Starting phenix.real_space_refine on Sun Feb 18 22:35:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/02_2024/6b48_7052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/02_2024/6b48_7052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/02_2024/6b48_7052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/02_2024/6b48_7052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/02_2024/6b48_7052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/02_2024/6b48_7052.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 0.748 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 786 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Se 5 7.20 5 P 59 5.49 5 S 18 5.16 5 C 13563 2.51 5 N 4184 2.21 5 O 4504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 222": "NH1" <-> "NH2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 166": "NH1" <-> "NH2" Residue "K ARG 6": "NH1" <-> "NH2" Residue "K PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22333 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, 'ASP:plan': 20, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 9, 'HIS:plan': 9, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 29} 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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASP:plan': 3} 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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2566 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "H" 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: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 786 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} 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: {'GLN:plan1': 9, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 10, 'GLU:plan': 11, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 414 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 19, 'rna3p': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 11.85, per 1000 atoms: 0.53 Number of scatterers: 22333 At special positions: 0 Unit cell: (131.04, 126.84, 161.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 5 33.99 S 18 16.00 P 59 15.00 O 4504 8.00 N 4184 7.00 C 13563 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.13 Conformation dependent library (CDL) restraints added in 4.1 seconds 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 40 sheets defined 29.2% alpha, 12.0% beta 1 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 7.02 Creating SS restraints... Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 33 through 48 removed outlier: 4.405A pdb=" N LYS A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 58 removed outlier: 4.247A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.808A pdb=" N LEU A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 213 through 222 removed outlier: 3.597A pdb=" N ALA A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.552A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 314 through 317 Processing helix chain 'A' and resid 318 through 342 removed outlier: 3.724A pdb=" N ALA A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 408 through 430 removed outlier: 3.834A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.651A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 removed outlier: 3.744A pdb=" N ARG B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.951A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 129 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 257 through 264 Processing helix chain 'C' and resid 303 through 313 removed outlier: 3.635A pdb=" N LEU C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.865A pdb=" N ASP D 34 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 70 removed outlier: 4.068A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.780A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 319 through 332 Processing helix chain 'E' and resid 32 through 36 removed outlier: 3.587A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.850A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 304 through 312 Processing helix chain 'E' and resid 319 through 332 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.768A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.604A pdb=" N ILE F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 129 Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 304 through 312 Processing helix chain 'F' and resid 319 through 332 Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 112 through 129 removed outlier: 3.653A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 190 through 204 removed outlier: 3.762A pdb=" N SER G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.750A pdb=" N ILE G 260 " --> pdb=" O HIS G 256 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 312 Processing helix chain 'G' and resid 319 through 332 Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 63 through 72 removed outlier: 3.591A pdb=" N