Starting phenix.real_space_refine on Mon Oct 26 18:03:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6b47_7051/10_2026/6b47_7051.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b47_7051/10_2026/6b47_7051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6b47_7051/10_2026/6b47_7051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b47_7051/10_2026/6b47_7051.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6b47_7051/10_2026/6b47_7051.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6b47_7051/10_2026/6b47_7051.cif" model { file = "/net/cci-nas-00/data/ceres_data/6b47_7051/10_2026/6b47_7051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b47_7051/10_2026/6b47_7051.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.010 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 59 5.49 5 S 20 5.16 5 C 13479 2.51 5 N 4171 2.21 5 O 4484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22213 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2079 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 310} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1373 Unresolved non-hydrogen angles: 1987 Unresolved non-hydrogen dihedrals: 884 Unresolved non-hydrogen chiralities: 392 Planarities with less than four sites: {'GLN:plan1': 29, 'GLU:plan': 24, 'ARG:plan': 29, 'PHE:plan': 11, 'ASP:plan': 20, 'HIS:plan': 9, 'TRP:plan': 9, 'ASN:plan1': 13, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 726 Chain: "B" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2374 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2561 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2561 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2557 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2557 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "K" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 668 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 758 Classifications: {'peptide': 189} Incomplete info: {'backbone_only': 173, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 173} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 806 Unresolved non-hydrogen angles: 1152 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'ASP:plan': 12, 'HIS:plan': 8, 'TYR:plan': 3, 'ARG:plan': 24, 'GLU:plan': 11, 'PHE:plan': 10, 'GLN:plan1': 9, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 414 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNAv2': 60} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 19, 'rna3p': 40} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.31, per 1000 atoms: 0.24 Number of scatterers: 22213 At special positions: 0 Unit cell: (152.281, 122.254, 153.353, 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 20 16.00 P 59 15.00 O 4484 8.00 N 4171 7.00 C 13479 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4550 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 47 sheets defined 32.3% alpha, 19.5% beta 1 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 removed outlier: 3.737A pdb=" N LYS A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.975A pdb=" N HIS A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 4.242A pdb=" N ARG A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.559A pdb=" N GLU A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 100' Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.805A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 317 through 341 removed outlier: 3.523A pdb=" N ARG A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.928A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 434 removed outlier: 3.869A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.951A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.685A pdb=" N LEU B 118 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 115 through 119' Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.638A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.839A pdb=" N GLU C 38 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP C 39 " --> pdb=" O SER C 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 35 through 39' Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 189 through 205 Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.671A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.502A pdb=" N GLN D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.514A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.582A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 314 removed outlier: 3.624A pdb=" N ARG D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 32 through 39 removed outlier: 3.682A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLN E 37 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TRP E 39 " --> pdb=" O SER E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 Processing helix chain 'E' and resid 112 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.622A pdb=" N ARG E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.610A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 removed outlier: 3.639A pdb=" N SER F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 3.561A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 190 through 204 removed outlier: 3.754A pdb=" N SER F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.555A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.527A pdb=" N SER