t0) REVERT: F 85 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8246 (mtmp) REVERT: F 205 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8546 (ttmm) REVERT: G 70 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7432 (tt0) REVERT: G 123 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: G 166 ASP cc_start: 0.7805 (t0) cc_final: 0.7582 (t0) REVERT: G 206 TYR cc_start: 0.7329 (p90) cc_final: 0.6999 (p90) REVERT: H 157 ILE cc_start: 0.8391 (mt) cc_final: 0.8153 (tt) REVERT: H 229 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8550 (tpt) REVERT: H 244 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8087 (mt-10) REVERT: M 103 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7482 (mmm160) outliers start: 72 outliers final: 50 residues processed: 607 average time/residue: 1.5093 time to fit residues: 1030.6093 Evaluate side-chains 642 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 586 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 156 GLU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 118 ILE 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 185 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 310 ASP 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 2 LEU Chi-restraints excluded: chain F residue 85 LYS 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 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 123 ASP 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 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 103 LYS Chi-restraints excluded: chain H residue 179 LEU 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 275 ILE Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain M residue 9 LYS 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 157 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 257 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 249 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 178 ASN C 80 GLN D 18 ASN D 308 ASN E 165 ASN E 207 GLN E 236 ASN F 51 ASN G 140 ASN H 18 ASN 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 = 0.3664 r_free = 0.3664 target = 0.117520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100252 restraints weight = 33093.852| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.54 r_work: 0.3334 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23734 Z= 0.212 Angle : 0.577 7.146 32605 Z= 0.307 Chirality : 0.044 0.235 3674 Planarity : 0.005 0.070 3838 Dihedral : 18.437 179.213 4253 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 3.23 % Allowed : 19.68 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2606 helix: 1.37 (0.19), residues: 745 sheet: 0.85 (0.23), residues: 510 loop : -2.02 (0.14), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 33 HIS 0.004 0.001 HIS A 317 PHE 0.024 0.002 PHE C 273 TYR 0.028 0.001 TYR G 206 ARG 0.008 0.000 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.05476 ( 634) hydrogen bonds : angle 4.47259 ( 1737) covalent geometry : bond 0.00514 (23734) covalent geometry : angle 0.57697 (32605) *********************** 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 661 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 589 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.8500 (t80) cc_final: 0.8037 (t80) REVERT: C 229 MET cc_start: 0.8646 (tpp) cc_final: 0.7759 (ttp) REVERT: E 160 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8461 (p) REVERT: F 20 ILE cc_start: 0.8489 (mt) cc_final: 0.8273 (mp) REVERT: F 83 ASP cc_start: 0.7870 (t0) cc_final: 0.7667 (t0) REVERT: F 85 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8323 (mtmp) REVERT: F 205 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8556 (ttmm) REVERT: G 70 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7484 (tt0) REVERT: G 166 ASP cc_start: 0.7789 (t0) cc_final: 0.7572 (t0) REVERT: H 157 ILE cc_start: 0.8438 (mt) cc_final: 0.8211 (tt) REVERT: H 244 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8127 (mt-10) REVERT: H 295 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7792 (mptm) REVERT: M 103 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7453 (mmm160) outliers start: 72 outliers final: 50 residues processed: 619 average time/residue: 1.4467 time to fit residues: 1011.4531 Evaluate side-chains 641 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 588 time to evaluate : 2.667 ------------------------------------------------------------------------------- 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 156 GLU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE 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 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 45 LEU 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 85 LYS Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 245 VAL 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 217 ILE 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 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 267 ASP Chi-restraints excluded: chain H residue 271 TYR Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 295 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 80 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 80 GLN D 18 ASN D 308 ASN E 14 ASN E 165 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 = 0.3698 r_free = 0.3698 target = 0.120000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102795 restraints weight = 32910.871| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.54 r_work: 0.3370 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23734 Z= 0.116 Angle : 0.529 8.153 32605 Z= 0.281 Chirality : 0.040 0.196 3674 Planarity : 0.005 0.072 3838 Dihedral : 18.389 179.259 4253 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 2.87 % Allowed : 20.35 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2606 helix: 1.53 (0.20), residues: 747 sheet: 0.77 (0.23), residues: 530 loop : -1.91 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 33 HIS 0.004 0.001 HIS A 317 PHE 0.022 0.001 PHE C 273 TYR 0.014 0.001 TYR G 265 ARG 0.009 0.000 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 634) hydrogen bonds : angle 4.19674 ( 1737) covalent geometry : bond 0.00261 (23734) covalent geometry : angle 0.52860 (32605) *********************** 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 657 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 593 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 229 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7825 (ttp) REVERT: E 160 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8407 (p) REVERT: F 20 ILE cc_start: 0.8421 (mt) cc_final: 0.8198 (mp) REVERT: F 62 MET cc_start: 0.8435 (tpp) cc_final: 0.8154 (mpp) REVERT: F 83 ASP cc_start: 0.7809 (t0) cc_final: 0.7488 (t0) REVERT: F 85 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8254 (mtmp) REVERT: F 205 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8543 (ttmm) REVERT: G 166 ASP cc_start: 0.7771 (t0) cc_final: 0.7547 (t0) REVERT: H 157 ILE cc_start: 0.8396 (mt) cc_final: 0.8158 (tt) REVERT: H 229 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8511 (tpt) REVERT: H 244 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7987 (mm-30) REVERT: H 310 ASP cc_start: 0.8282 (t0) cc_final: 0.8022 (t0) REVERT: M 103 ARG cc_start: 0.7994 (mmm160) cc_final: 0.7375 (mmm160) outliers start: 64 outliers final: 44 residues processed: 616 average time/residue: 1.5520 time to fit residues: 1083.1088 Evaluate side-chains 629 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 581 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 156 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE 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 184 GLU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 286 ILE 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 233 GLU Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 85 LYS 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 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 217 ILE Chi-restraints excluded: chain G residue 270 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 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 271 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 118 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 178 ASN C 75 ASN D 18 ASN D 308 ASN E 20 ASN E 165 ASN E 207 GLN F 51 ASN G 140 ASN H 18 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 = 0.3654 r_free = 0.3654 target = 0.116722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099477 restraints weight = 32906.583| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.52 r_work: 0.3322 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 23734 Z= 0.260 Angle : 0.615 7.745 32605 Z= 0.326 Chirality : 0.045 0.251 3674 Planarity : 0.005 0.066 3838 Dihedral : 18.388 179.425 4253 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 2.60 % Allowed : 20.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2606 helix: 1.41 (0.19), residues: 744 sheet: 0.73 (0.23), residues: 520 loop : -1.95 (0.14), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 33 HIS 0.005 0.001 HIS G 60 PHE 0.028 0.002 PHE C 273 TYR 0.023 0.002 TYR G 271 ARG 0.009 0.001 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.06112 ( 634) hydrogen bonds : angle 4.54664 ( 1737) covalent geometry : bond 0.00634 (23734) covalent geometry : angle 0.61508 (32605) *********************** 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 640 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 582 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 229 MET cc_start: 0.8644 (tpp) cc_final: 0.7760 (ttp) REVERT: E 160 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8461 (p) REVERT: F 20 ILE cc_start: 0.8496 (mt) cc_final: 0.8278 (mp) REVERT: F 85 LYS cc_start: 0.8726 (mttp) cc_final: 0.8320 (mtmp) REVERT: F 205 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8564 (ttmm) REVERT: G 70 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7538 (tt0) REVERT: G 166 ASP cc_start: 0.7772 (t0) cc_final: 0.7559 (t0) REVERT: H 157 ILE cc_start: 0.8469 (mt) cc_final: 0.8259 (tt) REVERT: H 229 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8534 (tpt) REVERT: H 244 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8109 (mt-10) REVERT: H 310 ASP cc_start: 0.8253 (t0) cc_final: 0.8006 (t0) REVERT: M 103 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7388 (mmm160) outliers start: 58 outliers final: 44 residues processed: 607 average time/residue: 1.4599 time to fit residues: 998.9384 Evaluate side-chains 619 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 573 time to evaluate : 