LEU H 67 " --> pdb=" O ASP H 63 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN H 72 " --> pdb=" O ASP H 68 " (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 190 through 203 Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.733A pdb=" N ARG H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.611A pdb=" N LEU H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 332 Processing helix chain 'K' and resid 60 through 66 Processing helix chain 'K' and resid 85 through 95 Processing helix chain 'L' and resid 16 through 31 removed outlier: 3.888A pdb=" N LEU L 20 " --> pdb=" O PRO L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 69 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.777A pdb=" N HIS L 82 " --> pdb=" O LEU L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 119 removed outlier: 4.639A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG L 113 " --> pdb=" O PRO L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.676A pdb=" N ARG B 278 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU B 281 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU B 308 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 242 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.997A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.847A pdb=" N VAL B 187 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 14 Processing sheet with id=AA7, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AA8, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.619A pdb=" N LEU D 12 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.886A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 24 through 26 removed outlier: 3.675A pdb=" N ARG D 94 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 46 through 51 Processing sheet with id=AB3, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.577A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 225 " --> pdb=" O ALA D 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 249 Processing sheet with id=AB5, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.597A pdb=" N VAL D 288 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.526A pdb=" N LEU E 12 " --> pdb=" O PHE E 336 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE E 14 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY E 334 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.504A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 19 through 20 removed outlier: 5.015A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA E 252 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 44 through 50 removed outlier: 3.727A pdb=" N ARG E 45 " --> pdb=" O VAL E 81 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 229 through 230 removed outlier: 4.563A pdb=" N THR E 245 " --> pdb=" O GLU E 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AC3, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.927A pdb=" N VAL E 288 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS E 293 " --> pdb=" O VAL E 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.353A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS F 164 " --> pdb=" O ARG F 172 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG F 172 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.789A pdb=" N ARG F 94 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 23 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 255 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA F 252 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 46 through 51 removed outlier: 3.803A pdb=" N ASN F 75 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC9, first strand: chain 'G' and resid 12 through 14 removed outlier: 3.760A pdb=" N PHE G 336 " --> pdb=" O LEU G 12 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AD2, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.303A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 46 through 50 Processing sheet with id=AD4, first strand: chain 'G' and resid 229 through 230 removed outlier: 3.961A pdb=" N THR G 245 " --> pdb=" O GLU G 230 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 248 through 249 Processing sheet with id=AD6, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD7, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.735A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY H 334 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 170 through 175 removed outlier: 3.899A pdb=" N ARG H 172 " --> pdb=" O HIS H 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 159 " --> pdb=" O PHE H 216 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE H 165 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AE1, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AE2, first strand: chain 'K' and resid 6 through 8 removed outlier: 3.969A pdb=" N ARG K 6 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL K 26 " --> pdb=" O ARG K 6 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 13 through 15 removed outlier: 3.780A pdb=" N PHE K 18 " --> pdb=" O ILE K 15 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 39 through 40 772 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 6.93 Time building geometry restraints manager: 8.