G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 190 through 205 removed outlier: 3.510A pdb=" N GLY G 205 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.528A pdb=" N ILE G 260 " --> pdb=" O HIS G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.513A pdb=" N SER H 36 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 73 removed outlier: 4.142A pdb=" N SER H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.527A pdb=" N ILE H 260 " --> pdb=" O HIS H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 278 Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'K' and resid 9 through 19 Processing helix chain 'K' and resid 57 through 68 Processing helix chain 'K' and resid 76 through 81 Processing helix chain 'K' and resid 81 through 86 Processing helix chain 'L' and resid 16 through 32 Processing helix chain 'L' and resid 33 through 35 No H-bonds generated for 'chain 'L' and resid 33 through 35' Processing helix chain 'L' and resid 67 through 71 removed outlier: 3.785A pdb=" N LEU L 70 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU L 71 " --> pdb=" O ARG L 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 67 through 71' Processing helix chain 'L' and resid 111 through 119 Processing helix chain 'L' and resid 123 through 131 removed outlier: 3.563A pdb=" N ALA L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 8.610A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 187 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 8.610A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 251 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232 removed outlier: 3.631A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 219 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 60 removed outlier: 5.773A pdb=" N GLY B 112 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.585A pdb=" N ARG B 65 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.634A pdb=" N ALA C 108 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 12 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 20 removed outlier: 4.533A pdb=" N VAL C 209 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 44 through 47 removed outlier: 3.616A pdb=" N LYS C 47 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 79 " --> pdb=" O LYS C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 229 through 230 removed outlier: 4.156A pdb=" N THR C 245 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.723A pdb=" N ALA C 252 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 266 through 268 removed outlier: 3.770A pdb=" N ILE C 280 " --> pdb=" O ASP C 268 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.587A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.497A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 160 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG D 175 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE D 162 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA D 173 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'D' and resid 45 through 51 removed outlier: 3.991A pdb=" N GLY D 51 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN D 75 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 229 through 230 removed outlier: 4.539A pdb=" N THR D 245 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.579A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.574A pdb=" N LEU E 12 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.541A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE E 162 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.547A pdb=" N ARG E 94 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 252 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 50 Processing sheet with id=AC7, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AC8, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AC9, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.581A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 12 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.492A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL F 158 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP F 177 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE F 162 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AD3, first strand: chain 'F' and resid 45 through 50 removed outlier: 4.572A pdb=" N ALA F 82 " --> pdb=" O VAL F 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AD5, first strand: chain 'F' and resid 287 through 288 Processing sheet with id=AD6, first strand: chain 'G' and resid 12 through 14 Processing sheet with id=AD7, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.352A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL G 160 " --> pdb=" O PHE G 176 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.861A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 45 through 50 removed outlier: 4.502A pdb=" N ALA G 82 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 45 through 50 removed outlier: 7.618A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.804A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 19 through 20 removed outlier: 4.456A pdb=" N VAL H 209 " --> pdb=" O VAL H 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 170 through 177 removed outlier: 3.557A pdb=" N ARG H 172 " --> pdb=" O HIS H 164 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA H 253 " --> pdb=" O