Starting phenix.real_space_refine on Wed Mar 20 20:35:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/03_2024/6uc2_20725_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/03_2024/6uc2_20725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/03_2024/6uc2_20725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/03_2024/6uc2_20725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/03_2024/6uc2_20725_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/03_2024/6uc2_20725_updated.pdb" } resolution = 4.48 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= 0.148 sd= 3.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 144 5.16 5 C 17688 2.51 5 N 4880 2.21 5 O 5624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "H ARG 153": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H ARG 412": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28408 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "C" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "D" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "E" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "F" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "G" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "H" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 14.68, per 1000 atoms: 0.52 Number of scatterers: 28408 At special positions: 0 Unit cell: (152.25, 152.25, 116.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 72 15.00 O 5624 8.00 N 4880 7.00 C 17688 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.19 Conformation dependent library (CDL) restraints added in 5.2 seconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 40 sheets defined 35.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.31 Creating SS restraints... Processing helix chain 'A' and resid 21 through 24 No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.951A pdb=" N GLU A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.851A pdb=" N PHE A 131 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 135 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.847A pdb=" N LYS A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 258 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.660A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 334 through 337 No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 removed outlier: 3.782A pdb=" N ALA A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 477 through 485 Processing helix chain 'A' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL A 499 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 24 No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 removed outlier: 3.951A pdb=" N GLU B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE B 131 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.848A pdb=" N LYS B 257 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 258 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.660A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 334 through 337 No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.782A pdb=" N ALA B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'B' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL B 499 " --> pdb=" O SER B 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 108 removed outlier: 3.952A pdb=" N GLU C 103 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE C 131 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 135 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.847A pdb=" N LYS C 257 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 removed outlier: 3.659A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 334 through 337 No H-bonds generated for 'chain 'C' and resid 334 through 337' Processing helix chain 'C' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 removed outlier: 3.782A pdb=" N ALA C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 477 through 485 Processing helix chain 'C' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL C 499 " --> pdb=" O SER C 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 24 No H-bonds generated for 'chain 'D' and resid 21 through 24' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 108 removed outlier: 3.952A pdb=" N GLU D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE D 131 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D 135 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.847A pdb=" N LYS D 257 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 258 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.660A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 334 through 337 No H-bonds generated for 'chain 'D' and resid 334 through 337' Processing helix chain 'D' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 removed outlier: 3.782A pdb=" N ALA D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'D' and resid 495 through 499 removed outlier: 4.188A pdb=" N VAL D 499 " --> pdb=" O SER D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 24 No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.539A pdb=" N ALA E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 108 removed outlier: 3.952A pdb=" N GLU E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE E 131 " --> pdb=" O ARG E 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA E 135 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.848A pdb=" N LYS E 257 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 258 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 3.659A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 334 through 337 No H-bonds generated for 'chain 'E' and resid 334 through 337' Processing helix chain 'E' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 removed outlier: 3.783A pdb=" N ALA E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 453 through 455 No H-bonds generated for 'chain 'E' and resid 453 through 455' Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 477 through 485 Processing helix chain 'E' and resid 495 through 499 removed outlier: 4.190A pdb=" N VAL E 499 " --> pdb=" O SER E 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 24 No H-bonds generated for 'chain 'F' and resid 21 through 24' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 removed outlier: 3.952A pdb=" N GLU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.851A pdb=" N PHE F 131 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA F 135 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.848A pdb=" N LYS F 257 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 3.659A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 316 Processing helix chain 'F' and resid 334 through 337 No H-bonds generated for 'chain 'F' and resid 334 through 337' Processing helix chain 'F' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 removed outlier: 3.782A pdb=" N ALA F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 453 through 455 No H-bonds generated for 'chain 'F' and resid 453 through 455' Processing helix chain 'F' and resid 457 through 471 Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'F' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL F 499 " --> pdb=" O SER F 496 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 24 No H-bonds generated for 'chain 'G' and resid 21 through 24' Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 108 removed outlier: 3.951A pdb=" N GLU G 103 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE G 131 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA G 135 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.848A pdb=" N LYS G 257 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 3.659A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 316 Processing helix chain 'G' and resid 334 through 337 No H-bonds generated for 'chain 'G' and resid 334 through 337' Processing helix chain 'G' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 removed outlier: 3.783A pdb=" N ALA G 374 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 453 through 455 No H-bonds generated for 'chain 'G' and resid 453 through 455' Processing helix chain 'G' and resid 457 through 471 Processing helix chain 'G' and resid 477 through 485 Processing helix chain 'G' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL G 499 " --> pdb=" O SER G 496 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 24 No H-bonds generated for 'chain 'H' and resid 21 through 24' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 108 removed outlier: 3.951A pdb=" N GLU H 103 " --> pdb=" O PHE H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE H 131 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA H 135 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 225 through 232 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.848A pdb=" N LYS H 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 258 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 3.660A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 334 through 337 No H-bonds generated for 'chain 'H' and resid 334 through 337' Processing helix chain 'H' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 removed outlier: 3.783A pdb=" N ALA H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 390 No H-bonds generated for 'chain 'H' and resid 388 through 390' Processing helix chain 'H' and resid 453 through 455 No H-bonds generated for 'chain 'H' and resid 453 through 455' Processing helix chain 'H' and resid 457 through 471 Processing helix chain 'H' and resid 477 through 485 Processing helix chain 'H' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL H 499 " --> pdb=" O SER H 496 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU A 36 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 491 " --> pdb=" O LEU A 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 321 through 323 Processing sheet with id= E, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= F, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU B 36 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 491 " --> pdb=" O LEU B 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 270 through 273 removed outlier: 6.671A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 321 through 323 Processing sheet with id= J, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= K, first strand: chain 'C' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU C 36 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU C 491 " --> pdb=" O LEU C 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 321 through 323 Processing sheet with id= O, first strand: chain 'C' and resid 142 through 145 Processing sheet with id= P, first strand: chain 'D' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU D 36 " --> pdb=" O GLU D 491 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU D 491 " --> pdb=" O LEU D 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 321 through 323 Processing sheet with id= T, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= U, first strand: chain 'E' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU E 36 " --> pdb=" O GLU E 491 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU E 491 " --> pdb=" O LEU E 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 187 through 189 removed outlier: 4.024A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 270 through 273 removed outlier: 6.671A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 321 through 323 Processing sheet with id= Y, first strand: chain 'E' and resid 142 through 145 Processing sheet with id= Z, first strand: chain 'F' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU F 36 " --> pdb=" O GLU F 491 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU F 491 " --> pdb=" O LEU F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 321 through 323 Processing sheet with id= AD, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AE, first strand: chain 'G' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU G 36 " --> pdb=" O GLU G 491 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU G 491 " --> pdb=" O LEU G 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'G' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'G' and resid 321 through 323 Processing sheet with id= AI, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AJ, first strand: chain 'H' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU H 36 " --> pdb=" O GLU H 491 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU H 491 " --> pdb=" O LEU H 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'H' and resid 187 through 189 removed outlier: 4.022A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'H' and resid 321 through 323 Processing sheet with id= AN, first strand: chain 'H' and resid 142 through 145 672 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.81 Time building geometry restraints manager: 12.