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7830 1.35 - 1.50: 6643 1.50 - 1.65: 8343 1.65 - 1.80: 21 1.80 - 1.95: 15 Bond restraints: 22852 Sorted by residual: bond pdb=" CG1 ILE G 327 " pdb=" CD1 ILE G 327 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.25e+00 bond pdb=" CG1 ILE F 327 " pdb=" CD1 ILE F 327 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.52e+00 bond pdb=" CG1 ILE D 327 " pdb=" CD1 ILE D 327 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.94e+00 bond pdb=" CB ASP K 17 " pdb=" CG ASP K 17 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.82e+00 bond pdb=" CG1 ILE E 327 " pdb=" CD1 ILE E 327 " ideal model delta sigma weight residual 1.513 1.424 0.089 3.90e-02 6.57e+02 5.21e+00 ... (remaining 22847 not shown) Histogram of bond angle deviations from ideal: 97.30 - 104.76: 562 104.76 - 112.22: 10575 112.22 - 119.67: 8292 119.67 - 127.13: 11296 127.13 - 134.59: 366 Bond angle restraints: 31091 Sorted by residual: angle pdb=" C GLU K 8 " pdb=" N ASN K 9 " pdb=" CA ASN K 9 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C SER A 252 " pdb=" N GLN A 253 " pdb=" CA GLN A 253 " ideal model delta sigma weight residual 121.54 130.82 -9.28 1.91e+00 2.74e-01 2.36e+01 angle pdb=" CA LEU B 181 " pdb=" CB LEU B 181 " pdb=" CG LEU B 181 " ideal model delta sigma weight residual 116.30 133.21 -16.91 3.50e+00 8.16e-02 2.33e+01 angle pdb=" C ASN K 16 " pdb=" N ASP K 17 " pdb=" CA ASP K 17 " ideal model delta sigma weight residual 126.45 134.59 -8.14 1.77e+00 3.19e-01 2.11e+01 angle pdb=" CA LEU H 231 " pdb=" CB LEU H 231 " pdb=" CG LEU H 231 " ideal model delta sigma weight residual 116.30 131.66 -15.36 3.50e+00 8.16e-02 1.93e+01 ... (remaining 31086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.19: 12760 32.19 - 64.37: 290 64.37 - 96.56: 33 96.56 - 128.74: 2 128.74 - 160.93: 2 Dihedral angle restraints: 13087 sinusoidal: 5483 harmonic: 7604 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 39.07 160.93 1 1.50e+01 4.44e-03 8.30e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 48.90 151.10 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" CA ARG A 222 " pdb=" C ARG A 222 " pdb=" N SER A 223 " pdb=" CA SER A 223 " ideal model delta harmonic sigma weight residual 180.00 143.32 36.68 0 5.00e+00 4.00e-02 5.38e+01 ... (remaining 13084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2727 0.077 - 0.153: 467 0.153 - 0.230: 38 0.230 - 0.307: 6 0.307 - 0.383: 2 Chirality restraints: 3240 Sorted by residual: chirality pdb=" CB ILE K 15 " pdb=" CA ILE K 15 " pdb=" CG1 ILE K 15 " pdb=" CG2 ILE K 15 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB VAL K 49 " pdb=" CA VAL K 49 " pdb=" CG1 VAL K 49 " pdb=" CG2 VAL K 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB ILE E 53 " pdb=" CA ILE E 53 " pdb=" CG1 ILE E 53 " pdb=" CG2 ILE E 53 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3237 not shown) Planarity restraints: 4040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 249 " 0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 250 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 250 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 250 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 25 " -0.048 5.00e-02 4.00e+02 7.21e-02 8.32e+00 pdb=" N PRO B 26 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 263 " 0.027 2.00e-02 2.50e+03 1.70e-02 7.22e+00 pdb=" CG TRP A 263 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 263 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 263 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 263 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 263 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 263 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 263 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 263 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 263 " 0.007 2.00e-02 2.50e+03 ... (remaining 4037 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3496 2.76 - 3.29: 19674 3.29 - 3.83: 35891 3.83 - 4.36: 40521 4.36 - 4.90: 69553 Nonbonded interactions: 169135 Sorted by model distance: nonbonded pdb=" O PHE H 14 " pdb=" O2' G M 5 " model vdw 2.223 2.440 nonbonded pdb=" O GLU D 283 " pdb=" OH TYR D 325 " model vdw 2.259 2.440 nonbonded pdb=" O PRO A 266 " pdb=" OG1 THR B 28 " model vdw 2.268 2.440 nonbonded pdb=" ND2 ASN D 262 " pdb=" OP2 G M 32 " model vdw 2.299 2.520 nonbonded pdb=" OH TYR D 305 " pdb=" O SER E 54 " model vdw 2.305 2.440 ... (remaining 169130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 4.300 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 61.650 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.090 