MET H 25 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 249 " --> pdb=" O ALA H 252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 44 through 50 removed outlier: 4.413A pdb=" N ALA H 82 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 44 through 50 removed outlier: 7.524A pdb=" N SER H 243 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR H 78 " --> pdb=" O SER H 243 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AE8, first strand: chain 'H' and resid 287 through 288 Processing sheet with id=AE9, first strand: chain 'K' and resid 23 through 27 Processing sheet with id=AF1, first strand: chain 'K' and resid 41 through 46 removed outlier: 3.628A pdb=" N ILE K 44 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 5 through 6 926 hydrogen bonds defined for protein. 2586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4584 1.32 - 1.45: 5677 1.45 - 1.57: 12320 1.57 - 1.69: 118 1.69 - 1.81: 30 Bond restraints: 22729 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.331 1.364 -0.033 7.90e-03 1.60e+04 1.72e+01 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.339 1.448 -0.109 3.40e-02 8.65e+02 1.03e+01 bond pdb=" CG1 ILE E 260 " pdb=" CD1 ILE E 260 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.09e+00 bond pdb=" CG1 ILE F 260 " pdb=" CD1 ILE F 260 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.31e+00 bond pdb=" C ARG B 85 " pdb=" N ASN B 86 " ideal model delta sigma weight residual 1.329 1.281 0.048 1.86e-02 2.89e+03 6.66e+00 ... (remaining 22724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 29373 2.27 - 4.54: 1320 4.54 - 6.81: 189 6.81 - 9.08: 34 9.08 - 11.35: 6 Bond angle restraints: 30922 Sorted by residual: angle pdb=" N GLN G 37 " pdb=" CA GLN G 37 " pdb=" C GLN G 37 " ideal model delta sigma weight residual 114.56 106.99 7.57 1.27e+00 6.20e-01 3.55e+01 angle pdb=" C SER A 252 " pdb=" N GLN A 253 " pdb=" CA GLN A 253 " ideal model delta sigma weight residual 122.08 130.02 -7.94 1.47e+00 4.63e-01 2.91e+01 angle pdb=" C LYS H 58 " pdb=" N THR H 59 " pdb=" CA THR H 59 " ideal model delta sigma weight residual 122.61 129.57 -6.96 1.56e+00 4.11e-01 1.99e+01 angle pdb=" C GLN G 32 " pdb=" N ARG G 33 " pdb=" CA ARG G 33 " ideal model delta sigma weight residual 120.38 126.82 -6.44 1.46e+00 4.69e-01 1.95e+01 angle pdb=" N GLN D 167 " pdb=" CA GLN D 167 " pdb=" C GLN D 167 " ideal model delta sigma weight residual 108.07 102.02 6.05 1.38e+00 5.25e-01 1.92e+01 ... (remaining 30917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 11799 15.65 - 31.30: 657 31.30 - 46.95: 211 46.95 - 62.60: 83 62.60 - 78.25: 29 Dihedral angle restraints: 12779 sinusoidal: 5212 harmonic: 7567 Sorted by residual: dihedral pdb=" C4' A M 3 " pdb=" C3' A M 3 " pdb=" C2' A M 3 " pdb=" C1' A M 3 " ideal model delta sinusoidal sigma weight residual 36.34 -38.17 74.52 1 3.10e+00 1.04e-01 7.32e+02 dihedral pdb=" C4' A M 7 " pdb=" C3' A M 7 " pdb=" C2' A M 7 " pdb=" C1' A M 7 " ideal model delta sinusoidal sigma weight residual 36.34 -36.82 73.17 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' C M 37 " pdb=" C3' C M 37 " pdb=" C2' C M 37 " pdb=" C1' C M 37 " ideal model delta sinusoidal sigma weight residual 36.34 -36.68 73.03 1 3.10e+00 1.04e-01 7.07e+02 ... (remaining 12776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2545 0.076 - 0.152: 539 0.152 - 0.228: 70 0.228 - 0.304: 54 0.304 - 0.381: 7 Chirality restraints: 3215 Sorted by residual: chirality pdb=" CB ILE H 267 " pdb=" CA ILE H 267 " pdb=" CG1 ILE H 267 " pdb=" CG2 ILE H 267 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB ILE F 267 " pdb=" CA ILE F 267 " pdb=" CG1 ILE F 267 " pdb=" CG2 ILE F 267 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C2' G M 15 " pdb=" C3' G M 15 " pdb=" O2' G M 15 " pdb=" C1' G M 15 " both_signs ideal model delta sigma weight residual False -2.79 -2.46 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 3212 not shown) Planarity restraints: 4018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 311 " -0.030 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP E 311 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP E 311 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP E 311 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 311 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 311 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 311 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 311 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 311 " -0.028 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP D 311 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP D 311 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 311 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 311 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 311 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 311 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 311 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 311 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 311 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 311 " 0.027 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP G 311 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP G 311 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 311 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 311 