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4872 1.31 - 1.44: 6832 1.44 - 1.56: 16697 1.56 - 1.69: 231 1.69 - 1.81: 232 Bond restraints: 28864 Sorted by residual: bond pdb=" C2' ATP D 603 " pdb=" C3' ATP D 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.34e+02 bond pdb=" C2' ATP E 603 " pdb=" C3' ATP E 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.32e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.32e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.31e+02 bond pdb=" C2' ATP C 603 " pdb=" C3' ATP C 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.31e+02 ... (remaining 28859 not shown) Histogram of bond angle deviations from ideal: 91.41 - 101.32: 104 101.32 - 111.24: 11098 111.24 - 121.15: 19983 121.15 - 131.07: 7805 131.07 - 140.99: 146 Bond angle restraints: 39136 Sorted by residual: angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 120.89 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 120.89 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 120.93 18.94 1.00e+00 1.00e+00 3.59e+02 ... (remaining 39131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 16637 33.77 - 67.55: 875 67.55 - 101.32: 45 101.32 - 135.10: 19 135.10 - 168.87: 24 Dihedral angle restraints: 17600 sinusoidal: 7264 harmonic: 10336 Sorted by residual: dihedral pdb=" CA GLU B 111 " pdb=" C GLU B 111 " pdb=" N GLN B 112 " pdb=" CA GLN B 112 " ideal model delta harmonic sigma weight residual -180.00 -131.80 -48.20 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CA GLU C 111 " pdb=" C GLU C 111 " pdb=" N GLN C 112 " pdb=" CA GLN C 112 " ideal model delta harmonic sigma weight residual -180.00 -131.81 -48.19 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CA GLU D 111 " pdb=" C GLU D 111 " pdb=" N GLN D 112 " pdb=" CA GLN D 112 " ideal model delta harmonic sigma weight residual 180.00 -131.83 -48.17 0 5.00e+00 4.00e-02 9.28e+01 ... (remaining 17597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3536 0.087 - 0.174: 807 0.174 - 0.261: 89 0.261 - 0.348: 24 0.348 - 0.436: 16 Chirality restraints: 4472 Sorted by residual: chirality pdb=" CB VAL A 479 " pdb=" CA VAL A 479 " pdb=" CG1 VAL A 479 " pdb=" CG2 VAL A 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CB VAL H 479 " pdb=" CA VAL H 479 " pdb=" CG1 VAL H 479 " pdb=" CG2 VAL H 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB VAL B 479 " pdb=" CA VAL B 479 " pdb=" CG1 VAL B 479 " pdb=" CG2 VAL B 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 4469 not shown) Planarity restraints: 4928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 72 " 0.019 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C THR C 72 " -0.063 2.00e-02 2.50e+03 pdb=" O THR C 72 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL C 73 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 72 " -0.019 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C THR D 72 " 0.063 2.00e-02 2.50e+03 pdb=" O THR D 72 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL D 73 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 72 " -0.019 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C THR G 72 " 0.063 2.00e-02 2.50e+03 pdb=" O THR G 72 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL G 73 " -0.020 2.00e-02 2.50e+03 ... (remaining 4925 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4162 2.75 - 3.29: 28651 3.29 - 3.82: 51766 3.82 - 4.36: 58394 4.36 - 4.90: 89307 Nonbonded interactions: 232280 Sorted by model distance: nonbonded pdb=" O PRO B 64 " pdb=" OG1 THR B 383 " model vdw 2.208 2.440 nonbonded pdb=" O PRO A 64 " pdb=" OG1 THR A 383 " model vdw 2.208 2.440 nonbonded pdb=" O PRO C 64 " pdb=" OG1 THR C 383 " model vdw 2.209 2.440 nonbonded pdb=" O PRO G 64 " pdb=" OG1 THR G 383 " model vdw 2.209 2.440 nonbonded pdb=" O PRO H 64 " pdb=" OG1 THR H 383 " model vdw 2.209 2.440 ... (remaining 232275 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.030 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 71.220 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.016 0.289 28864 Z= 1.076 Angle : 1.928 24.685 39136 Z= 1.081 Chirality : 0.078 0.436 4472 Planarity : 0.008 0.059 4928 Dihedral : 20.466 168.874 10976 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 14.82 % Allowed : 15.90 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.92 % 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: -4.41 (0.11), residues: 3576 helix: -3.27 (0.10), residues: 1192 sheet: -3.01 (0.27), residues: 272 loop : -2.79 (0.11), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS B 454 PHE 0.024 0.004 PHE B 456 TYR 0.027 0.004 TYR E 411 ARG 0.036 0.003 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1883 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 440 poor density : 1443 time to evaluate : 3.103 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8848 (tpp) cc_final: 0.8426 (tpp) REVERT: A 93 HIS cc_start: 0.9184 (p90) cc_final: 0.8812 (p90) REVERT: A 94 ASN cc_start: 0.8893 (t0) cc_final: 0.8654 (t0) REVERT: A 104 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.8886 (t) REVERT: A 108 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9200 (mtmt) REVERT: A 109 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8893 (tptp) REVERT: A 137 HIS cc_start: 0.9665 (m-70) cc_final: 0.9247 (m-70) REVERT: A 166 LEU cc_start: 0.9070 (pt) cc_final: 0.8338 (tp) REVERT: A 174 PHE cc_start: 0.9144 (m-80) cc_final: 0.8814 (m-80) REVERT: A 198 ASN cc_start: 0.9698 (m110) cc_final: 0.9320 (m110) REVERT: A 199 GLU cc_start: 0.9550 (OUTLIER) cc_final: 0.9254 (mp0) REVERT: A 209 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9045 (tm) REVERT: A 224 ARG cc_start: 0.8205 (tpt170) cc_final: 0.7522 (tpt-90) REVERT: A 229 LYS cc_start: 0.9411 (mttt) cc_final: 0.9157 (mmtt) REVERT: A 231 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8781 (ptm-80) REVERT: A 245 LEU cc_start: 0.9198 (mm) cc_final: 0.8768 (mm) REVERT: A 269 ASP cc_start: 0.9143 (t0) cc_final: 0.8334 (t0) REVERT: A 276 SER cc_start: 0.9206 (m) cc_final: 0.8968 (p) REVERT: A 283 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.9310 (mm-40) REVERT: A 296 ASN cc_start: 0.9208 (p0) cc_final: 0.8520 (p0) REVERT: A 297 LEU cc_start: 0.9300 (mm) cc_final: 0.8966 (mm) REVERT: A 298 GLN cc_start: 0.9199 (mm110) cc_final: 0.8715 (mm-40) REVERT: A 325 MET cc_start: 0.7463 (pmm) cc_final: 0.7089 (pmm) REVERT: A 351 SER cc_start: 0.8521 (p) cc_final: 0.8004 (p) REVERT: A 355 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8352 (ptt180) REVERT: A 372 HIS cc_start: 0.9573 (m170) cc_final: 0.9346 (m170) REVERT: A 402 PHE cc_start: 0.8531 (m-10) cc_final: 0.8265 (m-80) REVERT: A 450 LYS cc_start: 0.6934 (pttm) cc_final: 0.6189 (ptmm) REVERT: A 460 LEU cc_start: 0.9871 (mp) cc_final: 0.9646 (mt) REVERT: A 465 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8615 (pt0) REVERT: A 482 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8871 (tmm) REVERT: A 489 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8501 (ttpt) REVERT: B 82 MET cc_start: 0.8784 (tpp) cc_final: 0.8352 (tpp) REVERT: B 104 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8739 (t) REVERT: B 108 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9229 (mtmt) REVERT: B 109 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8791 (tptp) REVERT: B 137 HIS cc_start: 0.9680 (m-70) cc_final: 0.9279 (m-70) REVERT: B 154 LEU cc_start: 0.9764 (mm) cc_final: 0.9543 (mm) REVERT: B 166 LEU cc_start: 0.9021 (pt) cc_final: 0.8239 (tp) REVERT: B 174 PHE cc_start: 0.9064 (m-80) cc_final: 0.8713 (m-80) REVERT: B 198 ASN cc_start: 0.9634 (m110) cc_final: 0.9237 (m110) REVERT: B 199 GLU cc_start: 0.9518 (OUTLIER) cc_final: 0.9224 (mp0) REVERT: B 231 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8839 (ptm-80) REVERT: B 245 LEU cc_start: 0.9221 (mm) cc_final: 0.8852 (mm) REVERT: B 269 ASP cc_start: 0.9203 (t0) cc_final: 0.8243 (t0) REVERT: B 277 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 281 ILE cc_start: 0.9421 (mm) cc_final: 0.9118 (mm) REVERT: B 283 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.9253 (mm-40) REVERT: B 285 ASN cc_start: 0.9455 (m110) cc_final: 0.9195 (m110) REVERT: B 296 ASN cc_start: 0.9322 (p0) cc_final: 0.8550 (p0) REVERT: B 297 LEU cc_start: 0.9396 (mm) cc_final: 0.8918 (mm) REVERT: B 298 GLN cc_start: 0.9083 (mm110) cc_final: 0.8657 (mm-40) REVERT: B 321 LEU cc_start: 0.9795 (mm) cc_final: 0.9583 (mm) REVERT: B 325 MET cc_start: 0.7527 (pmm) cc_final: 0.7238 (pmm) REVERT: B 355 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8359 (ptt180) REVERT: B 372 HIS cc_start: 0.9538 (m170) cc_final: 0.9298 (m170) REVERT: B 402 PHE cc_start: 0.8351 (m-10) cc_final: 0.8092 (m-80) REVERT: B 450 LYS cc_start: 0.7039 (pttm) cc_final: 0.6255 (ptmm) REVERT: B 482 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8891 (tmm) REVERT: B 489 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8604 (ttpt) REVERT: C 14 PRO cc_start: 0.9109 (Cg_exo) cc_final: 0.8862 (Cg_endo) REVERT: C 82 MET cc_start: 0.8832 (tpp) cc_final: 0.8410 (tpp) REVERT: C 104 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8711 (p) REVERT: C 108 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9204 (mtmt) REVERT: C 109 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8887 (tptp) REVERT: C 112 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.6079 (mp10) REVERT: C 137 HIS cc_start: 0.9678 (m-70) cc_final: 0.9218 (m-70) REVERT: C 155 VAL cc_start: 0.9359 (t) cc_final: 0.9128 (t) REVERT: C 174 PHE cc_start: 0.9198 (m-80) cc_final: 0.8889 (m-80) REVERT: C 199 GLU cc_start: 0.9530 (OUTLIER) cc_final: 0.9107 (mp0) REVERT: C 209 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9028 (tm) REVERT: C 231 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8799 (ptm-80) REVERT: C 245 LEU cc_start: 0.9267 (mm) cc_final: 0.8922 (mm) REVERT: C 253 HIS cc_start: 0.9314 (m-70) cc_final: 0.9060 (m-70) REVERT: C 269 ASP cc_start: 0.9193 (t0) cc_final: 0.8403 (t0) REVERT: C 276 SER cc_start: 0.9215 (m) cc_final: 0.9010 (p) REVERT: C 283 GLN cc_start: 0.9509 (OUTLIER) cc_final: 0.9267 (mm-40) REVERT: C 297 LEU cc_start: 0.9303 (mm) cc_final: 0.8951 (mm) REVERT: C 298 GLN cc_start: 0.9161 (mm110) cc_final: 0.8655 (mm-40) REVERT: C 349 LYS cc_start: 0.9479 (mtmt) cc_final: 0.9236 (mtpt) REVERT: C 355 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8386 (ptt180) REVERT: C 402 PHE cc_start: 0.8336 (m-10) cc_final: 0.8130 (m-80) REVERT: C 450 LYS cc_start: 0.6896 (pttm) cc_final: 0.6186 (ptmm) REVERT: C 460 LEU cc_start: 0.9854 (mp) cc_final: 0.9627 (mt) REVERT: C 465 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: C 482 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8913 (tmm) REVERT: C 489 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8532 (ttpt) REVERT: D 82 MET cc_start: 0.8800 (tpp) cc_final: 0.8370 (tpp) REVERT: D 88 ILE cc_start: 0.7492 (mt) cc_final: 0.7290 (mp) REVERT: D 104 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8700 (t) REVERT: D 108 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9224 (mtmt) REVERT: D 109 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8841 (tptp) REVERT: D 137 HIS cc_start: 0.9664 (m-70) cc_final: 0.9259 (m-70) REVERT: D 154 LEU cc_start: 0.9778 (mm) cc_final: 0.9513 (mm) REVERT: D 166 LEU cc_start: 0.8953 (pt) cc_final: 0.8062 (tp) REVERT: D 198 ASN cc_start: 0.9634 (m110) cc_final: 0.9246 (m110) REVERT: D 199 GLU cc_start: 0.9515 (OUTLIER) cc_final: 0.9218 (mp0) REVERT: D 231 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8817 (ptm-80) REVERT: D 245 LEU cc_start: 0.9242 (mm) cc_final: 0.8844 (mm) REVERT: D 265 GLN cc_start: 0.9500 (mt0) cc_final: 0.9250 (tp40) REVERT: D 269 ASP cc_start: 0.9181 (t0) cc_final: 0.8228 (t0) REVERT: D 281 ILE cc_start: 0.9407 (mm) cc_final: 0.9099 (mm) REVERT: D 285 ASN cc_start: 0.9475 (m110) cc_final: 0.9214 (m110) REVERT: D 296 ASN cc_start: 0.9327 (p0) cc_final: 0.8628 (p0) REVERT: D 297 LEU cc_start: 0.9416 (mm) cc_final: 0.8940 (mm) REVERT: D 298 GLN cc_start: 0.9110 (mm110) cc_final: 0.8677 (mm-40) REVERT: D 321 LEU cc_start: 0.9784 (mm) cc_final: 0.9584 (mm) REVERT: D 325 MET cc_start: 0.7236 (pmm) cc_final: 0.6890 (pmm) REVERT: D 355 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8353 (ptt180) REVERT: D 372 HIS cc_start: 0.9592 (m170) cc_final: 0.9362 (m170) REVERT: D 401 PHE cc_start: 0.9309 (p90) cc_final: 0.9102 (p90) REVERT: D 402 PHE cc_start: 0.8360 (m-10) cc_final: 0.8087 (m-80) REVERT: D 450 LYS cc_start: 0.7001 (pttm) cc_final: 0.6266 (ptmm) REVERT: D 465 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8167 (pt0) REVERT: D 482 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8941 (tmm) REVERT: E 12 TYR cc_start: 0.9275 (t80) cc_final: 0.8922 (t80) REVERT: E 82 MET cc_start: 0.8844 (tpp) cc_final: 0.8434 (tpp) REVERT: E 104 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.8841 (t) REVERT: E 108 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9192 (mtmt) REVERT: E 109 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8836 (tptp) REVERT: E 137 HIS cc_start: 0.9692 (m-70) cc_final: 0.9268 (m-70) REVERT: E 154 LEU cc_start: 0.9763 (mm) cc_final: 0.9512 (mm) REVERT: E 166 LEU cc_start: 0.9027 (pt) cc_final: 0.8243 (tp) REVERT: E 174 PHE cc_start: 0.9092 (m-80) cc_final: 0.8778 (m-80) REVERT: E 198 ASN cc_start: 0.9673 (m110) cc_final: 0.9288 (m110) REVERT: E 199 GLU cc_start: 0.9539 (OUTLIER) cc_final: 0.9244 (mp0) REVERT: E 209 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9151 (tm) REVERT: E 229 LYS cc_start: 0.9403 (mttt) cc_final: 0.9152 (mmtt) REVERT: E 231 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8815 (ptm-80) REVERT: E 245 LEU cc_start: 0.9201 (mm) cc_final: 0.8796 (mm) REVERT: E 269 ASP cc_start: 0.9158 (t0) cc_final: 0.8329 (t0) REVERT: E 281 ILE cc_start: 0.9356 (mm) cc_final: 0.9139 (mm) REVERT: E 282 PHE cc_start: 0.8853 (m-80) cc_final: 0.8624 (m-80) REVERT: E 285 ASN cc_start: 0.9501 (m110) cc_final: 0.9281 (m110) REVERT: E 296 ASN cc_start: 0.9257 (p0) cc_final: 0.8581 (p0) REVERT: E 297 LEU cc_start: 0.9373 (mm) cc_final: 0.8999 (mm) REVERT: E 298 GLN cc_start: 0.9148 (mm110) cc_final: 0.8648 (mm-40) REVERT: E 321 LEU cc_start: 0.9770 (mm) cc_final: 0.9558 (mm) REVERT: E 325 MET cc_start: 0.7445 (pmm) cc_final: 0.7108 (pmm) REVERT: E 351 SER cc_start: 0.8581 (p) cc_final: 0.8084 (p) REVERT: E 355 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8407 (ptt180) REVERT: E 372 HIS cc_start: 0.9571 (m170) cc_final: 0.9314 (m170) REVERT: E 402 PHE cc_start: 0.8460 (m-10) cc_final: 0.8248 (m-80) REVERT: E 450 LYS cc_start: 0.6996 (pttm) cc_final: 0.6262 (ptmm) REVERT: E 460 LEU cc_start: 0.9869 (mp) cc_final: 0.9642 (mt) REVERT: E 465 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8671 (pt0) REVERT: E 482 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8935 (tmm) REVERT: E 489 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8513 (ttpt) REVERT: F 82 MET cc_start: 0.8784 (tpp) cc_final: 0.8338 (tpp) REVERT: F 88 ILE cc_start: 0.7440 (mt) cc_final: 0.7154 (mp) REVERT: F 109 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8896 (tptp) REVERT: F 137 HIS cc_start: 0.9666 (m-70) cc_final: 0.9280 (m-70) REVERT: F 174 PHE cc_start: 0.9056 (m-80) cc_final: 0.8688 (m-80) REVERT: F 198 ASN cc_start: 0.9660 (m110) cc_final: 0.9273 (m110) REVERT: F 199 GLU cc_start: 0.9528 (OUTLIER) cc_final: 0.9245 (mp0) REVERT: F 209 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9106 (tm) REVERT: F 231 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8839 (ptm-80) REVERT: F 232 ASP cc_start: 0.9204 (t70) cc_final: 0.8996 (m-30) REVERT: F 269 ASP cc_start: 0.9189 (t0) cc_final: 0.8279 (t0) REVERT: F 277 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8223 (tm-30) REVERT: F 281 ILE cc_start: 0.9418 (mm) cc_final: 0.9105 (mm) REVERT: F 283 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9253 (mm-40) REVERT: F 285 ASN cc_start: 0.9435 (m110) cc_final: 0.9169 (m110) REVERT: F 296 ASN cc_start: 0.9328 (p0) cc_final: 0.8573 (p0) REVERT: F 297 LEU cc_start: 0.9435 (mm) cc_final: 0.8999 (mm) REVERT: F 298 GLN cc_start: 0.9131 (mm110) cc_final: 0.8664 (mm-40) REVERT: F 321 LEU cc_start: 0.9802 (mm) cc_final: 0.9601 (mm) REVERT: F 325 MET cc_start: 0.7134 (pmm) cc_final: 0.6796 (pmm) REVERT: F 355 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8421 (ptt180) REVERT: F 372 HIS cc_start: 0.9599 (m170) cc_final: 0.9357 (m170) REVERT: F 402 PHE cc_start: 0.8361 (m-10) cc_final: 0.8085 (m-80) REVERT: F 482 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8999 (tmm) REVERT: G 22 GLN cc_start: 0.9262 (mt0) cc_final: 0.8634 (mp10) REVERT: G 65 LEU cc_start: 0.8977 (pt) cc_final: 0.8675 (pt) REVERT: G 82 MET cc_start: 0.8854 (tpp) cc_final: 0.8450 (tpp) REVERT: G 93 HIS cc_start: 0.9159 (p90) cc_final: 0.8745 (p90) REVERT: G 94 ASN cc_start: 0.8912 (t0) cc_final: 0.8663 (t0) REVERT: G 104 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.8868 (m) REVERT: G 108 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9206 (mtmt) REVERT: G 109 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8821 (tptp) REVERT: G 137 HIS cc_start: 0.9671 (m-70) cc_final: 0.9246 (m-70) REVERT: G 166 LEU cc_start: 0.9061 (pt) cc_final: 0.8328 (tp) REVERT: G 199 GLU cc_start: 0.9573 (OUTLIER) cc_final: 0.9183 (mp0) REVERT: G 209 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8941 (tm) REVERT: G 231 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8830 (ptm-80) REVERT: G 232 ASP cc_start: 0.9207 (t70) cc_final: 0.9006 (m-30) REVERT: G 245 LEU cc_start: 0.9226 (mm) cc_final: 0.8871 (mm) REVERT: G 269 ASP cc_start: 0.9142 (t0) cc_final: 0.8319 (t0) REVERT: G 276 SER cc_start: 0.9182 (m) cc_final: 0.8958 (p) REVERT: G 283 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.9326 (mm-40) REVERT: G 296 ASN cc_start: 0.9233 (p0) cc_final: 0.8561 (p0) REVERT: G 297 LEU cc_start: 0.9329 (mm) cc_final: 0.8999 (mm) REVERT: G 298 GLN cc_start: 0.9198 (mm110) cc_final: 0.8678 (mm-40) REVERT: G 351 SER cc_start: 0.8542 (p) cc_final: 0.8089 (p) REVERT: G 355 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8401 (ptt180) REVERT: G 401 PHE cc_start: 0.9311 (p90) cc_final: 0.9096 (p90) REVERT: G 402 PHE cc_start: 0.8515 (m-10) cc_final: 0.8245 (m-80) REVERT: G 450 LYS cc_start: 0.6987 (pttm) cc_final: 0.6351 (ptmm) REVERT: G 460 LEU cc_start: 0.9875 (mp) cc_final: 0.9645 (mt) REVERT: G 465 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8419 (pt0) REVERT: G 482 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9028 (tmm) REVERT: H 44 PHE cc_start: 0.7863 (p90) cc_final: 0.7581 (p90) REVERT: H 65 LEU cc_start: 0.8911 (pt) cc_final: 0.8600 (pt) REVERT: H 82 MET cc_start: 0.8827 (tpp) cc_final: 0.8409 (tpp) REVERT: H 88 ILE cc_start: 0.7461 (mt) cc_final: 0.7194 (mp) REVERT: H 104 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8690 (t) REVERT: H 108 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9219 (mtmt) REVERT: H 109 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8842 (tptp) REVERT: H 137 HIS cc_start: 0.9688 (m-70) cc_final: 0.9276 (m-70) REVERT: H 154 LEU cc_start: 0.9751 (mm) cc_final: 0.9501 (mm) REVERT: H 166 LEU cc_start: 0.8992 (pt) cc_final: 0.8112 (tp) REVERT: H 174 PHE cc_start: 0.9059 (m-80) cc_final: 0.8751 (m-80) REVERT: H 198 ASN cc_start: 0.9650 (m110) cc_final: 0.9245 (m110) REVERT: H 199 GLU cc_start: 0.9539 (OUTLIER) cc_final: 0.9262 (mp0) REVERT: H 209 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9052 (tm) REVERT: H 231 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8858 (ptm-80) REVERT: H 245 LEU cc_start: 0.9224 (mm) cc_final: 0.8915 (mm) REVERT: H 269 ASP cc_start: 0.9169 (t0) cc_final: 0.8242 (t0) REVERT: H 283 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.9266 (mm-40) REVERT: H 285 ASN cc_start: 0.9486 (m110) cc_final: 0.9238 (m110) REVERT: H 296 ASN cc_start: 0.9335 (p0) cc_final: 0.8619 (p0) REVERT: H 297 LEU cc_start: 0.9419 (mm) cc_final: 0.8988 (mm) REVERT: H 298 GLN cc_start: 0.9122 (mm110) cc_final: 0.8614 (mm-40) REVERT: H 321 LEU cc_start: 0.9783 (mm) cc_final: 0.9567 (mm) REVERT: H 325 MET cc_start: 0.7257 (pmm) cc_final: 0.6931 (pmm) REVERT: H 351 SER cc_start: 0.8605 (p) cc_final: 0.8165 (p) REVERT: H 355 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8364 (ptt180) REVERT: H 357 PHE cc_start: 0.9148 (m-80) cc_final: 0.8857 (m-80) REVERT: H 372 HIS cc_start: 0.9556 (m170) cc_final: 0.9335 (m170) REVERT: H 401 PHE cc_start: 0.9272 (p90) cc_final: 0.9061 (p90) REVERT: H 402 PHE cc_start: 0.8379 (m-10) cc_final: 0.8102 (m-80) REVERT: H 465 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8215 (pt0) REVERT: H 482 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8925 (tmm) REVERT: H 489 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8553 (ttpt) outliers start: 440 outliers final: 183 residues processed: 1615 average time/residue: 0.4086 time to fit residues: 1017.3478 Evaluate side-chains 1402 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1146 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 326 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 298 GLN A 466 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 298 GLN B 466 HIS C 230 ASN C 298 GLN C 343 GLN C 466 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 298 GLN D 466 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 298 GLN E 466 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN F 298 GLN F 465 GLN F 466 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN G 298 GLN G 466 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 298 GLN H 466 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28864 Z= 0.236 Angle : 0.859 10.085 39136 Z= 0.424 Chirality : 0.050 0.183 4472 Planarity : 0.005 0.042 4928 Dihedral : 19.199 168.757 4368 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.47 % Allowed : 6.10 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.49 (0.12), residues: 3576 helix: -2.26 (0.13), residues: 1208 sheet: -3.26 (0.20), residues: 424 loop : -2.11 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 137 PHE 0.017 0.002 PHE E 490 TYR 0.024 0.002 TYR F 233 ARG 0.004 0.001 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1397 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1383 time to evaluate : 2.859 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 SER cc_start: 0.9036 (m) cc_final: 0.8490 (t) REVERT: A 78 MET cc_start: 0.7798 (mpp) cc_final: 0.6943 (mpp) REVERT: A 93 HIS cc_start: 0.9199 (p90) cc_final: 0.8724 (p90) REVERT: A 94 ASN cc_start: 0.8856 (t0) cc_final: 0.8603 (t0) REVERT: A 154 LEU cc_start: 0.9587 (mm) cc_final: 0.9350 (mm) REVERT: A 166 LEU cc_start: 0.8879 (pt) cc_final: 0.8339 (tp) REVERT: A 230 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8844 (m-40) REVERT: A 253 HIS cc_start: 0.9192 (t-90) cc_final: 0.8991 (t-90) REVERT: A 269 ASP cc_start: 0.9152 (t0) cc_final: 0.8159 (t0) REVERT: A 276 SER cc_start: 0.9158 (m) cc_final: 0.8888 (p) REVERT: A 277 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 285 ASN cc_start: 0.9548 (m110) cc_final: 0.9344 (m110) REVERT: A 286 MET cc_start: 0.9050 (mtm) cc_final: 0.8807 (mtt) REVERT: A 296 ASN cc_start: 0.9231 (p0) cc_final: 0.8509 (p0) REVERT: A 297 LEU cc_start: 0.9206 (mm) cc_final: 0.8796 (mm) REVERT: A 298 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8283 (mm-40) REVERT: A 321 LEU cc_start: 0.9710 (mm) cc_final: 0.9483 (mm) REVERT: A 364 ASP cc_start: 0.8628 (t0) cc_final: 0.8087 (t0) REVERT: A 465 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8912 (pt0) REVERT: A 489 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7888 (ttpt) REVERT: A 492 LYS cc_start: 0.8264 (tptp) cc_final: 0.7881 (tptp) REVERT: B 66 VAL cc_start: 0.9142 (m) cc_final: 0.8803 (m) REVERT: B 67 SER cc_start: 0.9076 (m) cc_final: 0.8348 (t) REVERT: B 78 MET cc_start: 0.7862 (mpp) cc_final: 0.6841 (mpp) REVERT: B 88 ILE cc_start: 0.7208 (mt) cc_final: 0.6905 (mt) REVERT: B 93 HIS cc_start: 0.9240 (p90) cc_final: 0.8774 (p90) REVERT: B 166 LEU cc_start: 0.8809 (pt) cc_final: 0.8145 (tp) REVERT: B 174 PHE cc_start: 0.8997 (m-80) cc_final: 0.8656 (m-80) REVERT: B 269 ASP cc_start: 0.9171 (t0) cc_final: 0.8163 (t0) REVERT: B 277 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 285 ASN cc_start: 0.9479 (m110) cc_final: 0.9248 (m110) REVERT: B 291 LYS cc_start: 0.9662 (pttp) cc_final: 0.9453 (pttm) REVERT: B 296 ASN cc_start: 0.9312 (p0) cc_final: 0.8531 (p0) REVERT: B 297 LEU cc_start: 0.9343 (mm) cc_final: 0.8827 (mm) REVERT: B 298 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8278 (mm-40) REVERT: B 321 LEU cc_start: 0.9721 (mm) cc_final: 0.9464 (mm) REVERT: B 375 LYS cc_start: 0.9473 (ptpp) cc_final: 0.9214 (ptpp) REVERT: B 489 LYS cc_start: 0.8299 (ttpt) cc_final: 0.8003 (ttpt) REVERT: C 67 SER cc_start: 0.9067 (m) cc_final: 0.8651 (t) REVERT: C 78 MET cc_start: 0.7850 (mpp) cc_final: 0.7190 (mpp) REVERT: C 82 MET cc_start: 0.8708 (tpp) cc_final: 0.8342 (tpp) REVERT: C 93 HIS cc_start: 0.9177 (p90) cc_final: 0.8675 (p90) REVERT: C 94 ASN cc_start: 0.8951 (t0) cc_final: 0.8699 (t0) REVERT: C 103 GLU cc_start: 0.9215 (mp0) cc_final: 0.8957 (mp0) REVERT: C 132 GLU cc_start: 0.9441 (tm-30) cc_final: 0.9212 (tm-30) REVERT: C 137 HIS cc_start: 0.9548 (m-70) cc_final: 0.9105 (m-70) REVERT: C 166 LEU cc_start: 0.8846 (pt) cc_final: 0.8273 (tp) REVERT: C 269 ASP cc_start: 0.9131 (t0) cc_final: 0.8113 (t0) REVERT: C 276 SER cc_start: 0.9170 (m) cc_final: 0.8899 (p) REVERT: C 285 ASN cc_start: 0.9508 (m110) cc_final: 0.9301 (m110) REVERT: C 286 MET cc_start: 0.9052 (mtm) cc_final: 0.8819 (mtt) REVERT: C 291 LYS cc_start: 0.9495 (ptpp) cc_final: 0.9154 (ptpt) REVERT: C 297 LEU cc_start: 0.9282 (mm) cc_final: 0.8819 (mm) REVERT: C 298 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8306 (mm-40) REVERT: C 321 LEU cc_start: 0.9729 (mm) cc_final: 0.9489 (mm) REVERT: C 348 TYR cc_start: 0.8910 (t80) cc_final: 0.8086 (t80) REVERT: C 362 ILE cc_start: 0.9399 (tp) cc_final: 0.9191 (tp) REVERT: C 465 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8906 (pt0) REVERT: C 489 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8013 (ttpt) REVERT: C 492 LYS cc_start: 0.8124 (tptp) cc_final: 0.7840 (tptp) REVERT: D 66 VAL cc_start: 0.9129 (m) cc_final: 0.8766 (m) REVERT: D 67 SER cc_start: 0.9134 (m) cc_final: 0.8377 (t) REVERT: D 78 MET cc_start: 0.7882 (mpp) cc_final: 0.6910 (mpp) REVERT: D 88 ILE cc_start: 0.7700 (mt) cc_final: 0.7370 (mt) REVERT: D 119 VAL cc_start: 0.9308 (m) cc_final: 0.9082 (m) REVERT: D 137 HIS cc_start: 0.9552 (m-70) cc_final: 0.9192 (m-70) REVERT: D 163 ILE cc_start: 0.9471 (pt) cc_final: 0.9151 (pt) REVERT: D 166 LEU cc_start: 0.8809 (pt) cc_final: 0.8092 (tp) REVERT: D 253 HIS cc_start: 0.9109 (t-90) cc_final: 0.8905 (t-90) REVERT: D 269 ASP cc_start: 0.9158 (t0) cc_final: 0.8210 (t0) REVERT: D 277 GLN cc_start: 0.8511 (tm-30) cc_final: 0.7991 (tm-30) REVERT: D 281 ILE cc_start: 0.9483 (mm) cc_final: 0.9280 (mm) REVERT: D 285 ASN cc_start: 0.9498 (m110) cc_final: 0.9268 (m110) REVERT: D 296 ASN cc_start: 0.9320 (p0) cc_final: 0.8569 (p0) REVERT: D 297 LEU cc_start: 0.9373 (mm) cc_final: 0.8878 (mm) REVERT: D 298 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8233 (mm-40) REVERT: D 305 VAL cc_start: 0.8622 (m) cc_final: 0.7806 (p) REVERT: D 321 