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 22852 Z= 0.453 Angle : 0.979 16.907 31091 Z= 0.530 Chirality : 0.057 0.383 3240 Planarity : 0.006 0.081 4040 Dihedral : 13.640 160.929 8511 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.07 % Favored : 87.83 % Rotamer: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.93 (0.12), residues: 2950 helix: -3.03 (0.12), residues: 876 sheet: -2.63 (0.24), residues: 393 loop : -3.72 (0.12), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP F 311 HIS 0.019 0.003 HIS H 324 PHE 0.028 0.003 PHE H 216 TYR 0.025 0.003 TYR E 305 ARG 0.014 0.001 ARG G 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 418 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8647 (mtmt) REVERT: B 94 THR cc_start: 0.8553 (t) cc_final: 0.8159 (m) REVERT: B 263 LEU cc_start: 0.8911 (mm) cc_final: 0.8595 (tp) REVERT: B 290 LEU cc_start: 0.7581 (mt) cc_final: 0.7376 (mt) REVERT: B 310 ASP cc_start: 0.7289 (t70) cc_final: 0.7047 (m-30) REVERT: C 323 GLN cc_start: 0.6494 (mt0) cc_final: 0.5793 (mm110) REVERT: D 94 ARG cc_start: 0.6704 (ttt-90) cc_final: 0.6388 (ttp-170) REVERT: D 191 GLU cc_start: 0.6048 (tt0) cc_final: 0.5436 (pm20) REVERT: D 284 PRO cc_start: 0.8756 (Cg_exo) cc_final: 0.7903 (Cg_endo) REVERT: E 208 HIS cc_start: 0.7098 (t-90) cc_final: 0.6623 (t-90) REVERT: F 214 VAL cc_start: 0.8919 (t) cc_final: 0.8718 (m) REVERT: F 223 GLN cc_start: 0.7347 (tp-100) cc_final: 0.7133 (mm-40) REVERT: F 301 LYS cc_start: 0.8240 (mmpt) cc_final: 0.7913 (mmtm) REVERT: G 197 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7698 (tm-30) REVERT: G 301 LYS cc_start: 0.8513 (mmpt) cc_final: 0.8146 (mmtm) REVERT: H 285 TYR cc_start: 0.8029 (m-80) cc_final: 0.7583 (m-80) REVERT: K 31 ARG cc_start: 0.7822 (ptm-80) cc_final: 0.7361 (ptm-80) REVERT: K 78 PRO cc_start: 0.8641 (Cg_exo) cc_final: 0.8429 (Cg_endo) REVERT: K 84 THR cc_start: 0.8831 (p) cc_final: 0.8320 (p) outliers start: 2 outliers final: 0 residues processed: 420 average time/residue: 0.4442 time to fit residues: 270.8260 Evaluate side-chains 235 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 77 optimal weight: 40.0000 chunk 152 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 90 optimal weight: 40.0000 chunk 142 optimal weight: 2.9990 chunk 174 optimal weight: 0.2980 chunk 271 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS B 18 GLN B 19 ASN B 196 HIS C 120 GLN C 129 GLN C 141 ASN C 223 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN F 83 ASN F 120 GLN F 127 ASN F 129 GLN F 324 HIS G 120 GLN G 129 GLN H 129 GLN H 164 HIS K 37 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22852 Z= 0.206 Angle : 0.606 12.148 31091 Z= 0.319 Chirality : 0.042 0.252 3240 Planarity : 0.004 0.064 4040 Dihedral : 14.638 159.211 4155 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.37 % Allowed : 9.96 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.14), residues: 2950 helix: -1.31 (0.16), residues: 888 sheet: -2.31 (0.25), residues: 373 loop : -3.24 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 316 HIS 0.007 0.001 HIS D 324 PHE 0.021 0.002 PHE K 46 TYR 0.014 0.001 TYR H 271 ARG 0.007 0.001 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 286 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 SER cc_start: 0.7855 (m) cc_final: 0.7641 (m) REVERT: A 242 LYS cc_start: 0.9217 (mtpp) cc_final: 0.8554 (mtmt) REVERT: A 247 LYS cc_start: 0.7924 (tppt) cc_final: 0.7273 (mmtt) REVERT: B 27 LEU cc_start: 0.7894 (pp) cc_final: 0.7564 (mm) REVERT: B 77 ARG cc_start: 0.7269 (mtp-110) cc_final: 0.7008 (ttp-170) REVERT: B 93 SER cc_start: 0.7600 (p) cc_final: 0.7161 (p) REVERT: B 94 THR cc_start: 0.8290 (t) cc_final: 0.7796 (m) REVERT: B 263 LEU cc_start: 0.8914 (mm) cc_final: 0.8520 (tp) REVERT: B 310 ASP cc_start: 0.7303 (t70) cc_final: 0.7077 (m-30) REVERT: C 323 GLN cc_start: 0.6602 (mt0) cc_final: 0.5906 (mm110) REVERT: D 94 ARG cc_start: 0.6724 (ttt-90) cc_final: 0.6306 (ttp-170) REVERT: D 161 ARG cc_start: 0.5459 (mtt180) cc_final: 0.5228 (mtt180) REVERT: D 191 GLU cc_start: 0.6093 (tt0) cc_final: 0.5449 (pm20) REVERT: D 283 GLU cc_start: 0.7403 (tt0) cc_final: 0.6973 (tt0) REVERT: D 296 ARG cc_start: 0.4730 (mtt-85) cc_final: 0.4231 (mtp85) REVERT: E 208 HIS cc_start: 0.6886 (t-90) cc_final: 0.6499 (t-90) REVERT: E 271 TYR cc_start: 0.8321 (p90) cc_final: 0.8004 (p90) REVERT: F 83 ASN cc_start: 0.8312 (m-40) cc_final: 0.7654 (m110) REVERT: G 197 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7703 (tm-30) REVERT: G 301 LYS cc_start: 0.8452 (mmpt) cc_final: 0.8045 (mmtm) REVERT: K 31 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.7548 (ptm160) REVERT: K 51 TYR cc_start: 0.6937 (t80) cc_final: 0.6186 (t80) outliers start: 46 outliers final: 26 residues processed: 312 average time/residue: 0.3768 time to fit residues: 176.3691 Evaluate side-chains 262 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 184 ARG Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 74 optimal weight: 50.0000 chunk 272 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 overall best weight: 3.