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 311 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP G 311 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 311 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP G 311 " 0.001 2.00e-02 2.50e+03 ... (remaining 4015 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 770 2.69 - 3.24: 20059 3.24 - 3.79: 34769 3.79 - 4.35: 46103 4.35 - 4.90: 76746 Nonbonded interactions: 178447 Sorted by model distance: nonbonded pdb=" CB ALA L 0 " pdb=" N GLU L 170 " model vdw 2.133 3.540 nonbonded pdb=" OH TYR E 305 " pdb=" O SER F 54 " model vdw 2.278 3.040 nonbonded pdb=" O GLU E 283 " pdb=" OH TYR E 325 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR C 271 " pdb=" O GLY C 278 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR F 305 " pdb=" O SER G 54 " model vdw 2.286 3.040 ... (remaining 178442 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 'C' and (resid 6 through 272 or (resid 273 through 275 and (name N or nam \ e CA or name C or name O or name CB )) or resid 276 through 338)) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) } 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.490 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 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 : 0.010 0.389 22730 Z= 0.472 Angle : 1.074 11.348 30922 Z= 0.575 Chirality : 0.072 0.381 3215 Planarity : 0.006 0.061 4018 Dihedral : 12.682 78.251 8229 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.65 % Favored : 89.18 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.12), residues: 2939 helix: -2.54 (0.13), residues: 885 sheet: -1.24 (0.24), residues: 439 loop : -3.29 (0.12), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 102 TYR 0.036 0.004 TYR D 305 PHE 0.027 0.004 PHE C 216 TRP 0.064 0.006 TRP E 311 HIS 0.020 0.004 HIS F 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00923 / 0.40 (22729) covalent geometry : angle 1.07430 / 0.57 (30922) hydrogen bonds : bond 0.18535 / 13.84 ( 897) hydrogen bonds : angle 8.40107 / 6.22 ( 2592) Misc. bond : bond 0.38922 / 20.49 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ARG cc_start: 0.6502 (ttm110) cc_final: 0.6270 (ttm110) REVERT: B 108 SER cc_start: 0.7328 (m) cc_final: 0.6689 (p) REVERT: B 116 ASP cc_start: 0.5717 (p0) cc_final: 0.5095 (m-30) REVERT: C 124 THR cc_start: 0.8030 (m) cc_final: 0.7277 (m) REVERT: D 221 ASP cc_start: 0.7063 (m-30) cc_final: 0.6863 (m-30) REVERT: D 302 LEU cc_start: 0.7323 (mt) cc_final: 0.7006 (mt) REVERT: G 119 LEU cc_start: 0.8563 (mt) cc_final: 0.8327 (mt) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.1730 time to fit residues: 124.9610 Evaluate side-chains 236 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 256 ASN B 293 HIS C 83 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS C 329 ASN D 164 HIS E 164 HIS E 329 ASN F 75 ASN F 164 HIS F 291 GLN H 32 GLN H 129 GLN H 164 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099359 restraints weight = 34993.978| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.32 r_work: 0.3108 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22730 Z= 0.153 Angle : 0.844 15.653 30922 Z= 0.388 Chirality : 0.059 0.681 3215 Planarity : 0.005 0.055 4018 Dihedral : 10.903 150.487 3911 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.78 % Allowed : 8.62 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.14), residues: 2939 helix: -0.40 (0.16), residues: 927 sheet: -0.41 (0.24), residues: 447 loop : -2.85 (0.13), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 218 TYR 0.022 0.002 TYR C 114 PHE 0.022 0.002 PHE B 184 TRP 0.021 0.002 TRP F 311 HIS 0.008 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (22729) covalent geometry : angle 0.84363 / 0.39 (30922) hydrogen bonds : bond 0.03387 / 2.48 ( 897) hydrogen bonds : angle 5.17965 / 3.86 ( 2592) Misc. bond : bond 0.00706 / 0.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.6562 (mmm-85) cc_final: 0.6001 (mmm-85) REVERT: B 11 LEU cc_start: 0.8434 (tp) cc_final: 0.8213 (tt) REVERT: B 116 ASP cc_start: 0.6125 (p0) cc_final: 0.5434 (m-30) REVERT: B 124 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6947 (pm20) REVERT: B 137 MET cc_start: 0.8437 (mtp) cc_final: 0.8162 (mtp) REVERT: B 321 PHE cc_start: 0.4273 (t80) cc_final: 0.4017 (t80) REVERT: C 136 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7627 (ttp-110) REVERT: F 81 VAL cc_start: 0.8701 (m) cc_final: 0.8394 (p) REVERT: F 122 VAL cc_start: 0.9227 (t) cc_final: 0.9003 (m) REVERT: G 119 LEU cc_start: 0.8933 (mt) cc_final: 0.8714 (mt) REVERT: H 119 LEU cc_start: 0.8924 (mm) cc_final: 0.8627 (mm) REVERT: K 53 MET cc_start: 0.6261 (tmm) cc_final: 0.5815 (tmm) outliers start: 34 outliers final: 18 residues processed: 295 average time/residue: 0.1696 time to fit residues: 73.9678 Evaluate side-chains 213 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 270 TRP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: [267, 240, 98, 219, 149, 116, 12, 140, 30, 120, 17] chunk 267 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 12 optimal weight: 40.0000 chunk 140 optimal weight: 0.7980 chunk 30 optimal weight: 50.0000 chunk 120 optimal weight: 5.9990 chunk 17 optimal weight: 0.0770 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 203 HIS B 18 GLN B 133 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 151 ASN G 208 