LEU cc_start: 0.9700 (mm) cc_final: 0.9431 (mm) REVERT: D 353 TYR cc_start: 0.9183 (t80) cc_final: 0.8634 (t80) REVERT: D 362 ILE cc_start: 0.9391 (tp) cc_final: 0.9176 (tp) REVERT: D 401 PHE cc_start: 0.9300 (p90) cc_final: 0.9089 (p90) REVERT: D 450 LYS cc_start: 0.7368 (pttm) cc_final: 0.6373 (ptmm) REVERT: E 12 TYR cc_start: 0.9268 (t80) cc_final: 0.8816 (t80) REVERT: E 67 SER cc_start: 0.9008 (m) cc_final: 0.8266 (t) REVERT: E 78 MET cc_start: 0.7747 (mpp) cc_final: 0.6845 (mpp) REVERT: E 88 ILE cc_start: 0.6798 (mp) cc_final: 0.6586 (mp) REVERT: E 93 HIS cc_start: 0.9156 (p90) cc_final: 0.8807 (p90) REVERT: E 137 HIS cc_start: 0.9632 (m-70) cc_final: 0.9242 (m-70) REVERT: E 166 LEU cc_start: 0.8831 (pt) cc_final: 0.8215 (tp) REVERT: E 269 ASP cc_start: 0.9159 (t0) cc_final: 0.8275 (t0) REVERT: E 276 SER cc_start: 0.9080 (m) cc_final: 0.8788 (p) REVERT: E 285 ASN cc_start: 0.9494 (m110) cc_final: 0.9292 (m110) REVERT: E 286 MET cc_start: 0.8958 (mtm) cc_final: 0.8684 (mtt) REVERT: E 296 ASN cc_start: 0.9257 (p0) cc_final: 0.8539 (p0) REVERT: E 297 LEU cc_start: 0.9297 (mm) cc_final: 0.8857 (mm) REVERT: E 298 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8273 (mm-40) REVERT: E 321 LEU cc_start: 0.9676 (mm) cc_final: 0.9411 (mm) REVERT: E 353 TYR cc_start: 0.9128 (t80) cc_final: 0.8793 (t80) REVERT: E 465 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8958 (pt0) REVERT: E 489 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7841 (ttpt) REVERT: F 16 ASP cc_start: 0.8449 (m-30) cc_final: 0.8151 (m-30) REVERT: F 66 VAL cc_start: 0.9173 (m) cc_final: 0.8747 (m) REVERT: F 67 SER cc_start: 0.9146 (m) cc_final: 0.8444 (t) REVERT: F 78 MET cc_start: 0.7766 (mpp) cc_final: 0.6796 (mpp) REVERT: F 88 ILE cc_start: 0.7589 (mt) cc_final: 0.7236 (mt) REVERT: F 93 HIS cc_start: 0.9228 (p90) cc_final: 0.8687 (p90) REVERT: F 94 ASN cc_start: 0.8964 (t0) cc_final: 0.8755 (t0) REVERT: F 137 HIS cc_start: 0.9596 (m-70) cc_final: 0.9281 (m-70) REVERT: F 166 LEU cc_start: 0.8743 (pt) cc_final: 0.8012 (tp) REVERT: F 216 ASP cc_start: 0.9131 (t70) cc_final: 0.8903 (t0) REVERT: F 253 HIS cc_start: 0.9107 (t-90) cc_final: 0.8902 (t-90) REVERT: F 269 ASP cc_start: 0.9166 (t0) cc_final: 0.8181 (t0) REVERT: F 277 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8152 (tm-30) REVERT: F 285 ASN cc_start: 0.9462 (m110) cc_final: 0.9224 (m110) REVERT: F 296 ASN cc_start: 0.9308 (p0) cc_final: 0.8541 (p0) REVERT: F 297 LEU cc_start: 0.9370 (mm) cc_final: 0.8866 (mm) REVERT: F 298 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8265 (mm-40) REVERT: F 305 VAL cc_start: 0.8625 (m) cc_final: 0.7804 (p) REVERT: F 321 LEU cc_start: 0.9729 (mm) cc_final: 0.9444 (mm) REVERT: F 353 TYR cc_start: 0.9143 (t80) cc_final: 0.8664 (t80) REVERT: G 12 TYR cc_start: 0.9335 (t80) cc_final: 0.8952 (t80) REVERT: G 67 SER cc_start: 0.9042 (m) cc_final: 0.8284 (t) REVERT: G 78 MET cc_start: 0.7841 (mpp) cc_final: 0.7174 (mpp) REVERT: G 93 HIS cc_start: 0.9181 (p90) cc_final: 0.8696 (p90) REVERT: G 94 ASN cc_start: 0.8864 (t0) cc_final: 0.8609 (t0) REVERT: G 103 GLU cc_start: 0.9222 (mp0) cc_final: 0.8990 (mp0) REVERT: G 137 HIS cc_start: 0.9618 (m-70) cc_final: 0.9220 (m-70) REVERT: G 166 LEU cc_start: 0.8820 (pt) cc_final: 0.8212 (tp) REVERT: G 229 LYS cc_start: 0.9606 (mmtt) cc_final: 0.9261 (mmtm) REVERT: G 230 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8880 (m-40) REVERT: G 232 ASP cc_start: 0.9165 (t70) cc_final: 0.8882 (t0) REVERT: G 269 ASP cc_start: 0.9153 (t0) cc_final: 0.8108 (t0) REVERT: G 276 SER cc_start: 0.9092 (m) cc_final: 0.8821 (p) REVERT: G 285 ASN cc_start: 0.9566 (m110) cc_final: 0.9354 (m110) REVERT: G 286 MET cc_start: 0.9069 (mtm) cc_final: 0.8749 (mtt) REVERT: G 296 ASN cc_start: 0.9238 (p0) cc_final: 0.8537 (p0) REVERT: G 297 LEU cc_start: 0.9243 (mm) cc_final: 0.8897 (mm) REVERT: G 298 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8273 (mm110) REVERT: G 321 LEU cc_start: 0.9721 (mm) cc_final: 0.9468 (mm) REVERT: G 349 LYS cc_start: 0.9478 (mtpt) cc_final: 0.9266 (mtpt) REVERT: G 401 PHE cc_start: 0.9300 (p90) cc_final: 0.9076 (p90) REVERT: H 66 VAL cc_start: 0.9100 (m) cc_final: 0.8726 (m) REVERT: H 67 SER cc_start: 0.9072 (m) cc_final: 0.8385 (t) REVERT: H 78 MET cc_start: 0.7867 (mpp) cc_final: 0.7193 (mpp) REVERT: H 88 ILE cc_start: 0.7854 (mt) cc_final: 0.7637 (mt) REVERT: H 93 HIS cc_start: 0.9207 (p90) cc_final: 0.8759 (p90) REVERT: H 103 GLU cc_start: 0.9216 (mp0) cc_final: 0.8951 (mp0) REVERT: H 119 VAL cc_start: 0.9328 (m) cc_final: 0.9126 (m) REVERT: H 137 HIS cc_start: 0.9614 (m-70) cc_final: 0.9263 (m-70) REVERT: H 166 LEU cc_start: 0.8872 (pt) cc_final: 0.8088 (tp) REVERT: H 174 PHE cc_start: 0.8975 (m-80) cc_final: 0.8680 (m-80) REVERT: H 181 LYS cc_start: 0.9308 (mmpt) cc_final: 0.9074 (mmpt) REVERT: H 253 HIS cc_start: 0.9116 (t-90) cc_final: 0.8878 (t-90) REVERT: H 269 ASP cc_start: 0.9136 (t0) cc_final: 0.8160 (t0) REVERT: H 277 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7965 (tm-30) REVERT: H 281 ILE cc_start: 0.9472 (mm) cc_final: 0.8999 (tp) REVERT: H 285 ASN cc_start: 0.9508 (m110) cc_final: 0.9158 (m110) REVERT: H 286 MET cc_start: 0.8913 (mtm) cc_final: 0.8551 (mtt) REVERT: H 296 ASN cc_start: 0.9327 (p0) cc_final: 0.8568 (p0) REVERT: H 297 LEU cc_start: 0.9346 (mm) cc_final: 0.8860 (mm) REVERT: H 298 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8326 (mm-40) REVERT: H 321 LEU cc_start: 0.9694 (mm) cc_final: 0.9425 (mm) REVERT: H 351 SER cc_start: 0.8805 (p) cc_final: 0.8233 (p) REVERT: H 357 PHE cc_start: 0.9203 (m-80) cc_final: 0.8827 (m-10) REVERT: H 375 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9228 (ptpp) REVERT: H 450 LYS cc_start: 0.7341 (pttp) cc_final: 0.6871 (ptmm) REVERT: H 489 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7866 (ttpt) outliers start: 14 outliers final: 0 residues processed: 1384 average time/residue: 0.3624 time to fit residues: 801.7602 Evaluate side-chains 1084 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1079 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 0.5980 chunk 353 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 324 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 262 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 28864 Z= 0.265 Angle : 0.832 9.853 39136 Z= 0.410 Chirality : 0.048 0.165 4472 Planarity : 0.004 0.035 4928 Dihedral : 18.613 166.735 4368 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 28.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.03 (0.13), residues: 3576 helix: -1.69 (0.13), residues: 1192 sheet: -3.30 (0.20), residues: 424 loop : -1.88 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 372 PHE 0.032 0.002 PHE E 456 TYR 0.025 0.002 TYR F 233 ARG 0.003 0.001 ARG H 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1339 time to evaluate : 3.098 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 VAL cc_start: 0.8014 (t) cc_final: 0.7516 (m) REVERT: A 78 MET cc_start: 0.8020 (mpp) cc_final: 0.7489 (mpp) REVERT: A 93 HIS cc_start: 0.9220 (p90) cc_final: 0.8734 (p90) REVERT: A 94 ASN cc_start: 0.8880 (t0) cc_final: 0.8634 (t0) REVERT: A 106 LYS cc_start: 0.9179 (mtpt) cc_final: 0.8835 (mmtm) REVERT: A 132 GLU cc_start: 0.9527 (pp20) cc_final: 0.9325 (pp20) REVERT: A 166 LEU cc_start: 0.8878 (pt) cc_final: 0.8173 (tp) REVERT: A 216 ASP cc_start: 0.8378 (t70) cc_final: 0.7970 (t70) REVERT: A 253 HIS cc_start: 0.9229 (t-90) cc_final: 0.9007 (t-90) REVERT: A 269 ASP cc_start: 0.8916 (t0) cc_final: 0.7880 (t0) REVERT: A 276 SER cc_start: 0.9242 (m) cc_final: 0.8950 (p) REVERT: A 281 ILE cc_start: 0.9436 (mm) cc_final: 0.9029 (tp) REVERT: A 285 ASN cc_start: 0.9561 (m110) cc_final: 0.9277 (m110) REVERT: A 286 MET cc_start: 0.9046 (mtm) cc_final: 0.8801 (mtt) REVERT: A 296 ASN cc_start: 0.9133 (p0) cc_final: 0.8294 (p0) REVERT: A 297 LEU cc_start: 0.9185 (mm) cc_final: 0.8859 (mm) REVERT: A 298 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8225 (mm110) REVERT: A 321 LEU cc_start: 0.9663 (mm) cc_final: 0.9375 (mm) REVERT: A 368 GLN cc_start: 0.9158 (mp10) cc_final: 0.8883 (mp-120) REVERT: A 482 MET cc_start: 0.9310 (tmm) cc_final: 0.9086 (tmm) REVERT: A 492 LYS cc_start: 0.8527 (tptp) cc_final: 0.8166 (tptp) REVERT: A 493 ARG cc_start: 0.9359 (ttt90) cc_final: 0.9074 (ttm-80) REVERT: B 66 VAL cc_start: 0.9230 (m) cc_final: 0.9010 (m) REVERT: B 78 MET cc_start: 0.8002 (mpp) cc_final: 0.7163 (mpp) REVERT: B 103 GLU cc_start: 0.9135 (mp0) cc_final: 0.8899 (mp0) REVERT: B 134 LYS cc_start: 0.9402 (tppt) cc_final: 0.9175 (mmtt) REVERT: B 154 LEU cc_start: 0.9587 (mm) cc_final: 0.9311 (mm) REVERT: B 166 LEU cc_start: 0.8902 (pt) cc_final: 0.8140 (tp) REVERT: B 179 MET cc_start: 0.7586 (tpt) cc_final: 0.7382 (tpp) REVERT: B 241 LYS cc_start: 0.9484 (tptp) cc_final: 0.9179 (tptp) REVERT: B 243 GLN cc_start: 0.9056 (mp10) cc_final: 0.8706 (mp10) REVERT: B 269 ASP cc_start: 0.9061 (t0) cc_final: 0.8045 (t0) REVERT: B 277 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 281 ILE cc_start: 0.9486 (mm) cc_final: 0.9285 (mm) REVERT: B 285 ASN cc_start: 0.9501 (m110) cc_final: 0.9272 (m110) REVERT: B 286 MET cc_start: 0.8841 (mtm) cc_final: 0.8585 (mtt) REVERT: B 296 ASN cc_start: 0.9274 (p0) cc_final: 0.8411 (p0) REVERT: B 297 LEU cc_start: 0.9260 (mm) cc_final: 0.8751 (mm) REVERT: B 298 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8240 (mm-40) REVERT: B 321 LEU cc_start: 0.9709 (mm) cc_final: 0.9409 (mm) REVERT: B 375 LYS cc_start: 0.9541 (ptpp) cc_final: 0.9303 (ptpp) REVERT: B 450 LYS cc_start: 0.7354 (pttm) cc_final: 0.6160 (ptmm) REVERT: B 482 MET cc_start: 0.9328 (tmm) cc_final: 0.9120 (tmm) REVERT: B 492 LYS cc_start: 0.8592 (tptp) cc_final: 0.8143 (tptp) REVERT: B 493 ARG cc_start: 0.9358 (ttt90) cc_final: 0.9115 (ttm-80) REVERT: C 49 VAL cc_start: 0.8128 (t) cc_final: 0.7747 (m) REVERT: C 65 LEU cc_start: 0.9108 (pt) cc_final: 0.8887 (pt) REVERT: C 66 VAL cc_start: 0.9132 (m) cc_final: 0.8794 (m) REVERT: C 67 SER cc_start: 0.9034 (m) cc_final: 0.8477 (t) REVERT: C 75 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8369 (tm-30) REVERT: C 78 MET cc_start: 0.7861 (mpp) cc_final: 0.6636 (mpp) REVERT: C 82 MET cc_start: 0.8875 (tpp) cc_final: 0.8451 (tpp) REVERT: C 93 HIS cc_start: 0.9164 (p90) cc_final: 0.8627 (p90) REVERT: C 94 ASN cc_start: 0.8961 (t0) cc_final: 0.8703 (t0) REVERT: C 103 GLU cc_start: 0.9167 (mp0) cc_final: 0.8795 (mp0) REVERT: C 119 VAL cc_start: 0.9178 (m) cc_final: 0.8960 (m) REVERT: C 132 GLU cc_start: 0.9473 (tm-30) cc_final: 0.9230 (tm-30) REVERT: C 137 HIS cc_start: 0.9553 (m-70) cc_final: 0.9100 (m-70) REVERT: C 166 LEU cc_start: 0.8817 (pt) cc_final: 0.8152 (tp) REVERT: C 179 MET cc_start: 0.7240 (tpt) cc_final: 0.6807 (tpt) REVERT: C 269 ASP cc_start: 0.8998 (t0) cc_final: 0.8071 (t0) REVERT: C 276 SER cc_start: 0.9256 (m) cc_final: 0.8981 (p) REVERT: C 285 ASN cc_start: 0.9522 (m110) cc_final: 0.9322 (m110) REVERT: C 286 MET cc_start: 0.9051 (mtm) cc_final: 0.8788 (mtt) REVERT: C 297 LEU cc_start: 0.9152 (mm) cc_final: 0.8703 (mm) REVERT: C 298 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8276 (mm-40) REVERT: C 321 LEU cc_start: 0.9713 (mm) cc_final: 0.9413 (mm) REVERT: C 482 MET cc_start: 0.9326 (tmm) cc_final: 0.9123 (tmm) REVERT: C 489 LYS cc_start: 0.8262 (ttpt) cc_final: 0.8007 (ttpt) REVERT: D 42 ILE cc_start: 0.8855 (mp) cc_final: 0.8592 (mp) REVERT: D 66 VAL cc_start: 0.9259 (m) cc_final: 0.9024 (p) REVERT: D 78 MET cc_start: 0.8024 (mpp) cc_final: 0.7208 (mpp) REVERT: D 103 GLU cc_start: 0.9143 (mp0) cc_final: 0.8672 (mp0) REVERT: D 109 LYS cc_start: 0.9044 (tptp) cc_final: 0.8666 (tptp) REVERT: D 130 VAL cc_start: 0.9709 (m) cc_final: 0.9407 (m) REVERT: D 163 ILE cc_start: 0.9496 (pt) cc_final: 0.9076 (pt) REVERT: D 166 LEU cc_start: 0.8938 (pt) cc_final: 0.8126 (tp) REVERT: D 241 LYS cc_start: 0.9493 (tptp) cc_final: 0.9171 (tptp) REVERT: D 253 HIS cc_start: 0.9098 (t-90) cc_final: 0.8884 (t-90) REVERT: D 269 ASP cc_start: 0.9128 (t0) cc_final: 0.8246 (t0) REVERT: D 281 ILE cc_start: 0.9492 (mm) cc_final: 0.9284 (mm) REVERT: D 285 ASN cc_start: 0.9537 (m110) cc_final: 0.9301 (m110) REVERT: D 296 ASN cc_start: 0.9271 (p0) cc_final: 0.8323 (p0) REVERT: D 298 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8253 (mm-40) REVERT: D 305 VAL cc_start: 0.8727 (m) cc_final: 0.7933 (p) REVERT: D 321 LEU cc_start: 0.9703 (mm) cc_final: 0.9425 (mm) REVERT: D 375 LYS cc_start: 0.9561 (ptpp) cc_final: 0.9290 (ptpp) REVERT: D 482 MET cc_start: 0.9274 (tmm) cc_final: 0.9014 (tmm) REVERT: D 492 LYS cc_start: 0.8574 (tptp) cc_final: 0.8053 (tptp) REVERT: D 493 ARG cc_start: 0.9335 (ttt90) cc_final: 0.9020 (ttm-80) REVERT: E 12 TYR cc_start: 0.9316 (t80) cc_final: 0.8889 (t80) REVERT: E 49 VAL cc_start: 0.7942 (t) cc_final: 0.7495 (m) REVERT: E 66 VAL cc_start: 0.9266 (m) cc_final: 0.8755 (p) REVERT: E 78 MET cc_start: 0.8040 (mpp) cc_final: 0.7140 (mpp) REVERT: E 93 HIS cc_start: 0.9178 (p90) cc_final: 0.8737 (p90) REVERT: E 103 GLU cc_start: 0.9217 (mp0) cc_final: 0.8980 (mp0) REVERT: E 166 LEU cc_start: 0.8824 (pt) cc_final: 0.8106 (tp) REVERT: E 179 MET cc_start: 0.7545 (tpt) cc_final: 0.7089 (tpt) REVERT: E 241 LYS cc_start: 0.9493 (tptp) cc_final: 0.9200 (tptp) REVERT: E 269 ASP cc_start: 0.9057 (t0) cc_final: 0.8196 (t0) REVERT: E 276 SER cc_start: 0.9160 (m) cc_final: 0.8848 (p) REVERT: E 285 ASN cc_start: 0.9536 (m110) cc_final: 0.9330 (m110) REVERT: E 286 MET cc_start: 0.8960 (mtm) cc_final: 0.8634 (mtt) REVERT: E 296 ASN cc_start: 0.9209 (p0) cc_final: 0.8394 (p0) REVERT: E 297 LEU cc_start: 0.9237 (mm) cc_final: 0.8821 (mm) REVERT: E 298 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8232 (mm-40) REVERT: E 305 VAL cc_start: 0.8758 (m) cc_final: 0.7959 (p) REVERT: E 321 LEU cc_start: 0.9670 (mm) cc_final: 0.9372 (mm) REVERT: E 492 LYS cc_start: 0.8555 (tptp) cc_final: 0.8133 (tptp) REVERT: E 493 ARG cc_start: 0.9297 (ttt90) cc_final: 0.8984 (ttm-80) REVERT: F 42 ILE cc_start: 0.9004 (mp) cc_final: 0.8660 (mp) REVERT: F 66 VAL cc_start: 0.9262 (m) cc_final: 0.8794 (p) REVERT: F 75 GLU cc_start: 0.7926 (pp20) cc_final: 0.7562 (pp20) REVERT: F 78 MET cc_start: 0.8019 (mpp) cc_final: 0.7281 (mpp) REVERT: F 103 GLU cc_start: 0.9224 (mp0) cc_final: 0.8792 (mp0) REVERT: F 130 VAL cc_start: 0.9771 (m) cc_final: 0.9494 (m) REVERT: F 137 HIS cc_start: 0.9556 (m-70) cc_final: 0.9258 (m-70) REVERT: F 154 LEU cc_start: 0.9580 (mm) cc_final: 0.9349 (mm) REVERT: F 163 ILE cc_start: 0.9468 (pt) cc_final: 0.9032 (pt) REVERT: F 166 LEU cc_start: 0.8861 (pt) cc_final: 0.8070 (tp) REVERT: F 232 ASP cc_start: 0.9071 (t70) cc_final: 0.8712 (t0) REVERT: F 269 ASP cc_start: 0.9162 (t0) cc_final: 0.8450 (t0) REVERT: F 277 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8306 (tm-30) REVERT: F 285 ASN cc_start: 0.9498 (m110) cc_final: 0.9258 (m110) REVERT: F 296 ASN cc_start: 0.9293 (p0) cc_final: 0.8475 (p0) REVERT: F 298 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8222 (mm-40) REVERT: F 305 VAL cc_start: 0.8751 (m) cc_final: 0.7950 (p) REVERT: F 321 LEU cc_start: 0.9720 (mm) cc_final: 0.9435 (mm) REVERT: F 375 LYS cc_start: 0.9569 (ptpp) cc_final: 0.9319 (ptpp) REVERT: F 482 MET cc_start: 0.9289 (tmm) cc_final: 0.9053 (tmm) REVERT: F 492 LYS cc_start: 0.8561 (tptp) cc_final: 0.8050 (tptp) REVERT: F 493 ARG cc_start: 0.9337 (ttt90) cc_final: 0.9038 (ttm-80) REVERT: G 12 TYR cc_start: 0.9400 (t80) cc_final: 0.9038 (t80) REVERT: G 66 VAL cc_start: 0.9189 (m) cc_final: 0.8923 (p) REVERT: G 75 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8393 (tm-30) REVERT: G 78 MET cc_start: 0.7916 (mpp) cc_final: 0.6741 (mpp) REVERT: G 93 HIS cc_start: 0.9186 (p90) cc_final: 0.8671 (p90) REVERT: G 94 ASN cc_start: 0.8872 (t0) cc_final: 0.8608 (t0) REVERT: G 105 ARG cc_start: 0.8887 (mtt90) cc_final: 0.8596 (mmt90) REVERT: G 108 LYS cc_start: 0.9045 (pttm) cc_final: 0.8821 (pttm) REVERT: G 137 HIS cc_start: 0.9587 (m-70) cc_final: 0.9234 (m-70) REVERT: G 166 LEU cc_start: 0.8880 (pt) cc_final: 0.8201 (tp) REVERT: G 269 ASP cc_start: 0.8918 (t0) cc_final: 0.7977 (t0) REVERT: G 276 SER cc_start: 0.9204 (m) cc_final: 0.8922 (p) REVERT: G 281 ILE cc_start: 0.9441 (mm) cc_final: 0.9126 (tp) REVERT: G 285 ASN cc_start: 0.9561 (m110) cc_final: 0.9276 (m110) REVERT: G 286 MET cc_start: 0.9062 (mtm) cc_final: 0.8547 (mtt) REVERT: G 296 ASN cc_start: 0.9132 (p0) cc_final: 0.8289 (p0) REVERT: G 297 LEU cc_start: 0.9222 (mm) cc_final: 0.8813 (mm) REVERT: G 298 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8237 (mm-40) REVERT: G 321 LEU cc_start: 0.9711 (mm) cc_final: 0.9449 (mm) REVERT: G 482 MET cc_start: 0.9331 (tmm) cc_final: 0.9089 (tmm) REVERT: G 492 LYS cc_start: 0.8509 (tptp) cc_final: 0.8111 (tptp) REVERT: G 493 ARG cc_start: 0.9362 (ttt90) cc_final: 0.9069 (ttm-80) REVERT: H 66 VAL cc_start: 0.9239 (m) cc_final: 0.8984 (p) REVERT: H 75 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8174 (tm-30) REVERT: H 78 MET cc_start: 0.7950 (mpp) cc_final: 0.6862 (mpp) REVERT: H 105 ARG cc_start: 0.8776 (mtt90) cc_final: 0.8337 (mmt-90) REVERT: H 108 LYS cc_start: 0.8905 (pttm) cc_final: 0.8294 (pttm) REVERT: H 137 HIS cc_start: 0.9558 (m-70) cc_final: 0.9216 (m-70) REVERT: H 166 LEU cc_start: 0.8951 (pt) cc_final: 0.8135 (tp) REVERT: H 181 LYS cc_start: 0.9274 (mmpt) cc_final: 0.9068 (mmpt) REVERT: H 241 LYS cc_start: 0.9467 (tptp) cc_final: 0.9168 (tptp) REVERT: H 253 HIS cc_start: 0.9183 (t-90) cc_final: 0.8969 (t-90) REVERT: H 269 ASP cc_start: 0.9039 (t0) cc_final: 0.8196 (t0) REVERT: H 285 ASN cc_start: 0.9555 (m110) cc_final: 0.9309 (m110) REVERT: H 286 MET cc_start: 0.8901 (mtm) cc_final: 0.8327 (mtt) REVERT: H 296 ASN cc_start: 0.9255 (p0) cc_final: 0.8301 (p0) REVERT: H 298 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8308 (mm-40) REVERT: H 305 VAL cc_start: 0.8791 (m) cc_final: 0.7946 (p) REVERT: H 321 LEU cc_start: 0.9694 (mm) cc_final: 0.9406 (mm) REVERT: H 375 LYS cc_start: 0.9553 (ptpp) cc_final: 0.9294 (ptpp) REVERT: H 489 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7879 (ttpt) REVERT: H 492 LYS cc_start: 0.8599 (tptp) cc_final: 0.8167 (tptp) REVERT: H 493 ARG cc_start: 0.9373 (ttt90) cc_final: 0.9090 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 1339 average time/residue: 0.3906 time to fit residues: 822.1505 Evaluate side-chains 1065 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1065 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 219 optimal weight: 20.0000 chunk 328 optimal weight: 6.9990 chunk 347 optimal weight: 0.8980 chunk 171 optimal weight: 0.0970 chunk 311 optimal weight: 0.9980 chunk 93 optimal weight: 0.0170 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 265 GLN B 265 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 265 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN G 265 GLN G 283 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28864 Z= 0.204 Angle : 0.824 9.753 39136 Z= 0.394 Chirality : 0.049 0.223 4472 Planarity : 0.004 0.059 4928 Dihedral : 18.174 166.860 4368 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.10 % Allowed : 4.75 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.95 (0.13), residues: 3576 helix: -1.57 (0.13), residues: 1192 sheet: -3.31 (0.18), residues: 504 loop : -1.75 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 171 PHE 0.027 0.002 PHE G 456 TYR 0.026 0.002 TYR H 233 ARG 0.006 0.001 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1390 time to evaluate : 2.850 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7841 (mpp) cc_final: 0.7385 (mpp) REVERT: A 93 HIS cc_start: 0.9215 (p90) cc_final: 0.8754 (p90) REVERT: A 94 ASN cc_start: 0.8888 (t0) cc_final: 0.8643 (t0) REVERT: A 103 GLU cc_start: 0.9253 (mp0) cc_final: 0.9028 (mp0) REVERT: A 132 GLU cc_start: 0.9514 (pp20) cc_final: 0.9274 (pp20) REVERT: A 166 LEU cc_start: 0.8895 (pt) cc_final: 0.8167 (tp) REVERT: A 179 MET cc_start: 0.7303 (tpt) cc_final: 0.6812 (tpt) REVERT: A 216 ASP cc_start: 0.8399 (t70) cc_final: 0.8086 (t70) REVERT: A 230 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.8925 (m-40) REVERT: A 253 HIS cc_start: 0.9213 (t-90) cc_final: 0.9001 (t-90) REVERT: A 269 ASP cc_start: 0.9039 (t0) cc_final: 0.8176 (t0) REVERT: A 276 SER cc_start: 0.9255 (m) cc_final: 0.8946 (p) REVERT: A 281 ILE cc_start: 0.9405 (mm) cc_final: 0.8998 (tp) REVERT: A 285 ASN cc_start: 0.9549 (m110) cc_final: 0.9296 (m110) REVERT: A 286 MET cc_start: 0.9021 (mtm) cc_final: 0.8607 (mtt) REVERT: A 296 ASN cc_start: 0.9116 (p0) cc_final: 0.8231 (p0) REVERT: A 297 LEU cc_start: 0.9081 (mm) cc_final: 0.8706 (mm) REVERT: A 298 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8147 (mm-40) REVERT: A 321 LEU cc_start: 0.9684 (mm) cc_final: 0.9416 (mm) REVERT: A 482 MET cc_start: 0.9309 (tmm) cc_final: 0.9087 (tmm) REVERT: A 489 LYS cc_start: 0.7652 (ttpt) cc_final: 0.7212 (ttpt) REVERT: A 490 PHE cc_start: 0.8797 (m-80) cc_final: 0.8432 (m-80) REVERT: A 492 LYS cc_start: 0.8572 (tptp) cc_final: 0.8239 (tptp) REVERT: B 78 MET cc_start: 0.7915 (mpp) cc_final: 0.7355 (mpp) REVERT: B 93 HIS cc_start: 0.9282 (p90) cc_final: 0.8775 (p90) REVERT: B 120 VAL cc_start: 0.9548 (m) cc_final: 0.9293 (m) REVERT: B 121 LEU cc_start: 0.9026 (mp) cc_final: 0.8796 (tp) REVERT: B 132 GLU cc_start: 0.9483 (pp20) cc_final: 0.9244 (pp20) REVERT: B 134 LYS cc_start: 0.9378 (tppt) cc_final: 0.9151 (mmtt) REVERT: B 166 LEU cc_start: 0.8856 (pt) cc_final: 0.8057 (tp) REVERT: B 215 ASP cc_start: 0.9150 (m-30) cc_final: 0.8652 (t0) REVERT: B 216 ASP cc_start: 0.9258 (t0) cc_final: 0.8886 (t70) REVERT: B 229 LYS cc_start: 0.9454 (mttt) cc_final: 0.9046 (mttt) REVERT: B 241 LYS cc_start: 0.9385 (tptp) cc_final: 0.9009 (tptp) REVERT: B 261 ASP cc_start: 0.9321 (m-30) cc_final: 0.8782 (p0) REVERT: B 269 ASP cc_start: 0.9113 (t0) cc_final: 0.8091 (t70) REVERT: B 285 ASN cc_start: 0.9500 (m110) cc_final: 0.9266 (m110) REVERT: B 286 MET cc_start: 0.8801 (mtm) cc_final: 0.8388 (mtt) REVERT: B 296 ASN cc_start: 0.9223 (p0) cc_final: 0.8320 (p0) REVERT: B 297 LEU cc_start: 0.9197 (mm) cc_final: 0.8687 (mm) REVERT: B 298 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8236 (mm-40) REVERT: B 321 LEU cc_start: 0.9718 (mm) cc_final: 0.9467 (mm) REVERT: B 372 HIS cc_start: 0.9380 (m90) cc_final: 0.8783 (m90) REVERT: B 465 GLN cc_start: 0.9164 (mt0) cc_final: 0.8865 (pt0) REVERT: B 493 ARG cc_start: 0.9265 (ttt90) cc_final: 0.8979 (ttm-80) REVERT: C 65 LEU cc_start: 0.9044 (pt) cc_final: 0.8791 (pt) REVERT: C 66 VAL cc_start: 0.9146 (m) cc_final: 0.8691 (m) REVERT: C 78 MET cc_start: 0.8027 (mpp) cc_final: 0.7206 (mpp) REVERT: C 82 MET cc_start: 0.8756 (tpp) cc_final: 0.8514 (tpp) REVERT: C 93 HIS cc_start: 0.9222 (p90) cc_final: 0.8695 (p90) REVERT: C 94 ASN cc_start: 0.8886 (t0) cc_final: 0.8656 (t0) REVERT: C 115 ILE cc_start: 0.7108 (pt) cc_final: 0.6672 (pt) REVERT: C 132 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9262 (tm-30) REVERT: C 137 HIS cc_start: 0.9522 (m-70) cc_final: 0.9114 (m-70) REVERT: C 166 LEU cc_start: 0.8803 (pt) cc_final: 0.8134 (tp) REVERT: C 179 MET cc_start: 0.7072 (tpt) cc_final: 0.6794 (tpt) REVERT: C 216 ASP cc_start: 0.9070 (t70) cc_final: 0.8862 (t0) REVERT: C 276 SER cc_start: 0.9291 (m) cc_final: 0.9022 (p) REVERT: C 277 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8150 (tm-30) REVERT: C 285 ASN cc_start: 0.9514 (m110) cc_final: 0.9313 (m110) REVERT: C 286 MET cc_start: 0.8988 (mtm) cc_final: 0.8725 (mtt) REVERT: C 297 LEU cc_start: 0.9076 (mm) cc_final: 0.8724 (mm) REVERT: C 321 LEU cc_start: 0.9712 (mm) cc_final: 0.9455 (mm) REVERT: C 369 ASN cc_start: 0.9294 (p0) cc_final: 0.8793 (p0) REVERT: C 450 LYS cc_start: 0.6849 (pttm) cc_final: 0.5861 (ptmm) REVERT: C 482 MET cc_start: 0.9339 (tmm) cc_final: 0.9129 (tmm) REVERT: C 489 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7524 (ttpt) REVERT: C 490 PHE cc_start: 0.8900 (m-80) cc_final: 0.8590 (m-80) REVERT: C 492 LYS cc_start: 0.8469 (tptp) cc_final: 0.8128 (tptp) REVERT: D 42 ILE cc_start: 0.8628 (mp) cc_final: 0.8419 (mp) REVERT: D 78 MET cc_start: 0.8058 (mpp) cc_final: 0.7364 (mpp) REVERT: D 93 HIS cc_start: 0.9252 (p90) cc_final: 0.8718 (p90) REVERT: D 94 ASN cc_start: 0.8919 (t0) cc_final: 0.8705 (t0) REVERT: D 103 GLU cc_start: 0.9464 (mp0) cc_final: 0.9196 (mp0) REVERT: D 137 HIS cc_start: 0.9460 (m-70) cc_final: 0.9214 (m-70) REVERT: D 163 ILE cc_start: 0.9484 (pt) cc_final: 0.9100 (pt) REVERT: D 166 LEU cc_start: 0.8910 (pt) cc_final: 0.8066 (tp) REVERT: D 241 LYS cc_start: 0.9449 (tptp) cc_final: 0.9159 (tptp) REVERT: D 243 GLN cc_start: 0.9023 (mp10) cc_final: 0.8560 (mp10) REVERT: D 261 ASP cc_start: 0.9315 (m-30) cc_final: 0.8783 (p0) REVERT: D 269 ASP cc_start: 0.9059 (t0) cc_final: 0.8145 (t0) REVERT: D 276 SER cc_start: 0.9212 (m) cc_final: 0.8919 (p) REVERT: D 285 ASN cc_start: 0.9537 (m110) cc_final: 0.9312 (m110) REVERT: D 286 MET cc_start: 0.8854 (mtm) cc_final: 0.8066 (mtt) REVERT: D 296 ASN cc_start: 0.9260 (p0) cc_final: 0.8338 (p0) REVERT: D 298 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8283 (mm-40) REVERT: D 321 LEU cc_start: 0.9726 (mm) cc_final: 0.9445 (mm) REVERT: D 353 TYR cc_start: 0.9208 (t80) cc_final: 0.8882 (t80) REVERT: D 482 MET cc_start: 0.9232 (tmm) cc_final: 0.8992 (tmm) REVERT: D 493 ARG cc_start: 0.9303 (ttt90) cc_final: 0.8986 (ttm-80) REVERT: E 12 TYR cc_start: 0.9286 (t80) cc_final: 0.8673 (t80) REVERT: E 67 SER cc_start: 0.9323 (m) cc_final: 0.9023 (p) REVERT: E 78 MET cc_start: 0.7933 (mpp) cc_final: 0.7446 (mpp) REVERT: E 93 HIS cc_start: 0.9201 (p90) cc_final: 0.8765 (p90) REVERT: E 137 HIS cc_start: 0.9634 (m-70) cc_final: 0.9233 (m-70) REVERT: E 166 LEU cc_start: 0.8797 (pt) cc_final: 0.8072 (tp) REVERT: E 174 PHE cc_start: 0.8959 (m-80) cc_final: 0.8701 (m-80) REVERT: E 179 MET cc_start: 0.7431 (tpt) cc_final: 0.7029 (tpt) REVERT: E 198 ASN cc_start: 0.9711 (m110) cc_final: 0.9462 (m110) REVERT: E 202 GLN cc_start: 0.9405 (mp10) cc_final: 0.8683 (mp10) REVERT: E 230 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8974 (m-40) REVERT: E 241 LYS cc_start: 0.9429 (tptp) cc_final: 0.9133 (tptp) REVERT: E 269 ASP cc_start: 0.9057 (t0) cc_final: 0.8164 (t0) REVERT: E 276 SER cc_start: 0.9191 (m) cc_final: 0.8887 (p) REVERT: E 286 MET cc_start: 0.8982 (mtm) cc_final: 0.8454 (mtt) REVERT: E 296 ASN cc_start: 0.9181 (p0) cc_final: 0.8347 (p0) REVERT: E 297 LEU cc_start: 0.9164 (mm) cc_final: 0.8759 (mm) REVERT: E 298 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8126 (mm-40) REVERT: E 493 ARG cc_start: 0.9204 (ttt90) cc_final: 0.8897 (ttm-80) REVERT: F 42 ILE cc_start: 0.8953 (mp) cc_final: 0.8608 (mp) REVERT: F 67 SER cc_start: 0.9444 (m) cc_final: 0.9079 (m) REVERT: F 78 MET cc_start: 0.8120 (mpp) cc_final: 0.7354 (mpp) REVERT: F 93 HIS cc_start: 0.9230 (p90) cc_final: 0.8694 (p90) REVERT: F 94 ASN cc_start: 0.8905 (t0) cc_final: 0.8575 (t0) REVERT: F 103 GLU cc_start: 0.9438 (mp0) cc_final: 0.9231 (mp0) REVERT: F 137 HIS cc_start: 0.9599 (m-70) cc_final: 0.9356 (m-70) REVERT: F 166 LEU cc_start: 0.8854 (pt) cc_final: 0.8039 (tp) REVERT: F 198 ASN cc_start: 0.9711 (m110) cc_final: 0.9468 (m110) REVERT: F 199 GLU cc_start: 0.9464 (pt0) cc_final: 0.9263 (pt0) REVERT: F 202 GLN cc_start: 0.9389 (mp10) cc_final: 0.8662 (mp10) REVERT: F 261 ASP cc_start: 0.9344 (m-30) cc_final: 0.8804 (p0) REVERT: F 262 LEU cc_start: 0.9723 (tt) cc_final: 0.9483 (tt) REVERT: F 269 ASP cc_start: 0.9178 (t0) cc_final: 0.8427 (t0) REVERT: F 277 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8261 (tm-30) REVERT: F 296 ASN cc_start: 0.9249 (p0) cc_final: 0.8293 (p0) REVERT: F 298 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8265 (mm-40) REVERT: F 321 LEU cc_start: 0.9731 (mm) cc_final: 0.9458 (mm) REVERT: F 372 HIS cc_start: 0.9425 (m90) cc_final: 0.8821 (m90) REVERT: F 385 MET cc_start: 0.9038 (ttm) cc_final: 0.8742 (ttm) REVERT: F 482 MET cc_start: 0.9274 (tmm) cc_final: 0.9046 (tmm) REVERT: F 492 LYS cc_start: 0.8676 (tptp) cc_final: 0.8367 (tptp) REVERT: F 493 ARG cc_start: 0.9313 (ttt90) cc_final: 0.9103 (ttm-80) REVERT: G 12 TYR cc_start: 0.9408 (t80) cc_final: 0.8829 (t80) REVERT: G 42 ILE cc_start: 0.9021 (mp) cc_final: 0.8729 (mp) REVERT: G 66 VAL cc_start: 0.9353 (m) cc_final: 0.9126 (p) REVERT: G 75 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8252 (tm-30) REVERT: G 78 MET cc_start: 0.7796 (mpp) cc_final: 0.6575 (mpp) REVERT: G 93 HIS cc_start: 0.9198 (p90) cc_final: 0.8733 (p90) REVERT: G 94 ASN cc_start: 0.8878 (t0) cc_final: 0.8619 (t0) REVERT: G 137 HIS cc_start: 0.9609 (m-70) cc_final: 0.9248 (m-70) REVERT: G 166 LEU cc_start: 0.8882 (pt) cc_final: 0.8188 (tp) REVERT: G 179 MET cc_start: 0.7076 (tpt) cc_final: 0.6734 (tpt) REVERT: G 269 ASP cc_start: 0.8988 (t0) cc_final: 0.8093 (t0) REVERT: G 276 SER cc_start: 0.9207 (m) cc_final: 0.8883 (p) REVERT: G 281 ILE cc_start: 0.9436 (mm) cc_final: 0.9073 (tp) REVERT: G 285 ASN cc_start: 0.9564 (m110) cc_final: 0.9275 (m110) REVERT: G 286 MET cc_start: 0.9026 (mtm) cc_final: 0.8416 (mtt) REVERT: G 296 ASN cc_start: 0.9115 (p0) cc_final: 0.8220 (p0) REVERT: G 297 LEU cc_start: 0.9174 (mm) cc_final: 0.8819 (mm) REVERT: G 298 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8203 (mm-40) REVERT: G 385 MET cc_start: 0.9019 (ttm) cc_final: 0.8762 (ttm) REVERT: G 482 MET cc_start: 0.9289 (tmm) cc_final: 0.9050 (tmm) REVERT: G 490 PHE cc_start: 0.8873 (m-80) cc_final: 0.8245 (m-80) REVERT: G 493 ARG cc_start: 0.9293 (ttt90) cc_final: 0.9007 (ttm-80) REVERT: H 66 VAL cc_start: 0.9384 (m) cc_final: 0.9116 (m) REVERT: H 67 SER cc_start: 0.9267 (m) cc_final: 0.8799 (p) REVERT: H 75 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8164 (tm-30) REVERT: H 78 MET cc_start: 0.7844 (mpp) cc_final: 0.6622 (mpp) REVERT: H 93 HIS cc_start: 0.9246 (p90) cc_final: 0.8759 (p90) REVERT: H 130 VAL cc_start: 0.9770 (m) cc_final: 0.9466 (m) REVERT: H 137 HIS cc_start: 0.9620 (m-70) cc_final: 0.9316 (m-70) REVERT: H 166 LEU cc_start: 0.8940 (pt) cc_final: 0.8122 (tp) REVERT: H 174 PHE cc_start: 0.8939 (m-80) cc_final: 0.8737 (m-80) REVERT: H 181 LYS cc_start: 0.9208 (mmpt) cc_final: 0.9004 (mmpt) REVERT: H 241 LYS cc_start: 0.9334 (tptp) cc_final: 0.9033 (tptp) REVERT: H 253 HIS cc_start: 0.9139 (t-90) cc_final: 0.8935 (t-90) REVERT: H 261 ASP cc_start: 0.9303 (m-30) cc_final: 0.8694 (p0) REVERT: H 269 ASP cc_start: 0.9110 (t0) cc_final: 0.8295 (t0) REVERT: H 281 ILE cc_start: 0.9402 (mm) cc_final: 0.9155 (tp) REVERT: H 286 MET cc_start: 0.8900 (mtm) cc_final: 0.8552 (mtt) REVERT: H 296 ASN cc_start: 0.9239 (p0) cc_final: 0.8267 (p0) REVERT: H 298 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8261 (mm-40) REVERT: H 357 PHE cc_start: 0.9261 (m-80) cc_final: 0.8863 (m-10) REVERT: H 375 LYS cc_start: 0.9481 (ptpp) cc_final: 0.9279 (ptpp) REVERT: H 489 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7506 (ttpt) REVERT: H 490 PHE cc_start: 0.8892 (m-80) cc_final: 0.8546 (m-80) REVERT: H 492 LYS cc_start: 0.8650 (tptp) cc_final: 0.8292 (tptp) REVERT: H 493 ARG cc_start: 0.9320 (ttt90) cc_final: 0.9045 (ttm-80) outliers start: 3 outliers final: 0 residues processed: 1390 average time/residue: 0.3724 time to fit residues: 824.0275 Evaluate side-chains 1106 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1104 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 0.0770 chunk 197 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 296 optimal weight: 0.9990 chunk 240 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 0.6980 chunk 312 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 283 GLN A 343 GLN C 448 GLN D 283 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN F 283 GLN F 465 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28864 Z= 0.200 Angle : 0.807 9.519 39136 Z= 0.387 Chirality : 0.048 0.209 4472 Planarity : 0.004 0.042 4928 Dihedral : 17.856 166.754 4368 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.74 (0.13), residues: 3576 helix: -1.48 (0.14), residues: 1208 sheet: -3.23 (0.18), residues: 504 loop : -1.54 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 171 PHE 0.032 0.002 PHE G 456 TYR 0.028 0.002 TYR F 233 ARG 0.007 0.001 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1374 time to evaluate : 3.259 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7971 (mpp) cc_final: 0.7110 (mpp) REVERT: A 93 HIS cc_start: 0.9245 (p90) cc_final: 0.8830 (p90) REVERT: A 94 ASN cc_start: 0.8872 (t0) cc_final: 0.8638 (t0) REVERT: A 102 ASN cc_start: 0.9486 (m-40) cc_final: 0.9165 (m-40) REVERT: A 103 GLU cc_start: 0.9309 (mp0) cc_final: 0.9083 (mp0) REVERT: A 109 LYS cc_start: 0.8824 (tptp) cc_final: 0.8160 (tptp) REVERT: A 137 HIS cc_start: 0.9598 (m-70) cc_final: 0.9187 (m-70) REVERT: A 166 LEU cc_start: 0.8874 (pt) cc_final: 0.8113 (tp) REVERT: A 179 MET cc_start: 0.7169 (tpt) cc_final: 0.6758 (tpt) REVERT: A 216 ASP cc_start: 0.8428 (t70) cc_final: 0.8130 (t70) REVERT: A 253 HIS cc_start: 0.9218 (t-90) cc_final: 0.9006 (t-90) REVERT: A 265 GLN cc_start: 0.9588 (tp40) cc_final: 0.9306 (tp40) REVERT: A 269 ASP cc_start: 0.8958 (t0) cc_final: 0.8111 (t70) REVERT: A 276 SER cc_start: 0.9324 (m) cc_final: 0.8976 (p) REVERT: A 286 MET cc_start: 0.9046 (mtm) cc_final: 0.8443 (mtt) REVERT: A 296 ASN cc_start: 0.9106 (p0) cc_final: 0.8366 (p0) REVERT: A 297 LEU cc_start: 0.9022 (mm) cc_final: 0.8652 (mm) REVERT: A 298 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8198 (mm-40) REVERT: A 489 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7974 (ttmt) REVERT: A 490 PHE cc_start: 0.8905 (m-80) cc_final: 0.8591 (m-80) REVERT: B 43 ASP cc_start: 0.8881 (p0) cc_final: 0.8666 (p0) REVERT: B 66 VAL cc_start: 0.9222 (m) cc_final: 0.8983 (p) REVERT: B 67 SER cc_start: 0.9119 (p) cc_final: 0.8597 (p) REVERT: B 78 MET cc_start: 0.7973 (mpp) cc_final: 0.7138 (mpp) REVERT: B 93 HIS cc_start: 0.9314 (p90) cc_final: 0.8833 (p90) REVERT: B 132 GLU cc_start: 0.9472 (pp20) cc_final: 0.9230 (pp20) REVERT: B 134 LYS cc_start: 0.9381 (tppt) cc_final: 0.9127 (mmtt) REVERT: B 166 LEU cc_start: 0.8934 (pt) cc_final: 0.8137 (tp) REVERT: B 198 ASN cc_start: 0.9673 (m110) cc_final: 0.9473 (m110) REVERT: B 202 GLN cc_start: 0.9322 (mp10) cc_final: 0.8703 (mp10) REVERT: B 261 ASP cc_start: 0.9303 (m-30) cc_final: 0.8804 (p0) REVERT: B 265 GLN cc_start: 0.9465 (tp-100) cc_final: 0.9178 (tp40) REVERT: B 269 ASP cc_start: 0.9096 (t0) cc_final: 0.8139 (t70) REVERT: B 281 ILE cc_start: 0.9457 (mm) cc_final: 0.9241 (mm) REVERT: B 285 ASN cc_start: 0.9522 (m110) cc_final: 0.9310 (m110) REVERT: B 286 MET cc_start: 0.8834 (mtm) cc_final: 0.8240 (mtt) REVERT: B 296 ASN cc_start: 0.9230 (p0) cc_final: 0.8476 (p0) REVERT: B 297 LEU cc_start: 0.9152 (mm) cc_final: 0.8655 (mm) REVERT: B 298 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8165 (mm-40) REVERT: B 353 TYR cc_start: 0.9136 (t80) cc_final: 0.8862 (t80) REVERT: B 372 HIS cc_start: 0.9441 (m90) cc_final: 0.8823 (m90) REVERT: B 456 PHE cc_start: 0.9636 (t80) cc_final: 0.9430 (t80) REVERT: B 465 GLN cc_start: 0.9188 (mt0) cc_final: 0.8839 (pt0) REVERT: C 65 LEU cc_start: 0.9001 (pt) cc_final: 0.8728 (pt) REVERT: C 66 VAL cc_start: 0.9095 (m) cc_final: 0.8237 (m) REVERT: C 75 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8264 (tm-30) REVERT: C 78 MET cc_start: 0.8185 (mpp) cc_final: 0.7229 (mpp) REVERT: C 82 MET cc_start: 0.8705 (tpp) cc_final: 0.8425 (tpp) REVERT: C 93 HIS cc_start: 0.9249 (p90) cc_final: 0.8720 (p90) REVERT: C 94 ASN cc_start: 0.8848 (t0) cc_final: 0.8626 (t0) REVERT: C 103 GLU cc_start: 0.9538 (mp0) cc_final: 0.9294 (mp0) REVERT: C 115 ILE cc_start: 0.7250 (pt) cc_final: 0.6773 (pt) REVERT: C 130 VAL cc_start: 0.9739 (m) cc_final: 0.9451 (m) REVERT: C 137 HIS cc_start: 0.9520 (m-70) cc_final: 0.9131 (m-70) REVERT: C 166 LEU cc_start: 0.8821 (pt) cc_final: 0.8161 (tp) REVERT: C 202 GLN cc_start: 0.9351 (mp10) cc_final: 0.8714 (mp10) REVERT: C 203 ARG cc_start: 0.9403 (mmp80) cc_final: 0.9192 (mmp80) REVERT: C 232 ASP cc_start: 0.8995 (m-30) cc_final: 0.8766 (t0) REVERT: C 233 TYR cc_start: 0.8846 (m-10) cc_final: 0.8386 (m-10) REVERT: C 276 SER cc_start: 0.9398 (m) cc_final: 0.9117 (p) REVERT: C 277 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 286 MET cc_start: 0.9059 (mtm) cc_final: 0.8625 (mtt) REVERT: C 297 LEU cc_start: 0.9042 (mm) cc_final: 0.8789 (mm) REVERT: C 321 LEU cc_start: 0.9723 (mm) cc_final: 0.9499 (mm) REVERT: C 369 ASN cc_start: 0.9255 (p0) cc_final: 0.8751 (p0) REVERT: C 450 LYS cc_start: 0.6858 (pttm) cc_final: 0.5814 (ptmm) REVERT: C 482 MET cc_start: 0.9352 (tmm) cc_final: 0.9140 (tmm) REVERT: C 489 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7401 (mtpt) REVERT: C 490 PHE cc_start: 0.8985 (m-80) cc_final: 0.8629 (m-80) REVERT: D 66 VAL cc_start: 0.9242 (m) cc_final: 0.8999 (p) REVERT: D 67 SER cc_start: 0.9155 (p) cc_final: 0.8671 (p) REVERT: D 78 MET cc_start: 0.8251 (mpp) cc_final: 0.7723 (mpp) REVERT: D 93 HIS cc_start: 0.9299 (p90) cc_final: 0.8758 (p90) REVERT: D 137 HIS cc_start: 0.9447 (m-70) cc_final: 0.9191 (m-70) REVERT: D 163 ILE cc_start: 0.9479 (pt) cc_final: 0.9119 (pt) REVERT: D 166 LEU cc_start: 0.8973 (pt) cc_final: 0.8127 (tp) REVERT: D 241 LYS cc_start: 0.9392 (tptp) cc_final: 0.9097 (tptp) REVERT: D 261 ASP cc_start: 0.9313 (m-30) cc_final: 0.8804 (p0) REVERT: D 269 ASP cc_start: 0.9093 (t0) cc_final: 0.8105 (t70) REVERT: D 286 MET cc_start: 0.8856 (mtm) cc_final: 0.8141 (mtt) REVERT: D 296 ASN cc_start: 0.9226 (p0) cc_final: 0.8467 (p0) REVERT: D 297 LEU cc_start: 0.9186 (mm) cc_final: 0.8676 (mm) REVERT: D 298 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8204 (mm-40) REVERT: D 321 LEU cc_start: 0.9728 (mm) cc_final: 0.9478 (mm) REVERT: D 353 TYR cc_start: 0.9185 (t80) cc_final: 0.8907 (t80) REVERT: D 456 PHE cc_start: 0.9667 (t80) cc_final: 0.9431 (t80) REVERT: D 465 GLN cc_start: 0.9191 (mt0) cc_final: 0.8858 (pt0) REVERT: D 492 LYS cc_start: 0.8676 (tptp) cc_final: 0.8374 (tptp) REVERT: E 12 TYR cc_start: 0.9392 (t80) cc_final: 0.8964 (t80) REVERT: E 78 MET cc_start: 0.7993 (mpp) cc_final: 0.7179 (mpp) REVERT: E 93 HIS cc_start: 0.9220 (p90) cc_final: 0.8773 (p90) REVERT: E 137 HIS cc_start: 0.9684 (m-70) cc_final: 0.9296 (m-70) REVERT: E 166 LEU cc_start: 0.8873 (pt) cc_final: 0.8132 (tp) REVERT: E 174 PHE cc_start: 0.8902 (m-80) cc_final: 0.8672 (m-80) REVERT: E 241 LYS cc_start: 0.9351 (tptp) cc_final: 0.9067 (tptp) REVERT: E 269 ASP cc_start: 0.9091 (t0) cc_final: 0.8322 (t70) REVERT: E 276 SER cc_start: 0.9241 (m) cc_final: 0.8895 (p) REVERT: E 286 MET cc_start: 0.8977 (mtm) cc_final: 0.8384 (mtt) REVERT: E 296 ASN cc_start: 0.9167 (p0) cc_final: 0.8447 (p0) REVERT: E 297 LEU cc_start: 0.9153 (mm) cc_final: 0.8755 (mm) REVERT: E 298 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8173 (mm-40) REVERT: E 489 LYS cc_start: 0.7535 (ttpt) cc_final: 0.7062 (ttpt) REVERT: E 490 PHE cc_start: 0.8817 (m-80) cc_final: 0.8404 (m-80) REVERT: F 42 ILE cc_start: 0.8977 (mp) cc_final: 0.8635 (mp) REVERT: F 67 SER cc_start: 0.9393 (m) cc_final: 0.9165 (t) REVERT: F 75 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7612 (tm-30) REVERT: F 78 MET cc_start: 0.8093 (mpp) cc_final: 0.7190 (mpp) REVERT: F 93 HIS cc_start: 0.9290 (p90) cc_final: 0.8724 (p90) REVERT: F 94 ASN cc_start: 0.9026 (t0) cc_final: 0.8743 (t0) REVERT: F 95 CYS cc_start: 0.8753 (m) cc_final: 0.8550 (p) REVERT: F 137 HIS cc_start: 0.9577 (m-70) cc_final: 0.9348 (m-70) REVERT: F 166 LEU cc_start: 0.8906 (pt) cc_final: 0.8053 (tp) REVERT: F 232 ASP cc_start: 0.9027 (t70) cc_final: 0.8772 (m-30) REVERT: F 261 ASP cc_start: 0.9346 (m-30) cc_final: 0.8807 (p0) REVERT: F 269 ASP cc_start: 0.9155 (t0) cc_final: 0.8266 (t70) REVERT: F 286 MET cc_start: 0.8849 (mtm) cc_final: 0.8116 (mtt) REVERT: F 296 ASN cc_start: 0.9249 (p0) cc_final: 0.8419 (p0) REVERT: F 297 LEU cc_start: 0.9124 (mm) cc_final: 0.8607 (mm) REVERT: F 298 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8187 (mm-40) REVERT: F 353 TYR cc_start: 0.9184 (t80) cc_final: 0.8940 (t80) REVERT: F 372 HIS cc_start: 0.9426 (m90) cc_final: 0.8779 (m90) REVERT: F 482 MET cc_start: 0.9245 (tmm) cc_final: 0.9015 (tmm) REVERT: F 492 LYS cc_start: 0.8737 (tptp) cc_final: 0.8376 (tptp) REVERT: G 12 TYR cc_start: 0.9441 (t80) cc_final: 0.8802 (t80) REVERT: G 42 ILE cc_start: 0.9021 (mp) cc_final: 0.8696 (mp) REVERT: G 66 VAL cc_start: 0.9342 (m) cc_final: 0.9133 (p) REVERT: G 78 MET cc_start: 0.8033 (mpp) cc_final: 0.7038 (mpp) REVERT: G 93 HIS cc_start: 0.9233 (p90) cc_final: 0.8722 (p90) REVERT: G 94 ASN cc_start: 0.8858 (t0) cc_final: 0.8619 (t0) REVERT: G 137 HIS cc_start: 0.9652 (m-70) cc_final: 0.9347 (m-70) REVERT: G 166 LEU cc_start: 0.8930 (pt) cc_final: 0.8179 (tp) REVERT: G 179 MET cc_start: 0.6852 (tpt) cc_final: 0.6515 (tpt) REVERT: G 199 GLU cc_start: 0.9516 (pt0) cc_final: 0.9314 (pt0) REVERT: G 232 ASP cc_start: 0.9030 (t70) cc_final: 0.8779 (t0) REVERT: G 269 ASP cc_start: 0.8958 (t0) cc_final: 0.8041 (t70) REVERT: G 276 SER cc_start: 0.9255 (m) cc_final: 0.8919 (p) REVERT: G 281 ILE cc_start: 0.9394 (mm) cc_final: 0.9059 (tp) REVERT: G 285 ASN cc_start: 0.9552 (m110) cc_final: 0.9304 (m110) REVERT: G 286 MET cc_start: 0.9037 (mtm) cc_final: 0.8393 (mtt) REVERT: G 296 ASN cc_start: 0.9111 (p0) cc_final: 0.8350 (p0) REVERT: G 297 LEU cc_start: 0.9110 (mm) cc_final: 0.8685 (mm) REVERT: G 298 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8132 (mm-40) REVERT: G 364 ASP cc_start: 0.8565 (t0) cc_final: 0.8320 (t0) REVERT: G 372 HIS cc_start: 0.9419 (m170) cc_final: 0.9146 (m170) REVERT: G 385 MET cc_start: 0.9110 (ttm) cc_final: 0.8876 (ttm) REVERT: G 482 MET cc_start: 0.9281 (tmm) cc_final: 0.9002 (tmm) REVERT: G 490 PHE cc_start: 0.8885 (m-80) cc_final: 0.8273 (m-80) REVERT: G 493 ARG cc_start: 0.9247 (ttt90) cc_final: 0.8912 (ttm-80) REVERT: H 78 MET cc_start: 0.7985 (mpp) cc_final: 0.6933 (mpp) REVERT: H 93 HIS cc_start: 0.9275 (p90) cc_final: 0.8799 (p90) REVERT: H 137 HIS cc_start: 0.9580 (m-70) cc_final: 0.9298 (m-70) REVERT: H 166 LEU cc_start: 0.9012 (pt) cc_final: 0.8262 (tp) REVERT: H 241 LYS cc_start: 0.9384 (tptp) cc_final: 0.9123 (tptp) REVERT: H 261 ASP cc_start: 0.9301 (m-30) cc_final: 0.8731 (p0) REVERT: H 269 ASP cc_start: 0.9108 (t0) cc_final: 0.8159 (t0) REVERT: H 281 ILE cc_start: 0.9309 (mm) cc_final: 0.9023 (tp) REVERT: H 285 ASN cc_start: 0.9330 (m110) cc_final: 0.9050 (m110) REVERT: H 286 MET cc_start: 0.8899 (mtm) cc_final: 0.8505 (mtt) REVERT: H 296 ASN cc_start: 0.9233 (p0) cc_final: 0.8333 (p0) REVERT: H 297 LEU cc_start: 0.9195 (mm) cc_final: 0.8705 (mm) REVERT: H 298 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8168 (mm-40) REVERT: H 357 PHE cc_start: 0.9237 (m-80) cc_final: 0.8820 (m-10) REVERT: H 372 HIS cc_start: 0.9469 (m170) cc_final: 0.9266 (m170) REVERT: H 465 GLN cc_start: 0.9203 (mt0) cc_final: 0.8880 (pt0) REVERT: H 489 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7510 (mtpt) REVERT: H 490 PHE cc_start: 0.8905 (m-80) cc_final: 0.8628 (m-80) REVERT: H 492 LYS cc_start: 0.8687 (tptp) cc_final: 0.8361 (tptp) outliers start: 2 outliers final: 1 residues processed: 1375 average time/residue: 0.3717 time to fit residues: 816.0074 Evaluate side-chains 1092 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1091 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 2.9990 chunk 313 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 348 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 283 GLN A 343 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN C 283 GLN ** C 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 28864 Z= 0.405 Angle : 0.887 11.891 39136 Z= 0.451 Chirality : 0.051 0.298 4472 Planarity : 0.005 0.070 4928 Dihedral : 17.929 166.538 4368 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 35.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.77 (0.13), residues: 3576 helix: -1.44 (0.14), residues: 1200 sheet: -3.15 (0.19), residues: 504 loop : -1.64 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 466 PHE 0.025 0.002 PHE G 456 TYR 0.034 0.003 TYR E 459 ARG 0.014 0.001 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1262 time to evaluate : 3.350 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8492 (tm-30) REVERT: A 78 MET cc_start: 0.8302 (mpp) cc_final: 0.7588 (mpp) REVERT: A 93 HIS cc_start: 0.9203 (p90) cc_final: 0.8627 (p90) REVERT: A 94 ASN cc_start: 0.8895 (t0) cc_final: 0.8631 (t0) REVERT: A 102 ASN cc_start: 0.9532 (m-40) cc_final: 0.9231 (m-40) REVERT: A 103 GLU cc_start: 0.9434 (mp0) cc_final: 0.9230 (mp0) REVERT: A 105 ARG cc_start: 0.8967 (mmt180) cc_final: 0.8278 (mmt180) REVERT: A 108 LYS cc_start: 0.9349 (tptp) cc_final: 0.9115 (mtmm) REVERT: A 163 ILE cc_start: 0.9553 (pt) cc_final: 0.9249 (pt) REVERT: A 166 LEU cc_start: 0.9102 (pt) cc_final: 0.8341 (tp) REVERT: A 179 MET cc_start: 0.6924 (tpt) cc_final: 0.6624 (tpt) REVERT: A 269 ASP cc_start: 0.8929 (t0) cc_final: 0.8191 (t70) REVERT: A 286 MET cc_start: 0.9092 (mtm) cc_final: 0.8478 (mtt) REVERT: A 296 ASN cc_start: 0.9087 (p0) cc_final: 0.8239 (p0) REVERT: A 298 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8202 (mm-40) REVERT: A 321 LEU cc_start: 0.9670 (mm) cc_final: 0.9434 (mm) REVERT: B 75 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8357 (tm-30) REVERT: B 78 MET cc_start: 0.8479 (mpp) cc_final: 0.7656 (mpp) REVERT: B 109 LYS cc_start: 0.8874 (tptp) cc_final: 0.8341 (tptp) REVERT: B 132 GLU cc_start: 0.9482 (pp20) cc_final: 0.9271 (pp20) REVERT: B 163 ILE cc_start: 0.9581 (pt) cc_final: 0.9279 (pt) REVERT: B 166 LEU cc_start: 0.9163 (pt) cc_final: 0.8396 (tp) REVERT: B 202 GLN cc_start: 0.9410 (mp10) cc_final: 0.9198 (mp10) REVERT: B 265 GLN cc_start: 0.9495 (tp-100) cc_final: 0.9174 (tp40) REVERT: B 269 ASP cc_start: 0.9056 (t0) cc_final: 0.8234 (t70) REVERT: B 286 MET cc_start: 0.8948 (mtm) cc_final: 0.8595 (mtt) REVERT: B 296 ASN cc_start: 0.9194 (p0) cc_final: 0.8316 (p0) REVERT: B 298 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8326 (mm-40) REVERT: B 305 VAL cc_start: 0.8859 (m) cc_final: 0.8323 (p) REVERT: B 321 LEU cc_start: 0.9728 (mm) cc_final: 0.9514 (mm) REVERT: B 353 TYR cc_start: 0.9255 (t80) cc_final: 0.8908 (t80) REVERT: B 465 GLN cc_start: 0.9226 (mt0) cc_final: 0.8941 (pt0) REVERT: C 61 LEU cc_start: 0.8372 (mm) cc_final: 0.8100 (mm) REVERT: C 65 LEU cc_start: 0.8998 (pt) cc_final: 0.8796 (pt) REVERT: C 66 VAL cc_start: 0.8988 (m) cc_final: 0.8556 (m) REVERT: C 75 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8108 (tm-30) REVERT: C 78 MET cc_start: 0.8507 (mpp) cc_final: 0.7502 (mpp) REVERT: C 82 MET cc_start: 0.8825 (tpp) cc_final: 0.8484 (tpp) REVERT: C 93 HIS cc_start: 0.9142 (p90) cc_final: 0.8469 (p90) REVERT: C 94 ASN cc_start: 0.8882 (t0) cc_final: 0.8651 (t0) REVERT: C 102 ASN cc_start: 0.9500 (t0) cc_final: 0.9278 (t0) REVERT: C 137 HIS cc_start: 0.9503 (m-70) cc_final: 0.9126 (m-70) REVERT: C 163 ILE cc_start: 0.9474 (pt) cc_final: 0.9132 (pt) REVERT: C 166 LEU cc_start: 0.8969 (pt) cc_final: 0.8259 (tp) REVERT: C 179 MET cc_start: 0.6910 (tpt) cc_final: 0.6618 (tpt) REVERT: C 269 ASP cc_start: 0.9008 (t0) cc_final: 0.8360 (t0) REVERT: C 286 MET cc_start: 0.9091 (mtm) cc_final: 0.8146 (mtt) REVERT: C 298 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8252 (mm-40) REVERT: C 321 LEU cc_start: 0.9689 (mm) cc_final: 0.9441 (mm) REVERT: C 369 ASN cc_start: 0.9396 (p0) cc_final: 0.8797 (p0) REVERT: C 489 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7737 (mtmt) REVERT: D 42 ILE cc_start: 0.9088 (mp) cc_final: 0.8686 (mp) REVERT: D 61 LEU cc_start: 0.8558 (mm) cc_final: 0.8349 (mm) REVERT: D 75 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8012 (tm-30) REVERT: D 78 MET cc_start: 0.8571 (mpp) cc_final: 0.7940 (mpp) REVERT: D 109 LYS cc_start: 0.8865 (tptp) cc_final: 0.8393 (tptp) REVERT: D 137 HIS cc_start: 0.9511 (m-70) cc_final: 0.9204 (m-70) REVERT: D 163 ILE cc_start: 0.9544 (pt) cc_final: 0.9217 (pt) REVERT: D 166 LEU cc_start: 0.9183 (pt) cc_final: 0.8367 (tp) REVERT: D 269 ASP cc_start: 0.8993 (t0) cc_final: 0.8187 (t70) REVERT: D 286 MET cc_start: 0.8898 (mtm) cc_final: 0.8477 (mtt) REVERT: D 296 ASN cc_start: 0.9193 (p0) cc_final: 0.8338 (p0) REVERT: D 298 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8249 (mm-40) REVERT: D 305 VAL cc_start: 0.8874 (m) cc_final: 0.8422 (p) REVERT: D 321 LEU cc_start: 0.9707 (mm) cc_final: 0.9491 (mm) REVERT: D 351 SER cc_start: 0.8937 (p) cc_final: 0.8445 (p) REVERT: D 353 TYR cc_start: 0.9280 (t80) cc_final: 0.9032 (t80) REVERT: D 372 HIS cc_start: 0.9535 (m170) cc_final: 0.9254 (m170) REVERT: D 456 PHE cc_start: 0.9685 (t80) cc_final: 0.9463 (t80) REVERT: D 460 LEU cc_start: 0.9878 (mt) cc_final: 0.9676 (mt) REVERT: D 465 GLN cc_start: 0.9203 (mt0) cc_final: 0.8933 (pt0) REVERT: D 483 MET cc_start: 0.9628 (ptm) cc_final: 0.9342 (tmm) REVERT: D 492 LYS cc_start: 0.8755 (tptp) cc_final: 0.8481 (tptp) REVERT: E 12 TYR cc_start: 0.9446 (t80) cc_final: 0.8865 (t80) REVERT: E 78 MET cc_start: 0.8600 (mpp) cc_final: 0.8316 (mpp) REVERT: E 93 HIS cc_start: 0.9162 (p90) cc_final: 0.8619 (p90) REVERT: E 109 LYS cc_start: 0.8848 (tptp) cc_final: 0.8420 (tptp) REVERT: E 137 HIS cc_start: 0.9621 (m-70) cc_final: 0.9243 (m-70) REVERT: E 163 ILE cc_start: 0.9503 (pt) cc_final: 0.9185 (pt) REVERT: E 166 LEU cc_start: 0.9022 (pt) cc_final: 0.8272 (tp) REVERT: E 269 ASP cc_start: 0.9076 (t0) cc_final: 0.8313 (t70) REVERT: E 286 MET cc_start: 0.9024 (mtm) cc_final: 0.8651 (mtt) REVERT: E 296 ASN cc_start: 0.9159 (p0) cc_final: 0.8286 (p0) REVERT: E 298 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8239 (mm-40) REVERT: E 492 LYS cc_start: 0.8774 (tptp) cc_final: 0.8496 (tptp) REVERT: F 42 ILE cc_start: 0.9177 (mp) cc_final: 0.8817 (mp) REVERT: F 75 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8013 (tm-30) REVERT: F 78 MET cc_start: 0.8481 (mpp) cc_final: 0.7729 (mpp) REVERT: F 92 HIS cc_start: 0.8610 (p90) cc_final: 0.8385 (p90) REVERT: F 94 ASN cc_start: 0.9098 (t0) cc_final: 0.8797 (t0) REVERT: F 95 CYS cc_start: 0.8517 (m) cc_final: 0.8095 (p) REVERT: F 105 ARG cc_start: 0.8903 (mtt90) cc_final: 0.8452 (tpp-160) REVERT: F 137 HIS cc_start: 0.9574 (m-70) cc_final: 0.9271 (m-70) REVERT: F 163 ILE cc_start: 0.9496 (pt) cc_final: 0.9158 (pt) REVERT: F 166 LEU cc_start: 0.9097 (pt) cc_final: 0.8243 (tp) REVERT: F 269 ASP cc_start: 0.9085 (t0) cc_final: 0.8325 (t70) REVERT: F 286 MET cc_start: 0.8880 (mtm) cc_final: 0.8589 (mtt) REVERT: F 296 ASN cc_start: 0.9206 (p0) cc_final: 0.8362 (p0) REVERT: F 298 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8277 (mm-40) REVERT: F 305 VAL cc_start: 0.8858 (m) cc_final: 0.8399 (p) REVERT: F 321 LEU cc_start: 0.9756 (mm) cc_final: 0.9540 (mm) REVERT: F 353 TYR cc_start: 0.9228 (t80) cc_final: 0.8935 (t80) REVERT: F 482 MET cc_start: 0.9377 (tmm) cc_final: 0.9097 (tmm) REVERT: F 492 LYS cc_start: 0.8757 (tptp) cc_final: 0.8468 (tptp) REVERT: G 12 TYR cc_start: 0.9448 (t80) cc_final: 0.9081 (t80) REVERT: G 42 ILE cc_start: 0.9160 (mp) cc_final: 0.8801 (mp) REVERT: G 67 SER cc_start: 0.9597 (t) cc_final: 0.9351 (t) REVERT: G 75 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8375 (tm-30) REVERT: G 78 MET cc_start: 0.8335 (mpp) cc_final: 0.7433 (mpp) REVERT: G 93 HIS cc_start: 0.9085 (p90) cc_final: 0.8469 (p90) REVERT: G 94 ASN cc_start: 0.8892 (t0) cc_final: 0.8637 (t0) REVERT: G 109 LYS cc_start: 0.8943 (tptp) cc_final: 0.8635 (tptp) REVERT: G 137 HIS cc_start: 0.9598 (m-70) cc_final: 0.9258 (m-70) REVERT: G 163 ILE cc_start: 0.9506 (pt) cc_final: 0.9199 (pt) REVERT: G 166 LEU cc_start: 0.9069 (pt) cc_final: 0.8297 (tp) REVERT: G 179 MET cc_start: 0.6756 (tpt) cc_final: 0.6486 (tpt) REVERT: G 232 ASP cc_start: 0.9148 (t70) cc_final: 0.8726 (t0) REVERT: G 269 ASP cc_start: 0.8912 (t0) cc_final: 0.8119 (t70) REVERT: G 276 SER cc_start: 0.9397 (m) cc_final: 0.9104 (p) REVERT: G 281 ILE cc_start: 0.9461 (mm) cc_final: 0.9122 (tp) REVERT: G 285 ASN cc_start: 0.9578 (m110) cc_final: 0.9330 (m110) REVERT: G 286 MET cc_start: 0.9087 (mtm) cc_final: 0.8727 (mtt) REVERT: G 296 ASN cc_start: 0.9115 (p0) cc_final: 0.8262 (p0) REVERT: G 298 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8260 (mm-40) REVERT: G 372 HIS cc_start: 0.9549 (m170) cc_final: 0.9212 (m170) REVERT: H 67 SER cc_start: 0.9339 (m) cc_final: 0.9059 (m) REVERT: H 75 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8154 (tm-30) REVERT: H 78 MET cc_start: 0.8435 (mpp) cc_final: 0.7597 (mpp) REVERT: H 82 MET cc_start: 0.8956 (ttt) cc_final: 0.8617 (ttt) REVERT: H 137 HIS cc_start: 0.9555 (m-70) cc_final: 0.9202 (m-70) REVERT: H 163 ILE cc_start: 0.9516 (pt) cc_final: 0.9168 (pt) REVERT: H 166 LEU cc_start: 0.9085 (pt) cc_final: 0.8374 (tp) REVERT: H 181 LYS cc_start: 0.9339 (mmpt) cc_final: 0.9136 (mmmt) REVERT: H 269 ASP cc_start: 0.9034 (t0) cc_final: 0.8226 (t70) REVERT: H 281 ILE cc_start: 0.9373 (mm) cc_final: 0.9104 (tp) REVERT: H 285 ASN cc_start: 0.9363 (m110) cc_final: 0.9139 (m110) REVERT: H 286 MET cc_start: 0.8964 (mtm) cc_final: 0.8557 (mtt) REVERT: H 296 ASN cc_start: 0.9186 (p0) cc_final: 0.8321 (p0) REVERT: H 298 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8328 (mm-40) REVERT: H 372 HIS cc_start: 0.9512 (m170) cc_final: 0.9215 (m170) REVERT: H 465 GLN cc_start: 0.9219 (mt0) cc_final: 0.8940 (pt0) REVERT: H 492 LYS cc_start: 0.8758 (tptp) cc_final: 0.8524 (tptp) outliers start: 1 outliers final: 0 residues processed: 1262 average time/residue: 0.3806 time to fit residues: 758.9428 Evaluate side-chains 1051 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1051 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 346 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 283 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 448 GLN C 283 GLN ** C 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28864 Z= 0.264 Angle : 0.837 10.735 39136 Z= 0.406 Chirality : 0.049 0.289 4472 Planarity : 0.004 0.057 4928 Dihedral : 17.865 169.735 4368 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 29.