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 HIS H 223 GLN H 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22852 Z= 0.242 Angle : 0.603 12.295 31091 Z= 0.315 Chirality : 0.042 0.198 3240 Planarity : 0.004 0.065 4040 Dihedral : 14.451 159.280 4155 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.20 % Allowed : 11.46 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.15), residues: 2950 helix: -0.50 (0.17), residues: 887 sheet: -2.07 (0.26), residues: 387 loop : -3.00 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 316 HIS 0.008 0.001 HIS D 324 PHE 0.019 0.002 PHE D 304 TYR 0.013 0.002 TYR D 285 ARG 0.007 0.001 ARG D 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 252 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 SER cc_start: 0.7990 (m) cc_final: 0.7766 (m) REVERT: A 242 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8531 (mtmt) REVERT: A 247 LYS cc_start: 0.7958 (tppt) cc_final: 0.7393 (mmtt) REVERT: B 77 ARG cc_start: 0.7297 (mtp-110) cc_final: 0.7022 (ttp-110) REVERT: B 94 THR cc_start: 0.8295 (t) cc_final: 0.7977 (m) REVERT: B 310 ASP cc_start: 0.7368 (t70) cc_final: 0.7108 (m-30) REVERT: C 323 GLN cc_start: 0.6551 (mt0) cc_final: 0.5883 (mm110) REVERT: D 94 ARG cc_start: 0.6638 (ttt-90) cc_final: 0.6209 (ttp-170) REVERT: D 161 ARG cc_start: 0.5526 (mtt180) cc_final: 0.5217 (mtt180) REVERT: D 191 GLU cc_start: 0.6265 (tt0) cc_final: 0.5542 (pm20) REVERT: D 267 ILE cc_start: 0.3880 (mm) cc_final: 0.3674 (mm) REVERT: D 270 TRP cc_start: 0.5803 (m-90) cc_final: 0.5439 (m100) REVERT: D 283 GLU cc_start: 0.7514 (tt0) cc_final: 0.6959 (tt0) REVERT: D 293 LYS cc_start: 0.7555 (mttt) cc_final: 0.6276 (mtmt) REVERT: E 208 HIS cc_start: 0.6915 (t-90) cc_final: 0.6504 (t-90) REVERT: E 271 TYR cc_start: 0.8371 (p90) cc_final: 0.7984 (p90) REVERT: E 302 LEU cc_start: 0.8679 (tp) cc_final: 0.8334 (tt) REVERT: G 301 LYS cc_start: 0.8419 (mmpt) cc_final: 0.8028 (mmtm) REVERT: K 31 ARG cc_start: 0.7813 (ptm-80) cc_final: 0.7578 (ptm160) outliers start: 62 outliers final: 42 residues processed: 287 average time/residue: 0.3696 time to fit residues: 159.6062 Evaluate side-chains 272 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 230 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 50.0000 chunk 129 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 272 optimal weight: 0.0970 chunk 289 optimal weight: 40.0000 chunk 142 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN H 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22852 Z= 0.184 Angle : 0.559 12.020 31091 Z= 0.291 Chirality : 0.041 0.196 3240 Planarity : 0.004 0.061 4040 Dihedral : 14.281 158.877 4155 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.05 % Allowed : 12.60 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.15), residues: 2950 helix: 0.00 (0.18), residues: 890 sheet: -1.83 (0.27), residues: 376 loop : -2.86 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 316 HIS 0.005 0.001 HIS A 188 PHE 0.020 0.001 PHE K 46 TYR 0.025 0.001 TYR D 114 ARG 0.006 0.000 ARG D 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 247 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8517 (mtmt) REVERT: A 247 LYS cc_start: 0.7905 (tppt) cc_final: 0.7390 (mmtt) REVERT: B 27 LEU cc_start: 0.7944 (pp) cc_final: 0.7648 (mm) REVERT: B 77 ARG cc_start: 0.7276 (mtp-110) cc_final: 0.7047 (ttp-110) REVERT: B 94 THR cc_start: 0.8237 (t) cc_final: 0.7933 (m) REVERT: B 263 LEU cc_start: 0.8850 (mm) cc_final: 0.8400 (tp) REVERT: B 290 LEU cc_start: 0.7471 (mt) cc_final: 0.6800 (mt) REVERT: B 310 ASP cc_start: 0.7312 (t70) cc_final: 0.7068 (m-30) REVERT: C 323 GLN cc_start: 0.6520 (mt0) cc_final: 0.5855 (mm110) REVERT: D 94 ARG cc_start: 0.6605 (ttt-90) cc_final: 0.6215 (ttp-170) REVERT: D 191 GLU cc_start: 0.6229 (tt0) cc_final: 0.5515 (pm20) REVERT: D 283 GLU cc_start: 0.7601 (tt0) cc_final: 0.6983 (tt0) REVERT: D 293 LYS cc_start: 0.7468 (mttt) cc_final: 0.6212 (mtmt) REVERT: E 271 TYR cc_start: 0.8301 (p90) cc_final: 0.7923 (p90) REVERT: E 302 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8252 (tt) REVERT: G 301 LYS cc_start: 0.8342 (mmpt) cc_final: 0.8010 (mmtm) REVERT: K 31 ARG cc_start: 0.7812 (ptm-80) cc_final: 0.7539 (ptm160) REVERT: K 90 GLU cc_start: 0.8216 (pt0) cc_final: 0.7936 (pt0) outliers start: 59 outliers final: 39 residues processed: 282 average time/residue: 0.3711 time to fit residues: 160.7489 Evaluate side-chains 265 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 225 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 4 optimal weight: 40.0000 chunk 215 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN G 120 GLN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 22852 Z= 0.319 Angle : 0.628 12.250 31091 Z= 0.324 Chirality : 0.043 0.213 3240 Planarity : 0.004 0.059 4040 Dihedral : 14.263 159.649 