HIS H 32 GLN H 329 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095751 restraints weight = 34762.370| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.33 r_work: 0.3034 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22730 Z= 0.178 Angle : 0.768 14.641 30922 Z= 0.367 Chirality : 0.054 0.472 3215 Planarity : 0.005 0.062 4018 Dihedral : 11.252 162.398 3911 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.19 % Allowed : 11.02 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.15), residues: 2939 helix: 0.49 (0.17), residues: 930 sheet: -0.03 (0.25), residues: 438 loop : -2.51 (0.14), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 90 TYR 0.023 0.002 TYR C 114 PHE 0.018 0.002 PHE B 184 TRP 0.028 0.002 TRP B 147 HIS 0.005 0.001 HIS C 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (22729) covalent geometry : angle 0.76824 / 0.37 (30922) hydrogen bonds : bond 0.03778 / 2.80 ( 897) hydrogen bonds : angle 4.74277 / 3.53 ( 2592) Misc. bond : bond 0.00094 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 SER cc_start: 0.8995 (p) cc_final: 0.8794 (t) REVERT: A 222 ARG cc_start: 0.6697 (mmm-85) cc_final: 0.6155 (mmm-85) REVERT: B 11 LEU cc_start: 0.8730 (tp) cc_final: 0.8529 (tt) REVERT: B 133 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8644 (tp-100) REVERT: C 247 TYR cc_start: 0.8079 (t80) cc_final: 0.7819 (t80) REVERT: C 293 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7639 (tmtt) REVERT: D 44 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8466 (t) REVERT: D 283 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8100 (mt-10) REVERT: E 75 ASN cc_start: 0.8036 (t0) cc_final: 0.7576 (p0) REVERT: F 303 ASP cc_start: 0.8368 (t0) cc_final: 0.8032 (t0) REVERT: G 241 GLN cc_start: 0.8135 (pm20) cc_final: 0.6996 (tt0) REVERT: H 119 LEU cc_start: 0.9082 (mm) cc_final: 0.8600 (mm) REVERT: H 271 TYR cc_start: 0.8932 (p90) cc_final: 0.8660 (p90) REVERT: K 53 MET cc_start: 0.6626 (tmm) cc_final: 0.6193 (tmm) outliers start: 42 outliers final: 25 residues processed: 239 average time/residue: 0.1907 time to fit residues: 65.7277 Evaluate side-chains 166 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 48 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: [178, 277, 181, 109, 264, 218, 295, 135, 272, 177, 259] chunk 178 optimal weight: 0.6980 chunk 277 optimal weight: 0.0370 chunk 181 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 295 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 259 optimal weight: 0.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN A 249 GLN B 173 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN G 151 ASN G 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.094160 restraints weight = 35035.128| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.82 r_work: 0.2978 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22730 Z= 0.168 Angle : 0.701 13.776 30922 Z= 0.333 Chirality : 0.051 0.525 3215 Planarity : 0.004 0.033 4018 Dihedral : 10.976 153.524 3911 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.19 % Allowed : 11.54 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 2939 helix: 0.98 (0.17), residues: 929 sheet: 0.29 (0.26), residues: 427 loop : -2.34 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 169 TYR 0.022 0.002 TYR K 64 PHE 0.014 0.001 PHE B 184 TRP 0.016 0.002 TRP E 311 HIS 0.005 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (22729) covalent geometry : angle 0.70119 / 0.33 (30922) hydrogen bonds : bond 0.03262 / 2.40 ( 897) hydrogen bonds : angle 4.52870 / 3.36 ( 2592) Misc. bond : bond 0.00188 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: B 196 HIS cc_start: 0.7781 (t70) cc_final: 0.7501 (t70) REVERT: C 247 TYR cc_start: 0.8173 (t80) cc_final: 0.7909 (t80) REVERT: C 293 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7645 (tmtt) REVERT: D 44 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8510 (t) REVERT: E 75 ASN cc_start: 0.8072 (t0) cc_final: 0.7816 (p0) REVERT: G 241 GLN cc_start: 0.8035 (pm20) cc_final: 0.6849 (tt0) REVERT: H 119 LEU cc_start: 0.9121 (mm) cc_final: 0.8578 (mm) outliers start: 42 outliers final: 28 residues processed: 188 average time/residue: 0.1713 time to fit residues: 48.1464 Evaluate side-chains 171 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 38 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: [57, 232, 253, 66, 99, 260, 85, 230, 4, 0, 269] chunk 57 optimal weight: 0.7980 chunk 232 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 260 optimal weight: 0.8980 chunk 85 optimal weight: 0.0170 chunk 230 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 60.0000 chunk 269 optimal weight: 9.9990 overall best weight: 2.