2.400 ------------------------------------------------------------------------------- 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 156 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE 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 184 GLU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 168 GLU 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 169 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 103 LYS 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 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 267 ASP Chi-restraints excluded: chain H residue 271 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 147 optimal weight: 0.0370 chunk 151 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 228 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.9860 ------------------------------------------------------------------------------- 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 178 ASN C 80 GLN D 18 ASN D 308 ASN E 165 ASN H 18 ASN H 34 GLN H 178 ASN H 279 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.119139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.101935 restraints weight = 32930.619| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.54 r_work: 0.3350 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2768 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= 0.148 Angle : 0.554 8.452 32605 Z= 0.294 Chirality : 0.042 0.213 3674 Planarity : 0.005 0.078 3838 Dihedral : 18.357 179.202 4253 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 2.20 % Allowed : 21.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2606 helix: 1.55 (0.19), residues: 745 sheet: 0.73 (0.23), residues: 534 loop : -1.86 (0.15), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 33 HIS 0.004 0.001 HIS A 317 PHE 0.022 0.001 PHE C 273 TYR 0.015 0.001 TYR G 265 ARG 0.008 0.000 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 634) hydrogen bonds : angle 4.27661 ( 1737) covalent geometry : bond 0.00352 (23734) covalent geometry : angle 0.55404 (32605) ********************** 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 617 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 568 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 229 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7796 (ttp) REVERT: E 160 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8409 (p) REVERT: F 20 ILE cc_start: 0.8465 (mt) cc_final: 0.8246 (mp) REVERT: F 62 MET cc_start: 0.8444 (tpp) cc_final: 0.8148 (mpp) REVERT: F 85 LYS cc_start: 0.8523 (mttp) cc_final: 0.8239 (mtmp) REVERT: F 205 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8545 (ttmm) REVERT: G 70 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7494 (tt0) REVERT: H 157 ILE cc_start: 0.8417 (mt) cc_final: 0.8195 (tt) REVERT: H 229 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8502 (tpt) REVERT: H 244 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8087 (mt-10) REVERT: H 310 ASP cc_start: 0.8260 (t0) cc_final: 0.8022 (t0) REVERT: M 103 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7387 (mmm160) outliers start: 49 outliers final: 40 residues processed: 587 average time/residue: 1.5748 time to fit residues: 1039.7028 Evaluate side-chains 613 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 570 time to evaluate : 2.244 ------------------------------------------------------------------------------- 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 156 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 118 ILE 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 184 GLU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 168 GLU 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 169 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 103 LYS 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 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 98 LEU Chi-restraints excluded: chain M residue 151 THR 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 1 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 229 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN B 178 ASN D 18 ASN D 308 ASN E 165 ASN E 236 ASN H 18 ASN H 34 GLN H 279 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.117396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.100159 restraints weight = 32971.849| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.53 r_work: 0.3332 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23734 Z= 0.201 Angle : 0.586 10.296 32605 Z= 0.310 Chirality : 0.043 0.235 3674 Planarity : 0.005 0.076 3838 Dihedral : 18.338 179.204 4253 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.40 % Rotamer: Outliers : 2.47 % Allowed : 21.38 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2606 helix: 1.50 (0.19), residues: 745 sheet: 0.71 (0.23), residues: 534 loop : -1.86 (0.15), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 33 HIS 0.004 0.001 HIS H 250 PHE 0.026 0.001 PHE C 273 TYR 0.017 0.001 TYR G 271 ARG 0.009 0.000 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.05344 ( 634) hydrogen bonds : angle 4.40068 ( 1737) covalent geometry : bond 0.00488 (23734) covalent geometry : angle 0.58586 (32605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22881.08 seconds wall clock time: 389 minutes 45.41 seconds (23385.41 seconds total)