4155 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.12 % Favored : 88.85 % Rotamer: Outliers : 3.56 % Allowed : 13.32 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.15), residues: 2950 helix: 0.04 (0.18), residues: 885 sheet: -1.90 (0.26), residues: 394 loop : -2.84 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 270 HIS 0.007 0.001 HIS D 324 PHE 0.024 0.002 PHE K 46 TYR 0.012 0.002 TYR C 271 ARG 0.006 0.001 ARG D 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 238 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8574 (mtmt) REVERT: A 247 LYS cc_start: 0.7963 (tppt) cc_final: 0.7460 (mmtt) REVERT: B 77 ARG cc_start: 0.7290 (mtp-110) cc_final: 0.7055 (ttp-110) REVERT: B 120 ASP cc_start: 0.8070 (m-30) cc_final: 0.7609 (t0) REVERT: B 290 LEU cc_start: 0.7514 (mt) cc_final: 0.7226 (mt) REVERT: B 308 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8538 (mp0) REVERT: B 310 ASP cc_start: 0.7329 (t70) cc_final: 0.7108 (m-30) REVERT: C 184 ARG cc_start: 0.2600 (mtp-110) cc_final: 0.1676 (ptt90) REVERT: C 323 GLN cc_start: 0.6548 (mt0) cc_final: 0.5871 (mm110) REVERT: D 94 ARG cc_start: 0.6648 (ttt-90) cc_final: 0.6306 (ttp-170) REVERT: D 191 GLU cc_start: 0.6409 (tt0) cc_final: 0.5597 (pm20) REVERT: D 283 GLU cc_start: 0.7535 (tt0) cc_final: 0.6942 (tt0) REVERT: D 293 LYS cc_start: 0.7535 (mttt) cc_final: 0.6250 (mtmt) REVERT: E 271 TYR cc_start: 0.8390 (p90) cc_final: 0.8031 (p90) REVERT: E 302 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8355 (tt) REVERT: F 231 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8281 (tp) REVERT: G 301 LYS cc_start: 0.8374 (mmpt) cc_final: 0.8070 (mmtm) REVERT: K 31 ARG cc_start: 0.7800 (ptm-80) cc_final: 0.7567 (ptm160) REVERT: K 90 GLU cc_start: 0.8232 (pt0) cc_final: 0.7911 (pt0) outliers start: 69 outliers final: 52 residues processed: 277 average time/residue: 0.3649 time to fit residues: 155.4151 Evaluate side-chains 278 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 223 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 169 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 289 optimal weight: 50.0000 chunk 240 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN H 83 ASN H 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22852 Z= 0.272 Angle : 0.609 11.962 31091 Z= 0.314 Chirality : 0.042 0.205 3240 Planarity : 0.004 0.056 4040 Dihedral : 14.224 159.870 4155 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 3.67 % Allowed : 14.15 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.15), residues: 2950 helix: 0.19 (0.18), residues: 876 sheet: -1.80 (0.26), residues: 397 loop : -2.76 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 316 HIS 0.006 0.001 HIS A 188 PHE 0.024 0.002 PHE E 226 TYR 0.014 0.001 TYR H 285 ARG 0.006 0.000 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 230 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8627 (mtmt) REVERT: A 247 LYS cc_start: 0.7978 (tppt) cc_final: 0.7525 (mmtt) REVERT: B 77 ARG cc_start: 0.7286 (mtp-110) cc_final: 0.7083 (ttp-110) REVERT: B 94 THR cc_start: 0.8339 (t) cc_final: 0.8081 (m) REVERT: B 120 ASP cc_start: 0.8075 (m-30) cc_final: 0.7612 (t0) REVERT: B 288 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7531 (pt0) REVERT: B 308 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: B 310 ASP cc_start: 0.7315 (t70) cc_final: 0.7098 (m-30) REVERT: C 184 ARG cc_start: 0.2582 (mtp-110) cc_final: 0.1641 (ptt90) REVERT: C 323 GLN cc_start: 0.6521 (mt0) cc_final: 0.5853 (mm110) REVERT: D 94 ARG cc_start: 0.6653 (ttt-90) cc_final: 0.6310 (ttp-170) REVERT: D 191 GLU cc_start: 0.6433 (tt0) cc_final: 0.5593 (pm20) REVERT: D 270 TRP cc_start: 0.5719 (m-90) cc_final: 0.5355 (m-90) REVERT: E 302 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8350 (tt) REVERT: F 231 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8129 (tp) REVERT: G 301 LYS cc_start: 0.8384 (mmpt) cc_final: 0.8087 (mmtm) REVERT: K 31 ARG cc_start: 0.7824 (ptm-80) cc_final: 0.7564 (ptm160) REVERT: K 90 GLU cc_start: 0.8212 (pt0) cc_final: 0.7917 (pt0) outliers start: 71 outliers final: 54 residues processed: 272 average time/residue: 0.3775 time to fit residues: 158.0485 Evaluate side-chains 283 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 226 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 chunk 164 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 161 optimal weight: 0.0670 chunk 288 optimal weight: 20.0000 chunk 180 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 120 GLN H 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22852 Z= 0.210 Angle : 0.577 11.692 31091 Z= 0.296 Chirality : 0.041 0.200 3240 Planarity : 0.003 0.054 4040 Dihedral : 14.150 159.716 4155 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.61 % Allowed : 14.61 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.15), residues: 2950 helix: 0.36 (0.19), residues: 877 sheet: -1.67 (0.26), residues: 396 loop : -2.66 