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN B 18 GLN B 86 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS E 329 ASN G 129 GLN G 141 ASN K 5 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.093225 restraints weight = 34869.205| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.06 r_work: 0.2934 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22730 Z= 0.191 Angle : 0.714 13.823 30922 Z= 0.340 Chirality : 0.053 0.560 3215 Planarity : 0.004 0.037 4018 Dihedral : 11.139 157.906 3911 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.61 % Allowed : 12.90 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2939 helix: 1.14 (0.17), residues: 931 sheet: 0.25 (0.26), residues: 433 loop : -2.24 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 166 TYR 0.022 0.002 TYR H 285 PHE 0.015 0.002 PHE B 184 TRP 0.016 0.002 TRP F 311 HIS 0.005 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (22729) covalent geometry : angle 0.71393 / 0.34 (30922) hydrogen bonds : bond 0.03441 / 2.55 ( 897) hydrogen bonds : angle 4.50123 / 3.34 ( 2592) Misc. bond : bond 0.00265 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6970 (mtm180) REVERT: A 222 ARG cc_start: 0.6580 (mmm-85) cc_final: 0.6193 (mmm-85) REVERT: B 99 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: B 281 GLU cc_start: 0.6715 (tt0) cc_final: 0.6325 (mt-10) REVERT: C 231 LEU cc_start: 0.8487 (tp) cc_final: 0.8283 (tp) REVERT: C 247 TYR cc_start: 0.8189 (t80) cc_final: 0.7950 (t80) REVERT: C 293 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7657 (tmtt) REVERT: D 44 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8576 (t) REVERT: D 50 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7653 (ptt180) REVERT: E 66 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8477 (mtmm) REVERT: E 277 LEU cc_start: 0.7426 (mp) cc_final: 0.7158 (mp) REVERT: G 241 GLN cc_start: 0.8100 (pm20) cc_final: 0.7073 (tt0) REVERT: H 119 LEU cc_start: 0.9169 (mm) cc_final: 0.8626 (mm) REVERT: H 251 ASP cc_start: 0.7772 (m-30) cc_final: 0.7551 (m-30) outliers start: 50 outliers final: 35 residues processed: 188 average time/residue: 0.1742 time to fit residues: 49.0858 Evaluate side-chains 172 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 147 TRP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 38 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: [42, 70, 231, 126, 269, 128, 150, 65, 158, 194, 179] chunk 42 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 231 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 128 optimal weight: 0.2980 chunk 150 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 194 optimal weight: 0.0570 chunk 179 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN B 18 GLN B 114 HIS ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.097269 restraints weight = 34939.136| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.96 r_work: 0.3032 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22730 Z= 0.104 Angle : 0.633 12.935 30922 Z= 0.298 Chirality : 0.048 0.394 3215 Planarity : 0.003 0.035 4018 Dihedral : 10.807 148.308 3911 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.98 % Allowed : 13.58 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 2939 helix: 1.55 (0.18), residues: 930 sheet: 0.37 (0.25), residues: 431 loop : -2.14 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 172 TYR 0.021 0.001 TYR C 114 PHE 0.014 0.001 PHE A 211 TRP 0.037 0.001 TRP K 67 HIS 0.004 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (22729) covalent geometry : angle 0.63281 / 0.30 (30922) hydrogen bonds : bond 0.02905 / 2.14 ( 897) hydrogen bonds : angle 4.21155 / 3.13 ( 2592) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 HIS cc_start: 0.8518 (t70) cc_final: 0.8031 (t70) REVERT: A 235 TYR cc_start: 0.8063 (m-80) cc_final: 0.7826 (m-80) REVERT: A 258 ARG cc_start: 0.6455 (ptm160) cc_final: 0.6159 (ptt180) REVERT: B 99 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: C 181 ILE cc_start: 0.7670 (mp) cc_final: 0.7064 (mp) REVERT: C 186 PHE cc_start: 0.5164 (m-10) cc_final: 0.4947 (m-10) REVERT: C 231 LEU cc_start: 0.8499 (tp) cc_final: 0.8292 (tp) REVERT: C 293 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7696 (tmtt) REVERT: D 44 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8607 (t) REVERT: E 66 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8389 (mtmm) REVERT: E 277 LEU cc_start: 0.7407 (mp) cc_final: 0.7089 (mp) REVERT: F 38 GLU cc_start: 0.8404 (pm20) cc_final: 0.7976 (pp20) REVERT: F 295 TYR cc_start: 0.8838 (m-80) cc_final: 0.8521 (m-80) REVERT: G 241 GLN cc_start: 0.7968 (pm20) cc_final: 0.6957 (tt0) REVERT: H 119 LEU cc_start: 0.9184 (mm) cc_final: 0.8604 (mm) REVERT: H 271 TYR cc_start: 0.9104 (p90) cc_final: 0.8884 (p90) outliers start: 38 outliers final: 19 residues processed: 191 average time/residue: 0.1600 time to fit residues: 46.4943 Evaluate side-chains 162 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: [56, 162, 82, 23, 92, 183, 231, 188, 24, 170, 72] chunk 56 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 170 optimal weight: 0.0000 chunk 72 optimal weight: 0.7980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.091027 restraints weight = 34714.656| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.31 r_work: 0.2974 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.7353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22730 Z= 0.173 Angle : 0.679 12.352 30922 Z= 0.323 Chirality : 0.051 0.562 3215 Planarity : 0.004 0.038 4018 Dihedral : 10.934 152.847 3911 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.09 % Allowed : 13.73 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 2939 helix: 1.56 (0.18), residues: 931 sheet: 0.34 (0.25), residues: 436 loop : -2.14 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 184 TYR 0.018 0.002 TYR H 285 PHE 0.013 0.001 PHE C 147 TRP 0.045 0.002 TRP B 147 HIS 0.005 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (22729) covalent geometry : angle 0.67946 / 0.32 (30922) hydrogen bonds : bond 0.03245 / 2.40 ( 897) hydrogen bonds : angle 4.30894 / 3.21 ( 2592) Misc. bond : bond 0.00221 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 HIS cc_start: 0.8536 (t70) cc_final: 0.8031 (t70) REVERT: A 222 ARG cc_start: 0.6556 (mmm-85) cc_final: 0.6208 (mmm-85) REVERT: A 258 ARG cc_start: 0.6667 (ptm160) cc_final: 0.6251 (ptt180) REVERT: B 99 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: B 281 GLU cc_start: 0.6802 (tt0) cc_final: 0.6352 (mt-10) REVERT: C 247 TYR cc_start: 0.8190 (t80) cc_final: 0.7886 (t80) REVERT: C 293 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7881 (tmtt) REVERT: D 44 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8589 (t) REVERT: E 66 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8581 (mtmm) REVERT: E 277 LEU cc_start: 0.7434 (mp) cc_final: 0.7085 (mp) REVERT: F 38 GLU cc_start: 0.8352 (pm20) cc_final: 0.7942 (pp20) REVERT: G 241 GLN cc_start: 0.8012 (pm20) cc_final: 0.7017 (tt0) REVERT: H 119 LEU cc_start: 0.9153 (mm) cc_final: 0.8566 (mm) REVERT: H 251 ASP cc_start: 0.7816 (m-30) cc_final: 0.7488 (t0) outliers start: 40 outliers final: 30 residues processed: 181 average time/residue: 0.1525 time to fit residues: 42.0310 Evaluate side-chains 169 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain K residue 38 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: [30, 276, 173, 149, 258, 295, 0, 192, 228, 47, 223] chunk 30 optimal weight: 50.0000 chunk 276 optimal weight: 50.0000 chunk 173 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 258 optimal weight: 0.6980 chunk 295 optimal weight: 6.9990 chunk 0 optimal weight: 70.0000 chunk 192 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS A 249 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN D 262 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.090699 restraints weight = 35187.698| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.02 r_work: 0.2920 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.7628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 22730 Z= 0.240 Angle : 0.754 13.817 30922 Z= 0.359 Chirality : 0.056 0.723 3215 Planarity : 0.004 0.044 4018 Dihedral : 11.177 160.365 3911 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.14 % Allowed : 14.10 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.16), residues: 2939 helix: 1.37 (0.17), residues: 931 sheet: 0.21 (0.25), residues: 435 loop : -2.12 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 265 TYR 0.026 0.002 TYR C 305 PHE 0.016 0.002 PHE B 184 TRP 0.035 0.002 TRP B 147 HIS 0.006 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (22729) covalent geometry : angle 0.75387 / 0.36 (30922) hydrogen bonds : bond 0.03605 / 2.68 ( 897) hydrogen bonds : angle 4.51724 / 3.36 ( 2592) Misc. bond : bond 0.00098 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 HIS cc_start: 0.8483 (t70) cc_final: 0.8003 (t70) REVERT: A 222 ARG cc_start: 0.6820 (mmm-85) cc_final: 0.6301 (mmm-85) REVERT: A 258 ARG cc_start: 0.6477 (ptm160) cc_final: 0.6028 (ptt180) REVERT: B 99 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: B 281 GLU cc_start: 0.7173 (tt0) cc_final: 0.6666 (mt-10) REVERT: D 44 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8694 (t) REVERT: E 277 LEU cc_start: 0.7363 (mp) cc_final: 0.7027 (mp) REVERT: G 241 GLN cc_start: 0.8147 (pm20) cc_final: 0.7313 (tt0) REVERT: H 119 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8672 (mm) REVERT: K 1 MET cc_start: 0.5005 (ptt) cc_final: 0.0924 (ttt) REVERT: K 23 LYS cc_start: 0.7416 (ptpp) cc_final: 0.7097 (ptpp) REVERT: K 32 TYR cc_start: 0.8173 (m-10) cc_final: 0.7501 (m-80) outliers start: 41 outliers final: 33 residues processed: 178 average time/residue: 0.1691 time to fit residues: 45.0779 Evaluate side-chains 170 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 329 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 336 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: [276, 239, 156, 258, 184, 32, 223, 187, 250, 81, 89] chunk 276 optimal weight: 50.0000 chunk 239 optimal weight: 3.9990 chunk 156 optimal weight: 0.0870 chunk 258 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 223 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN D 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.096966 restraints weight = 34774.895| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.92 r_work: 0.3043 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.7791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 22730 Z= 0.106 Angle : 0.638 13.593 30922 Z= 0.301 Chirality : 0.047 0.423 3215 Planarity : 0.003 0.036 4018 Dihedral : 10.782 150.233 3911 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.51 % Allowed : 15.14 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2939 helix: 1.80 (0.18), residues: 927 sheet: 0.30 (0.25), residues: 442 loop : -2.06 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 184 TYR 0.017 0.001 TYR C 305 PHE 0.009 0.001 PHE B 184 TRP 0.027 0.001 TRP B 147 HIS 0.004 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (22729) covalent geometry : angle 0.63843 / 0.30 (30922) hydrogen bonds : bond 0.02897 / 2.13 ( 897) hydrogen bonds : angle 4.15056 / 3.09 ( 2592) Misc. bond : bond 0.00096 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8314 (mmtt) REVERT: A 200 HIS cc_start: 0.8487 (t70) cc_final: 