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.03 % Allowed : 1.68 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 (0.13), residues: 3576 helix: -1.35 (0.14), residues: 1184 sheet: -2.89 (0.21), residues: 424 loop : -1.68 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 466 PHE 0.033 0.002 PHE G 456 TYR 0.027 0.002 TYR B 233 ARG 0.009 0.001 ARG E 480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1288 time to evaluate : 3.039 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 HIS cc_start: 0.9187 (p90) cc_final: 0.8653 (p90) REVERT: A 94 ASN cc_start: 0.8856 (t0) cc_final: 0.8569 (t0) REVERT: A 102 ASN cc_start: 0.9488 (m-40) cc_final: 0.9185 (m-40) REVERT: A 103 GLU cc_start: 0.9493 (mp0) cc_final: 0.9261 (mp0) REVERT: A 105 ARG cc_start: 0.8968 (mmt180) cc_final: 0.8307 (mmt180) REVERT: A 137 HIS cc_start: 0.9656 (m-70) cc_final: 0.9252 (m-70) REVERT: A 163 ILE cc_start: 0.9457 (pt) cc_final: 0.9145 (pt) REVERT: A 166 LEU cc_start: 0.9012 (pt) cc_final: 0.8293 (tp) REVERT: A 179 MET cc_start: 0.6809 (tpt) cc_final: 0.6559 (tpt) REVERT: A 269 ASP cc_start: 0.8973 (t0) cc_final: 0.8106 (t70) REVERT: A 286 MET cc_start: 0.9070 (mtm) cc_final: 0.8355 (mtt) REVERT: A 296 ASN cc_start: 0.9085 (p0) cc_final: 0.8452 (p0) REVERT: A 297 LEU cc_start: 0.9011 (mm) cc_final: 0.8481 (mm) REVERT: A 298 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8314 (mm-40) REVERT: A 321 LEU cc_start: 0.9651 (mm) cc_final: 0.9413 (mm) REVERT: B 75 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8407 (tm-30) REVERT: B 78 MET cc_start: 0.8318 (mpp) cc_final: 0.7565 (mpp) REVERT: B 88 ILE cc_start: 0.6807 (pt) cc_final: 0.6471 (pt) REVERT: B 92 HIS cc_start: 0.8472 (p90) cc_final: 0.8266 (p90) REVERT: B 93 HIS cc_start: 0.9247 (p90) cc_final: 0.8672 (p90) REVERT: B 94 ASN cc_start: 0.8854 (t0) cc_final: 0.8523 (t0) REVERT: B 132 GLU cc_start: 0.9476 (pp20) cc_final: 0.9188 (pp20) REVERT: B 166 LEU cc_start: 0.9101 (pt) cc_final: 0.8385 (tp) REVERT: B 241 LYS cc_start: 0.9459 (tptp) cc_final: 0.9144 (tptp) REVERT: B 261 ASP cc_start: 0.9322 (m-30) cc_final: 0.8817 (p0) REVERT: B 265 GLN cc_start: 0.9483 (tp-100) cc_final: 0.9118 (tp40) REVERT: B 269 ASP cc_start: 0.9076 (t0) cc_final: 0.8117 (t70) REVERT: B 286 MET cc_start: 0.8913 (mtm) cc_final: 0.8536 (mtt) REVERT: B 296 ASN cc_start: 0.9174 (p0) cc_final: 0.8509 (p0) REVERT: B 297 LEU cc_start: 0.9164 (mm) cc_final: 0.8572 (mm) REVERT: B 298 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8392 (mm-40) REVERT: B 321 LEU cc_start: 0.9736 (mm) cc_final: 0.9499 (mm) REVERT: B 375 LYS cc_start: 0.9554 (ptpp) cc_final: 0.9342 (ptpp) REVERT: B 450 LYS cc_start: 0.7346 (pttm) cc_final: 0.6082 (ptmm) REVERT: B 460 LEU cc_start: 0.9878 (mt) cc_final: 0.9669 (mt) REVERT: B 465 GLN cc_start: 0.9216 (mt0) cc_final: 0.8912 (pt0) REVERT: B 489 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7310 (ttpt) REVERT: B 490 PHE cc_start: 0.8875 (m-80) cc_final: 0.8507 (m-80) REVERT: C 19 THR cc_start: 0.9414 (p) cc_final: 0.9039 (p) REVERT: C 42 ILE cc_start: 0.9113 (mp) cc_final: 0.8850 (mp) REVERT: C 66 VAL cc_start: 0.9015 (m) cc_final: 0.8623 (m) REVERT: C 75 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 78 MET cc_start: 0.8356 (mpp) cc_final: 0.7237 (mpp) REVERT: C 82 MET cc_start: 0.8800 (tpp) cc_final: 0.8517 (tpp) REVERT: C 93 HIS cc_start: 0.9186 (p90) cc_final: 0.8566 (p90) REVERT: C 94 ASN cc_start: 0.8799 (t0) cc_final: 0.8548 (t0) REVERT: C 103 GLU cc_start: 0.9594 (mp0) cc_final: 0.9368 (mp0) REVERT: C 137 HIS cc_start: 0.9484 (m-70) cc_final: 0.9136 (m-70) REVERT: C 163 ILE cc_start: 0.9475 (pt) cc_final: 0.9143 (pt) REVERT: C 166 LEU cc_start: 0.8911 (pt) cc_final: 0.8211 (tp) REVERT: C 265 GLN cc_start: 0.9631 (tp40) cc_final: 0.9418 (tp40) REVERT: C 277 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8126 (tm-30) REVERT: C 286 MET cc_start: 0.9047 (mtm) cc_final: 0.8170 (mtt) REVERT: C 321 LEU cc_start: 0.9669 (mm) cc_final: 0.9421 (mm) REVERT: C 369 ASN cc_start: 0.9312 (p0) cc_final: 0.8787 (p0) REVERT: D 42 ILE cc_start: 0.8921 (mp) cc_final: 0.8631 (mp) REVERT: D 75 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 78 MET cc_start: 0.8440 (mpp) cc_final: 0.7795 (mpp) REVERT: D 137 HIS cc_start: 0.9481 (m-70) cc_final: 0.9202 (m-70) REVERT: D 153 ARG cc_start: 0.9214 (ttp80) cc_final: 0.8778 (tmm-80) REVERT: D 154 LEU cc_start: 0.9262 (mm) cc_final: 0.8822 (mm) REVERT: D 163 ILE cc_start: 0.9529 (pt) cc_final: 0.9226 (pt) REVERT: D 166 LEU cc_start: 0.9111 (pt) cc_final: 0.8319 (tp) REVERT: D 261 ASP cc_start: 0.9298 (m-30) cc_final: 0.8839 (p0) REVERT: D 265 GLN cc_start: 0.9503 (tp40) cc_final: 0.9264 (tp40) REVERT: D 269 ASP cc_start: 0.9088 (t0) cc_final: 0.8290 (t70) REVERT: D 286 MET cc_start: 0.8860 (mtm) cc_final: 0.8525 (mtt) REVERT: D 296 ASN cc_start: 0.9162 (p0) cc_final: 0.8420 (p0) REVERT: D 298 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8411 (mm-40) REVERT: D 321 LEU cc_start: 0.9703 (mm) cc_final: 0.9471 (mm) REVERT: D 353 TYR cc_start: 0.9234 (t80) cc_final: 0.8954 (t80) REVERT: D 372 HIS cc_start: 0.9531 (m170) cc_final: 0.9141 (m170) REVERT: D 375 LYS cc_start: 0.9509 (ptpp) cc_final: 0.9301 (ptpp) REVERT: D 450 LYS cc_start: 0.7484 (pttm) cc_final: 0.6529 (ptmm) REVERT: D 465 GLN cc_start: 0.9203 (mt0) cc_final: 0.8912 (pt0) REVERT: D 492 LYS cc_start: 0.8726 (tptp) cc_final: 0.8495 (tptp) REVERT: E 12 TYR cc_start: 0.9441 (t80) cc_final: 0.8873 (t80) REVERT: E 44 PHE cc_start: 0.8263 (p90) cc_final: 0.7904 (p90) REVERT: E 78 MET cc_start: 0.8378 (mpp) cc_final: 0.8108 (mpp) REVERT: E 93 HIS cc_start: 0.9159 (p90) cc_final: 0.8584 (p90) REVERT: E 137 HIS cc_start: 0.9624 (m-70) cc_final: 0.9278 (m-70) REVERT: E 163 ILE cc_start: 0.9447 (pt) cc_final: 0.9145 (pt) REVERT: E 166 LEU cc_start: 0.8936 (pt) cc_final: 0.8201 (tp) REVERT: E 179 MET cc_start: 0.7346 (tpt) cc_final: 0.7097 (tpt) REVERT: E 269 ASP cc_start: 0.9074 (t0) cc_final: 0.8259 (t70) REVERT: E 276 SER cc_start: 0.9282 (m) cc_final: 0.8949 (p) REVERT: E 286 MET cc_start: 0.8995 (mtm) cc_final: 0.8706 (mtt) REVERT: E 296 ASN cc_start: 0.9172 (p0) cc_final: 0.8557 (p0) REVERT: E 297 LEU cc_start: 0.9103 (mm) cc_final: 0.8573 (mm) REVERT: E 298 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8398 (mm-40) REVERT: E 492 LYS cc_start: 0.8733 (tptp) cc_final: 0.8509 (tptp) REVERT: F 42 ILE cc_start: 0.9073 (mp) cc_final: 0.8655 (mp) REVERT: F 75 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8046 (tm-30) REVERT: F 78 MET cc_start: 0.8380 (mpp) cc_final: 0.7523 (mpp) REVERT: F 92 HIS cc_start: 0.8490 (p90) cc_final: 0.8200 (p90) REVERT: F 94 ASN cc_start: 0.9080 (t0) cc_final: 0.8770 (t0) REVERT: F 105 ARG cc_start: 0.8943 (mtt90) cc_final: 0.8487 (tpp-160) REVERT: F 137 HIS cc_start: 0.9544 (m-70) cc_final: 0.9283 (m-70) REVERT: F 163 ILE cc_start: 0.9485 (pt) cc_final: 0.9118 (pt) REVERT: F 166 LEU cc_start: 0.9048 (pt) cc_final: 0.8247 (tp) REVERT: F 261 ASP cc_start: 0.9305 (m-30) cc_final: 0.8833 (p0) REVERT: F 269 ASP cc_start: 0.9142 (t0) cc_final: 0.8321 (t70) REVERT: F 296 ASN cc_start: 0.9244 (p0) cc_final: 0.8488 (p0) REVERT: F 298 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8435 (mm-40) REVERT: F 321 LEU cc_start: 0.9758 (mm) cc_final: 0.9539 (mm) REVERT: F 353 TYR cc_start: 0.9201 (t80) cc_final: 0.8956 (t80) REVERT: F 375 LYS cc_start: 0.9555 (ptpp) cc_final: 0.9355 (ptpp) REVERT: F 450 LYS cc_start: 0.7481 (pttm) cc_final: 0.6427 (ptmm) REVERT: F 465 GLN cc_start: 0.9178 (mt0) cc_final: 0.8935 (pt0) REVERT: F 482 MET cc_start: 0.9301 (tmm) cc_final: 0.9066 (tmm) REVERT: F 492 LYS cc_start: 0.8765 (tptp) cc_final: 0.8436 (tptp) REVERT: G 12 TYR cc_start: 0.9453 (t80) cc_final: 0.8911 (t80) REVERT: G 42 ILE cc_start: 0.9162 (mp) cc_final: 0.8786 (mp) REVERT: G 66 VAL cc_start: 0.9206 (p) cc_final: 0.8895 (p) REVERT: G 75 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8346 (tm-30) REVERT: G 78 MET cc_start: 0.8220 (mpp) cc_final: 0.7390 (mpp) REVERT: G 93 HIS cc_start: 0.9129 (p90) cc_final: 0.8531 (p90) REVERT: G 94 ASN cc_start: 0.8826 (t0) cc_final: 0.8573 (t0) REVERT: G 137 HIS cc_start: 0.9563 (m-70) cc_final: 0.9259 (m-70) REVERT: G 163 ILE cc_start: 0.9481 (pt) cc_final: 0.9171 (pt) REVERT: G 166 LEU cc_start: 0.9005 (pt) cc_final: 0.8238 (tp) REVERT: G 214 GLU cc_start: 0.9461 (pm20) cc_final: 0.9257 (pm20) REVERT: G 232 ASP cc_start: 0.9151 (t70) cc_final: 0.8677 (t0) REVERT: G 269 ASP cc_start: 0.8920 (t0) cc_final: 0.8118 (t70) REVERT: G 276 SER cc_start: 0.9308 (m) cc_final: 0.9002 (p) REVERT: G 281 ILE cc_start: 0.9430 (mm) cc_final: 0.9067 (tp) REVERT: G 285 ASN cc_start: 0.9568 (m110) cc_final: 0.9322 (m110) REVERT: G 286 MET cc_start: 0.9086 (mtm) cc_final: 0.8736 (mtt) REVERT: G 296 ASN cc_start: 0.9049 (p0) cc_final: 0.8379 (p0) REVERT: G 297 LEU cc_start: 0.9105 (mm) cc_final: 0.8584 (mm) REVERT: G 298 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8208 (mm-40) REVERT: G 372 HIS cc_start: 0.9556 (m170) cc_final: 0.9150 (m170) REVERT: G 492 LYS cc_start: 0.8738 (tmtt) cc_final: 0.8481 (tmtt) REVERT: H 67 SER cc_start: 0.9348 (m) cc_final: 0.9124 (m) REVERT: H 75 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8140 (tm-30) REVERT: H 78 MET cc_start: 0.7973 (mpp) cc_final: 0.7163 (mpp) REVERT: H 82 MET cc_start: 0.8932 (ttt) cc_final: 0.8611 (ttt) REVERT: H 93 HIS cc_start: 0.9202 (p90) cc_final: 0.8609 (p90) REVERT: H 94 ASN cc_start: 0.8857 (t0) cc_final: 0.8643 (t0) REVERT: H 137 HIS cc_start: 0.9547 (m-70) cc_final: 0.9233 (m-70) REVERT: H 153 ARG cc_start: 0.9263 (ttp80) cc_final: 0.8816 (tmm-80) REVERT: H 154 LEU cc_start: 0.9309 (mm) cc_final: 0.8851 (mm) REVERT: H 163 ILE cc_start: 0.9494 (pt) cc_final: 0.9154 (pt) REVERT: H 166 LEU cc_start: 0.9033 (pt) cc_final: 0.8348 (tp) REVERT: H 184 ASP cc_start: 0.9360 (p0) cc_final: 0.9148 (p0) REVERT: H 261 ASP cc_start: 0.9302 (m-30) cc_final: 0.8814 (p0) REVERT: H 269 ASP cc_start: 0.9081 (t0) cc_final: 0.8288 (t70) REVERT: H 281 ILE cc_start: 0.9360 (mm) cc_final: 0.9063 (tp) REVERT: H 285 ASN cc_start: 0.9342 (m110) cc_final: 0.9074 (m110) REVERT: H 286 MET cc_start: 0.8945 (mtm) cc_final: 0.8559 (mtt) REVERT: H 296 ASN cc_start: 0.9167 (p0) cc_final: 0.8444 (p0) REVERT: H 298 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8391 (mm-40) REVERT: H 372 HIS cc_start: 0.9516 (m170) cc_final: 0.9150 (m170) REVERT: H 375 LYS cc_start: 0.9551 (ptpp) cc_final: 0.9334 (ptpp) REVERT: H 450 LYS cc_start: 0.7534 (pttm) cc_final: 0.6680 (ptmm) REVERT: H 465 GLN cc_start: 0.9209 (mt0) cc_final: 0.8918 (pt0) REVERT: H 493 ARG cc_start: 0.9131 (ttt90) cc_final: 0.8911 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 1289 average time/residue: 0.3778 time to fit residues: 765.4681 Evaluate side-chains 1071 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1071 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.0827 > 50: distance: 8 - 13: 17.116 distance: 13 - 14: 15.178 distance: 14 - 15: 18.230 distance: 14 - 17: 18.652 distance: 15 - 16: 17.680 distance: 15 - 20: 14.027 distance: 17 - 18: 26.319 distance: 17 - 19: 29.137 distance: 20 - 21: 17.397 distance: 21 - 22: 17.227 distance: 21 - 24: 20.792 distance: 22 - 23: 20.319 distance: 22 - 28: 40.634 distance: 24 - 25: 11.536 distance: 25 - 26: 12.958 distance: 25 - 27: 9.962 distance: 28 - 29: 33.918 distance: 29 - 30: 12.126 distance: 29 - 32: 30.954 distance: 30 - 31: 19.651 distance: 30 - 34: 12.443 distance: 32 - 33: 15.168 distance: 34 - 35: 10.175 distance: 34 - 40: 19.616 distance: 35 - 36: 6.578 distance: 35 - 38: 10.852 distance: 36 - 41: 4.153 distance: 38 - 39: 4.026 distance: 39 - 40: 7.910 distance: 41 - 42: 7.355 distance: 42 - 43: 6.202 distance: 42 - 45: 6.700 distance: 43 - 50: 8.054 distance: 45 - 46: 4.844 distance: 46 - 47: 5.589 distance: 47 - 48: 4.327 distance: 50 - 51: 15.284 distance: 51 - 52: 14.629 distance: 51 - 54: 18.309 distance: 52 - 53: 27.205 distance: 52 - 58: 19.209 distance: 54 - 55: 9.375 distance: 55 - 56: 8.184 distance: 55 - 57: 8.827 distance: 58 - 59: 7.027 distance: 59 - 60: 29.655 distance: 59 - 62: 13.835 distance: 60 - 61: 50.083 distance: 60 - 69: 22.569 distance: 62 - 63: 14.468 distance: 63 - 64: 10.079 distance: 64 - 65: 7.891 distance: 69 - 70: 24.847 distance: 70 - 71: 22.411 distance: 70 - 73: 23.505 distance: 71 - 72: 29.430 distance: 71 - 76: 25.557 distance: 72 - 95: 13.696 distance: 73 - 74: 36.375 distance: 73 - 75: 25.144 distance: 76 - 77: 8.463 distance: 77 - 78: 21.979 distance: 77 - 80: 31.617 distance: 78 - 79: 19.517 distance: 78 - 87: 19.765 distance: 80 - 81: 24.008 distance: 81 - 82: 13.975 distance: 82 - 83: 10.482 distance: 83 - 84: 5.231 distance: 84 - 85: 12.345 distance: 84 - 86: 8.713 distance: 87 - 88: 12.302 distance: 88 - 89: 4.438 distance: 88 - 91: 15.531 distance: 89 - 90: 13.311 distance: 89 - 95: 3.660 distance: 90 - 112: 13.188 distance: 91 - 92: 7.821 distance: 92 - 93: 11.073 distance: 92 - 94: 11.114