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 316 HIS 0.006 0.001 HIS A 188 PHE 0.026 0.001 PHE E 226 TYR 0.014 0.001 TYR H 285 ARG 0.007 0.000 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 243 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8609 (mtmt) REVERT: A 247 LYS cc_start: 0.7943 (tppt) cc_final: 0.7521 (mmtt) REVERT: B 94 THR cc_start: 0.8312 (t) cc_final: 0.8067 (m) REVERT: B 120 ASP cc_start: 0.8068 (m-30) cc_final: 0.7614 (t0) REVERT: B 263 LEU cc_start: 0.8861 (mm) cc_final: 0.8392 (tp) REVERT: B 310 ASP cc_start: 0.7288 (t70) cc_final: 0.7050 (m-30) REVERT: C 184 ARG cc_start: 0.2554 (mtp-110) cc_final: 0.1638 (ptt90) REVERT: C 323 GLN cc_start: 0.6493 (mt0) cc_final: 0.5817 (mm110) REVERT: D 94 ARG cc_start: 0.6616 (ttt-90) cc_final: 0.6264 (ttp-170) REVERT: D 191 GLU cc_start: 0.6403 (tt0) cc_final: 0.5589 (pm20) REVERT: D 283 GLU cc_start: 0.7601 (tt0) cc_final: 0.6916 (tt0) REVERT: D 293 LYS cc_start: 0.7513 (mttt) cc_final: 0.6248 (mtmt) REVERT: E 212 GLU cc_start: 0.7192 (pt0) cc_final: 0.6954 (tt0) REVERT: E 302 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8280 (tt) REVERT: F 231 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8030 (tp) REVERT: G 301 LYS cc_start: 0.8386 (mmpt) cc_final: 0.8030 (mmtm) REVERT: K 31 ARG cc_start: 0.7832 (ptm-80) cc_final: 0.7564 (ptm160) REVERT: K 90 GLU cc_start: 0.8201 (pt0) cc_final: 0.7887 (pt0) outliers start: 70 outliers final: 56 residues processed: 283 average time/residue: 0.3462 time to fit residues: 149.9498 Evaluate side-chains 279 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 221 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 86 optimal weight: 0.1980 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 196 optimal weight: 0.4980 chunk 142 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 chunk 226 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN F 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22852 Z= 0.150 Angle : 0.542 12.882 31091 Z= 0.278 Chirality : 0.040 0.194 3240 Planarity : 0.003 0.049 4040 Dihedral : 14.020 159.140 4155 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.05 % Allowed : 15.28 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.16), residues: 2950 helix: 0.62 (0.19), residues: 873 sheet: -1.46 (0.27), residues: 381 loop : -2.54 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 39 HIS 0.004 0.001 HIS G 324 PHE 0.023 0.001 PHE E 226 TYR 0.014 0.001 TYR H 285 ARG 0.008 0.000 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 255 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.7529 (mmt-90) REVERT: A 242 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8601 (mtmt) REVERT: B 94 THR cc_start: 0.8132 (t) cc_final: 0.7837 (m) REVERT: B 120 ASP cc_start: 0.8062 (m-30) cc_final: 0.7606 (t0) REVERT: B 263 LEU cc_start: 0.8759 (mm) cc_final: 0.8307 (tp) REVERT: B 310 ASP cc_start: 0.7399 (t70) cc_final: 0.7141 (m-30) REVERT: C 184 ARG cc_start: 0.2602 (mtp-110) cc_final: 0.1679 (ptt90) REVERT: C 323 GLN cc_start: 0.6476 (mt0) cc_final: 0.5823 (mm110) REVERT: D 94 ARG cc_start: 0.6565 (ttt-90) cc_final: 0.6220 (ttp-170) REVERT: D 191 GLU cc_start: 0.6273 (tt0) cc_final: 0.5534 (pm20) REVERT: D 271 TYR cc_start: 0.3787 (p90) cc_final: 0.3249 (p90) REVERT: D 293 LYS cc_start: 0.7481 (mttt) cc_final: 0.6170 (mtmt) REVERT: E 302 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8314 (tp) REVERT: F 283 GLU cc_start: 0.7946 (mp0) cc_final: 0.7583 (mt-10) REVERT: G 301 LYS cc_start: 0.8286 (mmpt) cc_final: 0.7968 (mmtm) REVERT: K 31 ARG cc_start: 0.7797 (ptm-80) cc_final: 0.7559 (ptm160) REVERT: K 90 GLU cc_start: 0.8187 (pt0) cc_final: 0.7866 (pt0) outliers start: 59 outliers final: 42 residues processed: 287 average time/residue: 0.3508 time to fit residues: 154.5006 Evaluate side-chains 271 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 228 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 0.0770 chunk 276 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 242 optimal weight: 7.9990 chunk 253 optimal weight: 0.9990 chunk 267 optimal weight: 20.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS B 86 ASN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22852 Z= 0.211 Angle : 0.571 13.141 31091 Z= 0.292 Chirality : 0.041 0.203 3240 Planarity : 0.004 0.057 4040 Dihedral : 14.000 159.457 4155 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 2.79 % Allowed : 16.26 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.16), residues: 2950 helix: 0.68 (0.19), residues: 872 sheet: -1.43 (0.27), residues: 383 loop : -2.50 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 263 HIS 0.005 0.001 HIS A 188 PHE 0.021 0.001 PHE E 226 TYR 0.013 0.001 TYR K 51 ARG 0.009 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 227 time to evaluate : 2.210 Fit side-chains revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7536 (pm20) cc_final: 0.7200 (pm20) REVERT: A 242 