0.8073 (t70) REVERT: A 222 ARG cc_start: 0.6704 (mmm-85) cc_final: 0.5826 (mpt180) REVERT: A 258 ARG cc_start: 0.6367 (ptm160) cc_final: 0.5934 (ptt180) REVERT: B 99 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: B 281 GLU cc_start: 0.6886 (tt0) cc_final: 0.6567 (mt-10) REVERT: C 293 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7736 (tmtt) REVERT: D 44 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8642 (t) REVERT: E 66 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8648 (mtmm) REVERT: F 38 GLU cc_start: 0.8295 (pm20) cc_final: 0.7536 (pp20) REVERT: G 241 GLN cc_start: 0.7990 (pm20) cc_final: 0.7227 (tt0) REVERT: H 119 LEU cc_start: 0.9216 (mm) cc_final: 0.8654 (mm) REVERT: H 259 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7148 (ptmt) REVERT: K 1 MET cc_start: 0.5047 (ptt) cc_final: 0.0956 (ttt) REVERT: K 32 TYR cc_start: 0.8170 (m-10) cc_final: 0.7194 (m-80) outliers start: 29 outliers final: 18 residues processed: 188 average time/residue: 0.1745 time to fit residues: 48.8144 Evaluate side-chains 164 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 336 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: [243, 175, 89, 198, 120, 79, 148, 189, 197, 8, 226] chunk 243 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 198 optimal weight: 0.3980 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 226 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096694 restraints weight = 34901.057| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.21 r_work: 0.2994 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.7853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22730 Z= 0.124 Angle : 0.641 12.581 30922 Z= 0.303 Chirality : 0.048 0.449 3215 Planarity : 0.003 0.033 4018 Dihedral : 10.752 149.123 3911 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.31 % Allowed : 15.51 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2939 helix: 1.87 (0.18), residues: 934 sheet: 0.42 (0.25), residues: 440 loop : -2.02 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 184 TYR 0.022 0.002 TYR C 305 PHE 0.010 0.001 PHE B 184 TRP 0.052 0.001 TRP K 67 HIS 0.004 0.001 HIS E 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (22729) covalent geometry : angle 0.64062 / 0.30 (30922) hydrogen bonds : bond 0.02958 / 2.19 ( 897) hydrogen bonds : angle 4.13217 / 3.08 ( 2592) Misc. bond : bond 0.00059 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8224 (mmtt) REVERT: A 200 HIS cc_start: 0.8519 (t70) cc_final: 0.8077 (t70) REVERT: A 222 ARG cc_start: 0.6704 (mmm-85) cc_final: 0.5836 (mpt180) REVERT: A 258 ARG cc_start: 0.6325 (ptm160) cc_final: 0.5971 (ptt180) REVERT: B 99 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: B 281 GLU cc_start: 0.6981 (tt0) cc_final: 0.6514 (mt-10) REVERT: C 283 GLU cc_start: 0.8406 (pm20) cc_final: 0.8142 (mm-30) REVERT: C 293 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7722 (tmtt) REVERT: D 44 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8587 (t) REVERT: E 66 LYS cc_start: 0.9024 (ttpt) cc_final: 0.8691 (mtmm) REVERT: F 38 GLU cc_start: 0.8309 (pm20) cc_final: 0.7550 (pp20) REVERT: F 295 TYR cc_start: 0.8883 (m-80) cc_final: 0.8539 (m-80) REVERT: G 241 GLN cc_start: 0.7979 (pm20) cc_final: 0.7206 (tt0) REVERT: H 119 LEU cc_start: 0.9212 (mm) cc_final: 0.8682 (mm) REVERT: H 250 ARG cc_start: 0.8017 (ptp90) cc_final: 0.7615 (ptt180) REVERT: H 259 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.6966 (ptmt) REVERT: K 1 MET cc_start: 0.4806 (ptt) cc_final: 0.0807 (ttt) REVERT: K 32 TYR cc_start: 0.8101 (m-10) cc_final: 0.7322 (m-80) outliers start: 25 outliers final: 22 residues processed: 163 average time/residue: 0.1664 time to fit residues: 41.1316 Evaluate side-chains 162 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 336 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: [14, 198, 104, 124, 219, 127, 194, 10, 146, 154, 170] chunk 14 optimal weight: 60.0000 chunk 198 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 219 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 10 optimal weight: 40.0000 chunk 146 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.134957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.095168 restraints weight = 34777.945| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.94 r_work: 0.2963 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.7915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22730 Z= 0.164 Angle : 0.672 12.508 30922 Z= 0.320 Chirality : 0.050 0.535 3215 Planarity : 0.003 0.030 4018 Dihedral : 10.848 152.235 3911 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.62 % Allowed : 15.56 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2939 helix: 1.79 (0.18), residues: 931 sheet: 0.41 (0.25), residues: 440 loop : -2.01 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 184 TYR 0.021 0.002 TYR C 305 PHE 0.011 0.001 PHE B 184 TRP 0.042 0.002 TRP K 67 HIS 0.004 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (22729) covalent geometry : angle 0.67235 / 0.32 (30922) hydrogen bonds : bond 0.03175 / 2.36 ( 897) hydrogen bonds : angle 4.23747 / 3.17 ( 2592) Misc. bond : bond 0.00075 / 0.04 ( 1) =============================================================================== Job complete usr+sys time: 6238.06 seconds wall clock time: 106 minutes 55.42 seconds (6415.42 seconds total)