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8312 (mtmt) REVERT: B 94 THR cc_start: 0.8213 (t) cc_final: 0.7951 (m) REVERT: B 99 GLU cc_start: 0.7501 (pt0) cc_final: 0.7296 (pt0) REVERT: B 120 ASP cc_start: 0.8065 (m-30) cc_final: 0.7620 (t0) REVERT: B 263 LEU cc_start: 0.8751 (mm) cc_final: 0.8283 (tp) REVERT: B 310 ASP cc_start: 0.7384 (t70) cc_final: 0.7121 (m-30) REVERT: C 184 ARG cc_start: 0.2601 (mtp-110) cc_final: 0.1665 (ptt90) REVERT: C 323 GLN cc_start: 0.6449 (mt0) cc_final: 0.5760 (mm110) REVERT: D 94 ARG cc_start: 0.6595 (ttt-90) cc_final: 0.6249 (ttp-170) REVERT: D 191 GLU cc_start: 0.6288 (tt0) cc_final: 0.5522 (pm20) REVERT: D 270 TRP cc_start: 0.5630 (m-90) cc_final: 0.5396 (m-90) REVERT: D 293 LYS cc_start: 0.7501 (mttt) cc_final: 0.6196 (mtmt) REVERT: E 34 ASP cc_start: 0.8329 (m-30) cc_final: 0.8097 (m-30) REVERT: E 302 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8347 (tt) REVERT: G 301 LYS cc_start: 0.8297 (mmpt) cc_final: 0.8020 (mmtm) REVERT: K 31 ARG cc_start: 0.7784 (ptm-80) cc_final: 0.7561 (ptm160) REVERT: K 90 GLU cc_start: 0.8209 (pt0) cc_final: 0.7885 (pt0) outliers start: 54 outliers final: 45 residues processed: 258 average time/residue: 0.3506 time to fit residues: 139.2717 Evaluate side-chains 258 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 212 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 4.9990 chunk 283 optimal weight: 20.0000 chunk 173 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 297 optimal weight: 50.0000 chunk 274 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN H 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22852 Z= 0.249 Angle : 0.596 13.532 31091 Z= 0.306 Chirality : 0.042 0.204 3240 Planarity : 0.004 0.049 4040 Dihedral : 14.027 159.944 4155 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 2.68 % Allowed : 16.47 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2950 helix: 0.62 (0.19), residues: 877 sheet: -1.40 (0.27), residues: 388 loop : -2.48 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 316 HIS 0.006 0.001 HIS A 188 PHE 0.022 0.002 PHE E 226 TYR 0.013 0.002 TYR E 271 ARG 0.010 0.000 ARG D 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 219 time to evaluate : 2.783 Fit side-chains revert: symmetry clash REVERT: A 232 PHE cc_start: 0.5393 (p90) cc_final: 0.5155 (p90) REVERT: A 234 GLU cc_start: 0.7576 (pm20) cc_final: 0.7213 (pm20) REVERT: A 242 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8300 (mtmt) REVERT: B 94 THR cc_start: 0.8246 (t) cc_final: 0.8019 (m) REVERT: B 99 GLU cc_start: 0.7521 (pt0) cc_final: 0.7279 (pt0) REVERT: B 120 ASP cc_start: 0.8069 (m-30) cc_final: 0.7628 (t0) REVERT: B 263 LEU cc_start: 0.8807 (mm) cc_final: 0.8324 (tp) REVERT: B 310 ASP cc_start: 0.7408 (t70) cc_final: 0.7135 (m-30) REVERT: C 184 ARG cc_start: 0.2635 (mtp-110) cc_final: 0.1660 (ptt90) REVERT: C 323 GLN cc_start: 0.6467 (mt0) cc_final: 0.5752 (mm110) REVERT: D 94 ARG cc_start: 0.6610 (ttt-90) cc_final: 0.6258 (ttp-170) REVERT: D 191 GLU cc_start: 0.6387 (tt0) cc_final: 0.5548 (pm20) REVERT: D 270 TRP cc_start: 0.5684 (m-90) cc_final: 0.5474 (m-90) REVERT: E 212 GLU cc_start: 0.7152 (pt0) cc_final: 0.6901 (tt0) REVERT: E 302 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8368 (tt) REVERT: G 301 LYS cc_start: 0.8332 (mmpt) cc_final: 0.8056 (mmtm) REVERT: K 31 ARG cc_start: 0.7785 (ptm-80) cc_final: 0.7556 (ptm160) REVERT: K 90 GLU cc_start: 0.8186 (pt0) cc_final: 0.7875 (pt0) outliers start: 52 outliers final: 48 residues processed: 250 average time/residue: 0.3577 time to fit residues: 139.2719 Evaluate side-chains 261 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 212 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 chunk 218 optimal weight: 0.0000 chunk 35 optimal weight: 0.0060 chunk 65 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 chunk 30 optimal weight: 50.0000 chunk 43 optimal weight: 3.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.187384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150240 restraints weight = 35827.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145643 restraints weight = 32433.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146793 restraints weight = 29198.898| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 22852 Z= 0.300 Angle : 0.742 59.200 31091 Z= 0.420 Chirality : 0.043 0.705 3240 Planarity : 0.004 0.049 4040 Dihedral : 14.032 159.945 4155 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 2.53 % Allowed : 16.73 % Favored : 80.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.16), residues: 2950 helix: 0.62 (0.19), residues: 877 sheet: -1.41 (0.27), residues: 389 loop : -2.48 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 316 HIS 0.005 0.001 HIS A 188 PHE 0.019 0.001 PHE E 226 TYR 0.012 0.001 TYR H 285 ARG 0.007 0.000 ARG D 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4218.37 seconds wall clock time: 77 minutes 42.44 seconds (4662.44 seconds total)